Correlation tab (v2)

.gitattributes

@@ -33,11 +33,3 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
-aggrescan3d/aggrescan/data/freesasa-2.0.1/src/structure.o filter=lfs diff=lfs merge=lfs -text
-aggrescan3d/aggrescan/data/freesasa.exe filter=lfs diff=lfs merge=lfs -text
-aggrescan3d/aggrescan/data/freesasa-2.0.1/src/example filter=lfs diff=lfs merge=lfs -text
-aggrescan3d/aggrescan/data/freesasa-2.0.1/src/freesasa filter=lfs diff=lfs merge=lfs -text
-aggrescan3d/aggrescan/data/freesasa-2.0.1/src/freesasa.exe filter=lfs diff=lfs merge=lfs -text
-aggrescan3d/aggrescan/data/freesasa-2.0.1/src/freesasa_Darwin filter=lfs diff=lfs merge=lfs -text
-aggrescan3d/aggrescan/data/freesasa-2.0.1/src/libfreesasa.a filter=lfs diff=lfs merge=lfs -text
-aggrescan3d/aggrescan/data/freesasa-2.0.1/src/main.o filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -1,8 +1,4 @@
 .envrc
-**/__pycache__/
+__pycache__/
 output/
-sequences/
-boltz_results/
-
-*.ipynb
-*.npz
+sequences/

Dockerfile

@@ -34,11 +34,16 @@ RUN uv sync --locked --no-dev
 
 # COPY pred.cif /app/boltz_results/pred_model_0.cif
 # COPY plddt_0.npz /app/boltz_results/plddt_0.npz
-COPY spr_af_scores_mapped.csv /app/spr_af_scores_mapped.csv
 
 EXPOSE 7860
 ENV GRADIO_SERVER_NAME="0.0.0.0"
 ARG FOLDING_PROJECT_CODE="folding_dev"
 ENV FOLDING_PROJECT_CODE=$FOLDING_PROJECT_CODE
 
+# Create directory for HTML output
+RUN mkdir -p ./output/html
+
+# Create volume for HTML output
+VOLUME ["/app/output/html"]
+
 CMD ["uv", "run", "folding-studio-demo"]

Dockerfile.secretion

@@ -1,20 +0,0 @@
-# Use official Rosetta as base image
-FROM rosettacommons/rosetta:latest
-
-# Install system dependencies
-RUN apt-get update && apt-get install -y \
-    build-essential \
-    wget \
-    && rm -rf /var/lib/apt/lists/*
-
-# Set up working directory
-WORKDIR /app
-
-# Copy Aggrescan3D package
-COPY aggrescan3d /app/aggrescan3d
-
-# Install Aggrescan3D and its dependencies
-RUN pip install --no-cache-dir /app/aggrescan3d
-
-# Default command
-CMD ["/bin/bash"]

aggrescan3d/Aggrescan3D.egg-info/PKG-INFO

@@ -1,11 +0,0 @@
-Metadata-Version: 2.1
-Name: Aggrescan3D
-Version: 1.1.0
-Summary: Aggrescan3D - protein aggregation analysis standalone application
-Home-page: https://bitbucket.org/lcbio/aggrescan3d
-Author: Laboratory of Computational Biology
-License: free for non-commercial users
-License-File: LICENCE
-Requires-Dist: numpy
-Requires-Dist: matplotlib>=2.0
-Requires-Dist: requests

aggrescan3d/Aggrescan3D.egg-info/SOURCES.txt

@@ -1,31 +0,0 @@
-LICENCE
-README.md
-setup.py
-Aggrescan3D.egg-info/PKG-INFO
-Aggrescan3D.egg-info/SOURCES.txt
-Aggrescan3D.egg-info/dependency_links.txt
-Aggrescan3D.egg-info/entry_points.txt
-Aggrescan3D.egg-info/not-zip-safe
-Aggrescan3D.egg-info/requires.txt
-Aggrescan3D.egg-info/top_level.txt
-aggrescan/__init__.py
-aggrescan/__main__.py
-aggrescan/aggrescan_3d.py
-aggrescan/analysis.py
-aggrescan/auto_mutation.py
-aggrescan/dynamic_module.py
-aggrescan/foldx_module.py
-aggrescan/logger.py
-aggrescan/newRunJob.py
-aggrescan/optparser.py
-aggrescan/paintit.py
-aggrescan/pdb.py
-aggrescan/postProcessing.py
-aggrescan/data/buildModel.txt
-aggrescan/data/freesasa.exe
-aggrescan/data/paintit.py
-aggrescan/data/repairPDB.txt
-aggrescan/data/rotabase.txt
-aggrescan/data/superimpose.pml
-aggrescan/data/freesasa-2.0.1/src/freesasa
-aggrescan/data/matrices/aggrescan.mat

aggrescan3d/Aggrescan3D.egg-info/dependency_links.txt

@@ -1 +0,0 @@
-

aggrescan3d/Aggrescan3D.egg-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-aggrescan = aggrescan.__main__:run_program

aggrescan3d/Aggrescan3D.egg-info/not-zip-safe

@@ -1 +0,0 @@
-

aggrescan3d/Aggrescan3D.egg-info/requires.txt

@@ -1,3 +0,0 @@
-numpy
-matplotlib>=2.0
-requests

aggrescan3d/Aggrescan3D.egg-info/top_level.txt

@@ -1 +0,0 @@
-aggrescan

aggrescan3d/LICENCE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2018 Mateusz Kurcinski
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

aggrescan3d/README.md

@@ -1,370 +0,0 @@
-![Aggrescan3D logo](https://bitbucket.org/lcbio/aggrescan3d/wiki/logo.png "Aggrescan3D logo")
-
-This is a repository for Aggrescan3D standalone application developed by the [Laboratory of Computational Biology at University of Warsaw](http://lcbio.pl) in cooperation with the [Laboratory of Protein Folding and Conformational Diseases at Univesity of Barcelona](https://ibb.uab.cat/wp-content/themes/viral/modules/ibb_membres/view_grup.php?CodiGrup=36). 
-
-## Detailed instructions and tutorials are provided on [Aggrescan3D WIKI PAGE](https://bitbucket.org/lcbio/aggrescan3d/wiki/Home) ##
-
--------------------------------------------
-### Table of contents
-[1. Introduction](#markdown-header-introduction)
-
-[2. Windows installation guide](#markdown-header-windows-users)
-
-[3. Linux installation guide](#markdown-header-linux-users)  
-  
-[4. macOS installation guide](#markdown-header-macos-users)
-
-[5. Docker image](#markdown-header-docker-image)
-
----
-
-## Introduction
-*Aggrescan3D* can be installed on Linux, macOS or Windows. This comprehensive tutorial is aimed to guide users through the installation process and is split into three parts for corresponding systems. 
-
-*Aggrescan3D* is a python package using *Python 2.7* version. We *highly* recommend that you use the scientific Anaconda distribution that comes with pre-installed packages 
-and conda package manager which allows for an easier and less error prone installation. If you choose to use Anaconda simply go to [their web page](https://www.anaconda.com/download/)
-and download a Python 2.7 installation for your target operating system (the installer will suggest installing only for current user for Windows systems we also advise that as managing an all-user install can be more challenging 
-and this guide assumes that the user chooses the recommended option). Further steps will give specific instructions for conda users as well as for vanilla python.
-
-##### Tips for users who are not familiar with Python or using command prompt/terminal:
-- *Python3.X* is **NOT** the latest version of *Python2.7* and you should always use *Python2.7* to run Aggrescan3D.
-- Throughout this tutorial a PATH will be frequently mentioned. PATH is a variable that tells the system where to look for your installed programs when you issue commands. Detailed instructions on how to modify it will be given in appropriate parts of this guide.
-- Most sections of this guide contain a correctness test step which can be executed to see wether or not the isntallation was successful. When in doubt run the test. 
-- While this tutorial attempts to covers much ground as possible if something goes wrong please contact us for assistance this will also help us improve our software and this guide too!
-
----
-
-## Windows users
-
-#### 1. Python 2.7 
-
-##### Anaconda distribution 
-
-If you have chosen to use Anaconda this step is already done. 
-
-* Please do note that at this point you should always use  the Anaconda Prompt available in the start menu under that name instead of the regular command prompt.
-
-##### Vanilla Python distribution   
-
-- Follow instructions on [python.org](https://python.org). During the installation process select to include pip and setuptools as those will be necessary. 
-- Add Python27/Scripts (by default under C:\Python27\Scripts) folder to your PATH. This folder contains pip which will install Aggrescan3D as well as it is the folder which will contain the Aggrescan3D program once its installed.
-
-Follow the steps described in GFortran section. The folder should be located at ```C:\Python27\Scripts``` by default so either follow the steps in the Control Panel or type:
-
-```
-set PATH=%PATH%;C:\Python27\Scripts
-``` 
-
-- Note that you have to re-type that in each command prompt in which you want to use *pip* or *Aggrescan3D*.  
-
-##### pip not installed with Python
-
-If you chose not to install pip with your Python installation you need to do that manually. 
-Assuming you've already made Python2.7 accessible under command "python", download [this](https://bootstrap.pypa.io/get-pip.py) script, 
-change to the directory with downloaded script and run:
-
-```python get-pip.py```
- 
-##### Correctness test 
-To check if pip (hence also Python) are working open a  `command
-prompt` (press `cmd + R`; enter "cmd"; hit `enter`) and run the following command:
-
-```pip freeze```
-
-This should list all the packages that you have currently installed.
-
-If you wish to check that you have the correct Python version add the Python binary (python.exe) replacing the example path with your respective one:
-
-```set PATH=%PATH%;C:\Python27``` 
-
-And then type:
-
-```python --version```
-
-Minimum recommended python version for Aggrescan3D is 2.7.12 but as low as 2.7.6 should work. We recommend that you download the latest version from
-[python.org](https://python.org).
-
-#### 2. FoldX (optional)
-
- In order to run stability calculations or mutant calculations FoldX has to be present on the system and PATH to it provided to the program upon running a calculation. 
- 
- FoldX is free for academic use and the licence can be obtained at http://foldxsuite.crg.eu/ 
-
-#### 3. *CABS-flex* (optional)
-
- In order to run the dynamic mode (*highly recommneded*) one has to install *CABS-flex*. Detailed instructions how to do so can be found [here](https://bitbucket.org/lcbio/cabsflex/src/master/README.md)
-
-#### 4. *Aggrescan3D*
-##### Anaconda users
-In your Anaconda Prompt type:
-
-```conda install -c lcbio aggrescan3d```
-
-##### Vanilla Python
-In the regular command prompt type:
-
-```pip install aggrescan3d```
-
-##### Correctness test 
-Run a simulation of lcbio's favorite 2gb1 with:
-
-```aggrescan -i 2gb1 -w test_run -v 4```
-
-- If the result is `'aggrescan3d' is not recognized as an internal or external command, operable program or batch file.` it means that your Python's Scripts folder is not on the PATH variable.
-- If you see a ```Simulation completed successfully``` message, congratulations you have completed your first *aggrescan3d* simulation. 
-
-To check if the server app works:
-
-```a3d_server```
-
-- Open your favourite web browser (Be warned though - Internet Explorer will not be able to provide full functionality)
-- Go to localhost:5000
-- ** Some of the app functionality might not work on the Windows system (namely job stopping) and the app is generally less responsive and more prone to hang should work well in most cases though ** 
-
----
-
-## Linux users ##
-
-#### 1. Python 2.7 
-
-##### Anaconda distribution 
-
-If you have chosen to use Anaconda this step is already done. Anaconda installer should ask you if you want it to be added to your PATH, 
-for most users this is desirable because it means that when typing ```python``` it will call Anaconda's Python rather than regular one.  
-
-* Check if the ```python``` command refers to Anaconda Python type:
-
-```python --version```
-
-The output should be something like ```Python 2.7.14 :: Anaconda, Inc. ```. If it is not add a following line to your ~/.bashrc file (found in the user's home directory) 
-replacing the path with your anaconda's installation path:
-
-```export $PATH="/absolute/path/to/anaconda2/bin:$PATH"```
-
-and then close and reopen the terminal or simply run:
-
-```source ~/.bashrc```
-
-##### Vanilla Python distribution   
-
-Python 2.7 should be present on all unix systems, to verify the version, open your terminal and type:
-
-```python --version```
-
-We recommended python version for 2.7.12 or higher but earlier releases might also work. 
-
-##### pip not installed with Python
-
-pip should also be installed by default on most unix systems, verify that it works issuing the following command:
-
-```pip freeze```
-
-This should return a list of installed packages for your Python. 
-if that is not the case install it using your system's package manager:
-
-```sudo apt-get install python-pip```
-
-#### 2. FoldX (optional)
-
- In order to run stability calculations or mutant calculations FoldX has to be present on the system and PATH to it provided to the program upon running a calculation. 
- 
- FoldX is free for academic use and the licence can be obtained at http://foldxsuite.crg.eu/ 
-
-#### 3. *CABS-flex* (optional)
-
- In order to run the dynamic mode (*highly recommneded*) one has to install *CABS-flex*. Detailed instructions how to do so can be found [here](https://bitbucket.org/lcbio/cabsflex/src/master/README.md)
-
-#### 4. *Aggrescan3D*
-##### Anaconda users
-Simply type:
-
-```conda install -c lcbio aggrescan3d```
-
-##### Vanilla Python
-Simply type:
-
-```pip install aggrescan3d```
-
-##### **Troubleshooting**
-
-- If pip install fails due to writing rights **do not use sudo pip install.** 
-
-- Depending on your privileges and the way your system is managed you might want or need to install *Aggrescan3D* just for the current user:
-
-```pip install --user aggrescan3d```
-
-- When using the --user flag the binary is placed in a folder that is usually not on your PATH. Usually it is located in your 
-```$HOME/.local/bin``` but check if that is the case before continuing. Once you located the binary add its location to your path via editing your .bashrc folder in home directory. Add the line:
-
-```export PATH="$HOME/.local/bin:$PATH"```
-
-##### Correctness test 
-Run a simulation of lcbio's favorite 2gb1 with:
-
-```aggrescan -i 2gb1 -w test_run -v 4```
-
-- If the result is `'aggrescan3d' is not recognized as an internal or external command, operable program or batch file.` it means that your Python's Scripts folder is not on the PATH variable.
-- If you see a ```Simulation completed successfully``` message, congratulations you have completed your first *aggrescan3d* simulation. 
-
-To check if the server app works:
-
-```a3d_server```
-
-- Open your favourite web browser
-- Go to 0.0.0.0:5000 (if the server is not responding depending on the loopback settings localhost:5000 might work)
-
----
-
-## macOS users
-
-#### 1. Python 2.7 
-
-##### Anaconda distribution 
-If you have chosen to use Anaconda this step is already done. Anaconda installer should ask you if you want it to be added to your PATH, 
-for most users this is desirable because it means that when typing ```python``` it will call Anaconda's Python rather than regular one.  
-* Check if the ```python``` command refers to Anaconda Python type:
-
-```python --version```
-
-If the result doesnt include the word Anaconda it means your system is using other Python version by default this can be changed by prepending Anaconda to your PATH.
-
-- Move into home directory
-- Create a .bash_profile file using a text editor (like nano) ```nano .bash_profile```
-- Add the line ```export PATH="/absolute/path/to/anaconda2/bin:$PATH"``` with your respective path to anaconda2 installation
-- Save the file and relaunch the terminal 
-
-##### Vanilla Python distribution   
-
-macOS comes with *Python2.7* already installed. To check if you have the correct Python version open the `Terminal.app` and type:
-
-```python --version```
-
-If you get the message: `bash: python: command not found` it may mean that your system doesn't have Python installed, or
-Python's binary is not in the system `PATH`. To check this run in the `Terminal.app` the following command:
-
-```/Library/Frameworks/Python.framework/Versions/2.7/bin/python --version```
-
-If you still get the message: `bash: python: command not found` you need to install *Python2.7*. Otherwise add Python's
-binary to the system's `PATH` by running in the `Terminal.app` the following command and then reopen the terminal:
-
-```echo "export PATH=/Library/Frameworks/Python.framework/Versions/2.7/bin/:$PATH" >> ~/.bash_profile```
-
-##### pip not installed with Python
-
-Assuming you've already installed Python2.7 and made it accessible under command "python" simply install pip via setuptools by:
-
-```sudo easy_install pip```
-
-#### 2. FoldX (optional)
-
- In order to run stability calculations or mutant calculations FoldX has to be present on the system and PATH to it provided to the program upon running a calculation. 
- 
- FoldX is free for academic use and the licence can be obtained at http://foldxsuite.crg.eu/ 
-
-#### 3. *CABS-flex* (optional)
-
- In order to run the dynamic mode (*highly recommneded*) one has to install *CABS-flex*. Detailed instructions how to do so can be found [here](https://bitbucket.org/lcbio/cabsflex/src/master/README.md)
-
-#### 4. *Aggrescan3D*
-##### Anaconda users
-Simply type:
-
-```conda install -c lcbio aggrescan3d```
-
-##### Vanilla Python
-Simply type:
-
-```pip install aggrescan3d```
-
-*For macOS "El Captian" are newer `six` library comes preinstalled and may cause installation erros. Try running: `pip install aggrescan3d --ignore-installed six` instead.*
-
-##### Correctness test 
-Run a simulation of lcbio's favorite 2gb1 with:
-
-```aggrescan -i 2gb1 -w test_run -v 4```
-
-- If the result is `'aggrescan3d' is not recognized as an internal or external command, operable program or batch file.` it means that your Python's Scripts folder is not on the PATH variable.
-- If you see a ```Simulation completed successfully``` message, congratulations you have completed your first *aggrescan3d* simulation. 
-
-To check if the server app works:
-
-```a3d_server```
-
-- Open your favourite web browser
-- Go to 0.0.0.0:5000 (if the server is not responding depending on the loopback settings localhost:5000 might work)
-
----
-
-## Docker image
-
-*Aggrescan3D* is also available as a docker image and this tutorial will guide the user through how to create a local, always available *Aggrescan3D* server on their PC using the Docker technology. This could also be a good workaround for
-users facing compatibility and installation issues.
- 
-*Please note we cannot include FoldX nor Modeller software in distributed images as they require a licence to run. We however explain how to get those running easly and unlok the full potentail of Aggrescan3D inside a Docker container*
- 
-- ```lcbio/a3d_server``` - [conda](https://hub.docker.com/r/lcbio/a3d_server/) based distribution. Included Dockerfile should allow the users to build a Docker Image with dynamic mode support
-
- 
-### Beginner's tutorial
- 
- While we cannot provide a ground-up guide on Docker usage we do provide basic instructions and further reading material that should make it possible to use this without prior experience. This tutorial is Linux oriented but Docker is also available on Windows10 Pro.
- 
-#### 1. Installing Docker
- 
- Please refer to the [docs](https://docs.docker.com/install/) which contain detailed and well written guides for different systems:
- 
- We also recommend you read [this](https://docs.docker.com/get-started/) starter article on the docker docs
- 
- And [this](https://docs.docker.com/install/linux/linux-postinstall/) post-installation tips (especially if you get permission errors and have to always run docker with sudo)
- 
-#### 2. Using dynamic mode in the container
- 
- To do that one has to create their own image based on our conda image.
- 
- - Create a new folder and cd into it ```mkdir docker_build && cd docker_build```
- - Create a Dockerfile and copy the contents which can be found [here](https://hub.docker.com/r/lcbio/a3d_server/)
- - Uncomment the suggested lines and replace XXXX with your Modeller licence key
- - Run ```docker build -t image_name .``` 
- - If the process is successful the image will be available under 'image_name'
- 
-#### 3. Get the *Aggrescan3D* image (skip if you did point 2)
-  
- To make the image available on your system run:
-```
-#!bash
-docker pull lcbio/a3d_server
-```
-#### 4. Running the Docker container
- 
- The basic goal of the conatiner is to provide a server-like service locally. We recommend to use a following command (explained below):
- 
-```
-#!bash
-docker run --name a3d_service -p 5000:5000 -v /your/absolute/path/to/FoldX:/home/FoldX --restart unless-stopped -d a3d_server
-```
- - The name command will assign a name to your container which will make it easier to manipulate it in the future
- - The -p option exposes your container's 5000 port to your machine's 5000 port. This will mean that you can access the service from your machine. 
- - The -v option mounts your FoldX folder inside the container which makes it available to the service. This is necessary if you wish to use the stability calculations or mutations. Please leave the second part (after ':') unchanged and make sure you provide an absoulte path.
- - The restrart unless-stopped will restart the container on system restart meaning it will be always available (Blocking port 5000 though). 
- - The -d options means detach - the container will run in the background  
- 
- Addition interaction with the container can be performed as follows:
-
- - To stop the service: ```docker stop a3d_service```
- - To start it again: ```docker start a3d_service```
- - To restart a running container (in case it hung, etc): ```docker start a3d_service ```
- - To copy files from container to local system (results on the container are stored inside /opt/conda/lib/python2.7/site-packages/a3d_gui/computations/): ```docker cp a3d_service:path/inside/the/container local/path```
- - To delete the container (*this will delete all the simulation results that were not copied to the filesystem!*): ```docker rm a3d_service```
-
- To interact with the container's console for purposes other than the server run it via which will give access to a shell with aggrescan installed: 
- 
-```docker run --name my_container a3d_server /bin/bash```
- 
-#### 5. Further reading 
- 
- - Running docker images [explained](https://www.pluralsight.com/guides/docker-a-beginner-guide)
- - We found [this](https://docker-curriculum.com/) guide to be quite informative and well-written. 
-
-
-
-

aggrescan3d/aggrescan/__init__.py

@@ -1,45 +0,0 @@
-"""Module for simple AGGRESCAN3D method."""
-
-from __future__ import annotations
-import pathlib
-from aggrescan import analysis
-from aggrescan.aggrescan_3d import Residue
-
-
-def run_aggrescan3d(
-    structure_path: str,
-    distance: float = 10,
-) -> list[Residue]:
-    """Run AGGRESCAN3D on the input structure.
-
-    Args:
-        structure_path: Path to pdb structure.
-        distance: Radius around the central atom within which atoms are included in the
-        aggrescan3d score calculation.
-
-    Returns:
-        List of aggrescan3D `Residue` objects.
-        `Residue` objects have the following attributes:
-        - chain: Chain ID.
-        - rsa: Relative surface area. Value in range [0, 100].
-        - score: Aggrescan3D score.
-        - resi: Residue index.
-        - resn: One letter residue type.
-        - coords: Tuple of (x, y, z) coordinates.
-
-    """
-    struct_path = pathlib.Path(structure_path)
-    # Check if structure exists. If it doesn't, it only gets caught by freeSASA and it
-    # throws a confusing error message.
-    if not struct_path.exists():
-        raise RuntimeError(f"Structure '{structure_path}' does not exist.")
-    config = {
-        "distance": distance,
-        "naccess": False,
-        "ph": False,
-    }
-    analysis._run_free_sasa(target=structure_path, agg=".")
-    residues: list[Residue] = analysis._run_aggrescan(
-        target=structure_path, working_dir=".", config=config,
-    )
-    return residues

aggrescan3d/aggrescan/__main__.py

@@ -1,63 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys,shutil
-from . import logger
-from .newRunJob import Job
-from . import optparser as opt
-import traceback as _tr
-
-_name = "Main"
-
-
-def _cleanup(aggrescan_job_instance):
-    """
-    Done to prevent a situation where Job raises an error on initialization and there is nothing to delete
-    Normally deletes or keeps the simulations temporary directory depending on verbosity settings
-    (Can't check for Exceptions in finally block, hence the function)
-    """
-    try:
-        if logger.get_log_level() < 4:
-            shutil.rmtree(aggrescan_job_instance.get_tempdir(),ignore_errors=True)
-            logger.log_file(module_name=_name, msg="Removing temporary files")
-        else:
-            logger.log_file(module_name=_name,
-                            msg="Verbosity higher than 3 - temporary files kept in %s"
-                                % aggrescan_job_instance.get_tempdir())
-    except AttributeError:
-        pass
-
-
-def run_program():
-    try:
-        a = "dummy"  # to avoid cleanup on empty instances
-        options = opt.parse(options=sys.argv[1:])
-        logger.setup(log_level=options['verbose'], remote=options['remote'], work_dir=options["work_dir"])
-        a = Job(config=options)
-        a.run_job()
-        _cleanup(a)
-        logger.info(module_name="Main", msg="Simulation completed successfully.")
-
-    except KeyboardInterrupt:
-        _cleanup(a)
-        logger.info(module_name=_name, msg="Interrupted by user")
-
-    except logger.AggrescanError as custom_error:
-        _cleanup(a)
-        custom_error.generate_error_file()
-        logger.exit_program(module_name=custom_error.module_name,
-                            msg=custom_error.logger_msg,
-                            traceback=None,
-                            exc=custom_error)
-
-    except Exception as e:
-        _cleanup(a)
-        logger.record_exception(trace_stack=_tr.format_exc())
-        logger.critical(module_name=_name,
-                        msg="Unhandled Exception caught: %s." % e.message)
-        if logger.get_log_level() > 2:
-            logger.info(module_name=_name,
-                        msg="Verbosity higher than 2 - raising the Exception to provide traceback.")
-            raise
-        else:
-            logger.exit_program()

aggrescan3d/aggrescan/aggrescan_3d.py

@@ -1,309 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import math
-import csv
-from . import logger
-
-# minimum and maximum surface exposition to be considered
-min_surf = 10
-max_surf = 55
-_name = "agg3D"
-
-
-class Residue:
-    def __init__(self, chain, resi, resn, coords, rsa, score_matrix, ph):
-        if chain == ' ':
-            self.chain = '-'
-        else:
-            self.chain = chain
-        self.resi = resi
-        self.resn = get_one_letter(resn)   # we store it in one-letter code
-        self.coords = coords
-        self.score_matrix = score_matrix
-        self.agg_sup = self.calc_res_agg_fin(rsa=rsa)
-        self.agg_fin = 0
-        self.rsa = 0
-        self.ph = ph
-        self.const_ph_scores = {
-            "A": 0.66,
-            "N": -0.84,
-            "C": 1.66,
-            "Q": -0.87,
-            "G": 0,
-            "I": 2.75,
-            "L": 1.77,
-            "M": 1.30,
-            "F": 3.99,
-            "P": 1.69,
-            "S": -0.99,
-            "T": 0.12,
-            "W": 3.29,
-            "Y": 1.33,
-            "V": 1.45
-        }
-
-        self.aa_data = {
-            'R': {'pKa': 12.5, "R": 0.857546950885663, "PN": 10 ** (-3.66), "PI": 10 ** (-7.38)},
-            'D': {'pKa': 3.5, "R": 0.622376926398327, "PN": 10 ** (-3.18), "PI": 10 ** (-8.54)},
-            'E': {'pKa': 4.2, 'R': 0.940369170156725, 'PN': 10 ** (-3.79), 'PI': 10 ** (-6.2)},
-            'H': {'pKa': 6.6, 'R': 0.812212007706225, 'PN': 10 ** (-4.67), 'PI': 10 ** (-5.97)},
-            'K': {'pKa': 10.5, 'R': 0.9093172437, 'PN': 10 ** (-2.19), 'PI': 10 ** (-6.81)},
-        }
-
-    def __str__(self):
-        return self.chain+self.resn
-
-    def set_agg_fin(self, agg_dis_sum):
-        self.agg_fin = self.agg_sup + agg_dis_sum
-
-    def id(self):
-        return self.chain+self.resn+self.resi
-
-    def set_rsa(self, rsa):
-        self.rsa = rsa
-        self.agg_sup = self.calc_res_agg_fin(rsa=rsa)
-
-    def calc_res_agg_fin(self, rsa):
-        if rsa < min_surf:
-            return 0
-        else:
-            if rsa > max_surf:
-                rsa = max_surf
-            if not self.ph:
-                return float(self.score_matrix[self.resn]) * 0.0599 * math.exp(0.0521 * rsa)
-            else:
-                return self.calc_ph_score() * 0.0599 * math.exp(0.0521 * rsa)
-
-    def calc_ph_score(self):
-        correction_value = -3.13
-        try:
-            return self.const_ph_scores[self.resn]
-        except KeyError:
-            res_data = self.aa_data[self.resn]
-            term1, term2 = self.calc_terms(res_data)
-            corrected_1 = term1 * res_data['R']
-            return (corrected_1 - term2) - correction_value
-
-    def calc_terms(self, data):
-        first = math.log10(data['PN'] + (data['PI'] * 10 ** (abs(data['pKa'] - self.ph))))
-        second = math.log10(1 + 10 ** (abs(data['pKa'] - self.ph)))
-        return first, second
-    
-    @property
-    def score(self):
-        return self.agg_fin
-
-
-class Protein:
-    def __init__(self, pdb_code, residues, out_dir, max_dist):
-        self.name = pdb_code
-        self.residues = residues
-        self.out_dir = out_dir
-        self.max_dist = max_dist
-
-    def __str__(self):
-        return self.name
-
-    def add_residue(self, res):
-        self.residues.append(res)
-
-    def change_res_rsa(self, res_number, res_id, rsa):
-        if self.residues[res_number].id() == res_id:
-            self.residues[res_number].set_rsa(rsa)
-        else:
-            logger.critical(module_name=_name,
-                            msg="Error while parsing freeSasa output. Probably freeSasa failed quietly.")
-            logger.critical(module_name=_name,
-                            msg="Failed to assign rsa to %s proper id is: %s " %
-                                (res_id, self.residues[res_number].id()) +
-                            "(ChainID, residue's one letter code, residue's ID)")
-            raise logger.AggrescanError("Failed to parse freeSasa output. Qutting.",
-                                        module_name=_name)
-
-    def calc_agg_fin(self):
-        """Calculate the agg_dis_sum for every Residue in the Protein"""
-        dist_correction = -2.56 / self.max_dist
-        for central in self.residues:
-            agg_dis_sum = 0
-            if not central.agg_sup == 0:
-                for peripheric in self.residues:
-                    dist = get_distance(central.coords, peripheric.coords)
-                    if dist < self.max_dist and not dist == 0:
-                        agg_dis_sum += peripheric.agg_sup * 1.2915 * math.exp(dist_correction*dist)
-            central.set_agg_fin(agg_dis_sum)
-
-    def short_summary(self):
-        """Return a short summarized output and identify it with a leading #"""
-        total_sum = 0
-        maximum = 0
-        minimum = 0
-        pos_auc = 0
-        neg_auc = 0
-        prev_score = 0
-        res_number = len(self.residues)
-        for res in self.residues:
-            total_sum += res.agg_fin
-            if res.agg_fin > maximum:
-                maximum = res.agg_fin
-            if res.agg_fin < minimum:
-                minimum = res.agg_fin
-            if res.agg_fin != 0:
-                if prev_score != 0:
-                    auc = (res.agg_fin + prev_score)/2
-                    if auc > 0:
-                        pos_auc += abs(auc)
-                    else:
-                        neg_auc += abs(auc)
-                prev_score = res.agg_fin
-        return '#' + self.name + " " + ' '.join(str("%.4f" % round(val, 4))
-                                                for val in (total_sum,
-                                                total_sum/res_number,
-                                                maximum,
-                                                minimum,
-                                                pos_auc))
-
-    def long_output(self):
-        """Return the complete output and identify it with a leading //"""
-        output = ""
-        for res in self.residues:
-            output += '//' + " ".join((res.chain, res.resi, res.resn)) + " %.4f\n" % round(res.agg_fin, 4)
-        return output
-
-    def out_csv(self):
-        """Save the complete output in a csv file"""
-        csv_file = os.path.join(self.out_dir, "A3D.csv")
-        c = csv.writer(open(csv_file, "w"))
-        if os.stat(csv_file).st_size == 0:
-            c.writerow(["protein", "chain", "residue", "residue_name", "score"])
-        for res in self.residues:
-            c.writerow([self.name.split("/")[-1], res.chain, res.resi, res.resn, "%.4f" % round(res.agg_fin, 4)])
-
-    def get_residues(self):
-        return self.residues
-
-
-def get_one_letter(raw):
-    """Return the one letter code for a residue"""
-    if len(raw) > 3:
-        aa = raw[-3:]
-    else:
-        aa = raw
-
-    three_letters = aa.capitalize()
-
-    conversion = {"Ala": "A", "Arg": "R", "Asn": "N", "Asp": "D", "Cys": "C",
-                  "Glu": "E", "Gln": "Q", "Gly": "G", "His": "H", "Ile": "I",
-                  "Leu": "L", "Lys": "K", "Met": "M", "Phe": "F", "Pro": "P",
-                  "Ser": "S", "Thr": "T", "Trp": "W", "Tyr": "Y", "Val": "V"}
-    try:
-        one_letter = conversion[three_letters]
-    except KeyError:
-        logger.warning(module_name=_name,
-                       msg='Could not recognize the following residue symbol: "%s"' % raw)
-        one_letter = None
-    return one_letter
-
-
-def get_distance(a, b):
-    """Return the distance between two cartesian tri dimensional points"""
-    return math.sqrt((a[0] - b[0])**2 +
-                     (a[1] - b[1])**2 +
-                     (a[2] - b[2])**2)
-
-
-def parse_matrix(filename=''):
-    """Parse the matrix input into a dictionary"""
-    with open(filename, 'r') as fh:
-        matdict = {}
-        for line in fh.readlines():
-            if not line == '\n':
-                pair = line.strip().split(" ")
-                matdict[pair[0]] = pair[1]
-
-    return matdict
-
-
-def parse_naccess(pdb_code, work_dir, score_matrix, max_dist, ph):
-    """Parse the output of naccess into an object of class Protein"""
-    with open(os.path.join(work_dir,pdb_code) + ".rsa", "r") as fh:
-        rsa_dict = {line[3:8].strip() +  # resn
-                    line[8] +   # chain
-                    line[9:16].strip():  # resi
-                    float(line[22:28].strip())  # rsa
-                    for line in fh.readlines()
-                    if line.startswith('RES')}
-
-    my_protein = Protein(pdb_code=pdb_code, residues=[], out_dir=work_dir, max_dist=max_dist)
-    center_atom = 'CA'  # atom to be considered the center of the residue
-
-    with open(os.path.join(work_dir,pdb_code) + '.asa', 'r') as fh:
-        for line in fh.readlines():
-            # use data only from alpha carbons
-            if line[12:16].strip() == center_atom:
-                # extract the data according to the characteristics of the pdb format
-                my_chain = line[21]
-                my_resi = line[22:29].strip()
-                my_resn = line[17:20].strip()
-                x = float(line[30:38].strip())
-                y = float(line[38:46].strip())
-                z = float(line[46:54].strip())
-                res_id = my_resn + my_chain + my_resi
-                my_rsa = rsa_dict[res_id]
-                my_protein.add_residue(Residue(chain=my_chain,
-                                               resi=my_resi,
-                                               resn=my_resn,
-                                               coords=(x, y, z),
-                                               rsa=my_rsa,
-                                               score_matrix=score_matrix,
-                                               ph=ph))
-    return my_protein
-
-
-def parse_freesasa(pdb_code, work_dir, filename, score_matrix, max_dist, ph):
-    my_protein = Protein(pdb_code=pdb_code, residues=[], out_dir=work_dir, max_dist=max_dist)
-    residue_count = 0
-    central_atom = 'CA'   # atom to be considered the center of the residue
-    with open(os.path.join(work_dir, filename), 'r') as f:
-        for line in f:
-            if line.startswith("ATOM "):  # this is the same as naccess asa file
-                if line[12:16].strip() == central_atom:
-                    # extract the data according to the characteristics of the pdb format
-                    my_chain = line[21]
-                    my_resi = line[22:29].strip()
-                    my_resn = line[17:20].strip()
-                    x = float(line[30:38].strip())
-                    y = float(line[38:46].strip())
-                    z = float(line[46:54].strip())
-                    my_protein.add_residue(Residue(chain=my_chain,
-                                                   resi=my_resi,
-                                                   resn=my_resn,
-                                                   coords=(x, y, z),
-                                                   rsa=0,
-                                                   score_matrix=score_matrix,
-                                                   ph=ph))
-            elif line.startswith("RES"):   # equivalent to naccess rsa file
-                this_id = line[8] + get_one_letter(line[3:8].strip()) + line[9:16].strip()
-                rsa = float(line[22:28].strip())
-                my_protein.change_res_rsa(res_number=residue_count, res_id=this_id, rsa=rsa)
-                residue_count += 1
-
-    return my_protein
-
-
-def run(pdb_file='', mat_file='', max_dist='', work_dir='', naccess=False, ph=None):
-    score_matrix = parse_matrix(filename=mat_file)
-    pdb_code = pdb_file.split(".")[0]
-    if naccess:
-        my_protein = parse_naccess(pdb_code=pdb_code, work_dir=work_dir,
-                                   score_matrix=score_matrix, max_dist=max_dist, ph=ph)
-    else:
-        my_protein = parse_freesasa(pdb_code=pdb_code, work_dir=work_dir,
-                                    filename="sasa.out", score_matrix=score_matrix, max_dist=max_dist, ph=ph)
-    my_protein.calc_agg_fin()
-    my_protein.out_csv()
-    # short_summary = my_protein.short_summary()+"\n"
-    # long_summary = my_protein.long_output()
-    # return short_summary + long_summary
-    return my_protein.residues

aggrescan3d/aggrescan/analysis.py

@@ -1,82 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import os
-from os.path import join, abspath
-from subprocess import PIPE, Popen
-from pkg_resources import resource_filename
-from .aggrescan_3d import run as run_aggrescan_3d
-from . import logger
-import platform
-
-_name = "Analysis"
-if platform.system() == "Windows":
-    _bin_name = "freesasa.exe"
-elif platform.system() == "Darwin":
-    _bin_name = "freesasa_Darwin"
-else:
-    _bin_name = "freesasa"
-
-
-def aggregation_analysis(config, target="input.pdb", working_dir=".", agg_work_dir=""):
-    """Takes Aggrescaan3D Job class config as an argument and should never change it"""
-    os.chdir(working_dir)  # Just in case one of the programs handles abspaths poorly
-    if config["naccess"]:
-        _run_naccess(target=target, agg=agg_work_dir, naccess_dir=config["naccess"])
-    else:
-        _run_free_sasa(target=target, agg=agg_work_dir)
-    residues = _run_aggrescan(target=target, working_dir=working_dir, config=config)
-    return residues
-
-
-def _run_aggrescan(target, working_dir, config):
-    """
-    Takes target pdb file, working directory for analysis
-    and aggrescan config dict as arguments so need the two in sync
-    """
-    matrix_dir = resource_filename('aggrescan', join("data", "matrices", "aggrescan.mat"))
-    residues = run_aggrescan_3d(target, matrix_dir, config["distance"], working_dir, naccess=config["naccess"], ph=config['ph'])
-    # logger.to_file(filename=join(config["tmp_dir"], "input_output"), content=out, allow_err=False)
-    return residues
-
-
-def _run_free_sasa(target="folded.pdb", agg=""):
-    sasa_dir = resource_filename('aggrescan', join("data", "freesasa-2.0.1", "src", _bin_name))
-    sasa_cmd = [sasa_dir, "--resolution", "100", target, "--radii", "naccess", "--format", "pdb", "--format", "rsa"]
-    logger.debug(module_name="freeSasa", msg="Starting freeSasa with %s" % " ".join(sasa_cmd))
-    _fname = join(agg, "ASA.error")
-    out, err = Popen(sasa_cmd, stdout=PIPE, stderr=PIPE).communicate()
-    if err:
-        logger.to_file(_fname, content=err)
-        try:
-            err = err.decode()
-        except (UnicodeDecodeError, AttributeError):
-            pass
-        for line in err.split("\n"):
-            if "warning" in line:
-                logger.critical(module_name="freeSasa", msg="Warning detected: %s" % line)
-                logger.critical(module_name="freeSasa", msg="Attempting to continue.")
-            else:
-                raise logger.ASAError(program_name="freeSasa", filename=_fname)
-    logger.to_file(filename="sasa.out", content=out, allow_err=False)
-
-
-def _run_naccess(target="folded.pdb", agg="", naccess_dir=""):
-    naccess_cmd = [naccess_dir, target, "-p", "1.4", "-z", "0.05"]
-    logger.debug(module_name=_name, msg="running naccess program with %s" % " ".join(naccess_cmd))
-    _fname = join(agg, "ASA.error")
-    try:
-        out, err = Popen(naccess_cmd, stdout=PIPE, stderr=PIPE).communicate()
-    except OSError:
-        raise logger.AggrescanError("Couldn't start the naccess program. Naccess requires csh shell to be present on the system."
-                                    " If it is present please run the program in debug mode and see if the path printed in "
-                                    "Naccess command actually contains the file.", module_name="Naccess")
-    if err:
-        logger.to_file(filename=_fname, content=err)
-        raise logger.ASAError(program_name="Naccess", filename=_fname)
-    try:
-        for msg in out.split("\n"):
-            if msg:
-                logger.debug(module_name="Naccess", msg=msg)
-    except AttributeError:
-        pass
-

aggrescan3d/aggrescan/auto_mutation.py

@@ -1,182 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-import multiprocessing as mp
-from subprocess import Popen, PIPE
-from collections import OrderedDict
-from os.path import join, isfile
-from .postProcessing import make_auto_mut_plot
-import os
-import re
-import shutil
-from . import logger
-
-_name = "Auto_mut"
-
-# Define some variables that dictate how some properties of this - maybe they get to be parameters in the future
-_score_threshold = -0.2  # How high an A3D score has to be for the residue to be considered for mutation
-_energy_threshold = 0.0   # When a mutation is considered "good"
-_score_diff_threshold = 5  # When a mutation is considered to increase solubility  +5 should accept all while 0 would
-                           # already be qutite restrictive
-_target_mutations = ["E", "K", "D", "R"]  # Glutamic acid, lysine,  aspartic acid, arginine
-
-# The slicing in this code can be hard to read so here is a short summary:
-# Chain ID and residue names come as one letter shorts while the number can have more than one char
-# Final mutation code is <Old residue><New residue><Residue number><Chain ID>
-# The auto_mutation to_exclude argument comes as <Residue number><Chain ID>
-# The one that comes from A3D file comes as < Old residue><Residue number><Chain ID>
-
-
-def run_auto_mutation(work_dir, options, foldx_loc, distance, ph):
-    n_mutations = options[0]
-    n_processes = options[1]
-    to_exclude = []     # Not to worry about it even exists
-    if len(options) > 2:
-        to_exclude = options[2]
-    pool = mp.Pool(n_processes)
-    mutations, avg_score = _mutation_list(work_dir=work_dir, excluded_list=to_exclude, n_mutations=n_mutations)
-    if not mutations:
-        with open(join(work_dir, "Mutations_summary.csv"), "w") as f:   # leave an empty file for the server
-            pass
-        return
-    pool.map(_run_job, [(i, foldx_loc, work_dir, str(distance), ph) for i in mutations])
-
-    _analyze_results(work_dir=work_dir, output_file="Mutations_summary.csv", mutation_list=mutations,
-                     base_avg_score=avg_score)
-    _cleanup(work_dir=work_dir, mutation_list=mutations)
-    try:
-        _plots(work_dir=work_dir)
-    except Exception as e:  # This is hopefully not needed but in case something happens the user will at least see a
-                            # message rather than a traceback
-        logger.critical(module_name=_name, msg="It seems that all the mutation attempts failed or some other unexpected"
-                                               " error arisen while trying to plot the automated mutations.")
-        raise
-
-
-def _mutation_list(work_dir, excluded_list, n_mutations):
-    scores = _parse_a3dcsv(os.path.join(work_dir, "A3D.csv"))
-    avg_score = sum(scores.values())/len(list(scores.values()))
-    mutation_list = []
-    counter = 0
-    for residue, value in list(scores.items()):
-        if value > _score_threshold and residue[1:] not in excluded_list and residue[0] not in _target_mutations \
-                and value != 0:
-            mutation_list.extend(["%s%s%s" % (residue[0], i, residue[1:]) for i in _target_mutations])
-            logger.info(module_name=_name, msg="Residue number %s from chain %s and a score of %.3f (%s) selected "
-                                               "for automated muatation" % (residue[1:-1], residue[-1], value,
-                                                                            _aa_dict_F[residue[0]]))
-            counter += 1
-            if counter >= n_mutations:
-                break
-        elif value > _score_threshold and residue[1:] in excluded_list:
-            logger.info(module_name=_name, msg="Residue number %s from chain %s and a score of %.3f omitted "
-                                               "from automated muatation (excluded by the user)." % (residue[1:-1], residue[-1], value))
-    if not mutation_list:
-        logger.critical(module_name=_name, msg="Couldn't find residues suitable for automated mutations (exceeding a "
-                                               "threshold of %.2f). No automated mutations performed." % _score_threshold)
-    return mutation_list, avg_score
-
-
-def _parse_a3dcsv(filepath):  #TODO this is done on muttiple occasions so maybe should be unified somwhere
-    """
-    Return an OrderedDict of label:score type. The dict is sorted by score so highest is on top
-    """
-    pattern = re.compile(r"^(.*),(.*),(.*),(.*),(.*)$", re.M)
-    scores = OrderedDict()
-    try:
-        with open(filepath, 'r') as f:
-            data = pattern.findall(f.read().replace("\r", ""))[1:]  #
-    except IOError:
-        return False    # The mutation likely failed this should pass the info to analyze_results
-    for line in data:
-        label = line[3] + line[2] + line[1]  # One letter code + residue ID + chain ID (the mutation syntax)
-        aggScore = float(line[4])
-        scores[label] = aggScore
-    scores = OrderedDict(sorted(list(scores.items()), key=lambda x: x[1], reverse=True))
-    return scores
-
-
-def _run_job(args):
-    """
-    Run a single A3D job with a specific mutation
-    args go as follows: mutation code, FoldX location, main job's work dir, a3d distance argument
-    """
-    mutation, foldx, work_dir, distance, ph = args
-    os.chdir(work_dir)
-    if ph:
-        cmd = ["aggrescan", "-i", "output.pdb", "-v", "4", "-w", mutation, "-m", mutation, "-f", foldx,
-               "--subprocess", "--distance", distance]
-    else:
-        cmd = ["aggrescan", "-i", "output.pdb", "-v", "4", "-w", mutation, "-m", mutation, "-f", foldx,
-               "--subprocess", "--distance", distance, "-ph", ph]
-    logger.info(module_name=_name, msg="Mutating residue number %s from chain %s (%s) into %s "
-                                       " " % (mutation[2:-1], mutation[-1], _aa_dict_F[mutation[0]],
-                                              _aa_dict_F[mutation[1]]))  # converting letters into full names
-    proc = Popen(cmd, stdout=PIPE, stderr=PIPE)
-    proc.communicate()
-    if proc.returncode != 0:
-        logger.warning(module_name=_name, msg="Mutation %s could have failed (this can be ignored if the main program "
-                                              "reports the energy difference). Simulation log for that run should be "
-                                               "available at %s" % (mutation,
-                                                                    os.path.join(work_dir, mutation, "Aggrescan.error")))
-
-
-def _analyze_results(work_dir, output_file, mutation_list, base_avg_score):
-    """
-    Analyze the results and select all of those that are not relevant on keeping top X mutations and return the rest
-    to the cleaner that will get rid of them, but keeping their scores in the output_file
-    """
-    data = OrderedDict()
-    unnecessary_results = []
-    for mutation in mutation_list:
-        scores = _parse_a3dcsv(os.path.join(work_dir, mutation, "A3D.csv"))
-        if not scores:
-            continue
-        with open(os.path.join(work_dir, mutation, "MutantEnergyDiff"), 'r') as f:
-            mutation_energy = float(f.read().split()[0])    # This should be guaranteed to work given the check above
-        avg_score = sum(scores.values())/len(list(scores.values()))
-        data[mutation] = [mutation_energy, avg_score, avg_score - base_avg_score]
-        if mutation_energy > _energy_threshold or avg_score - base_avg_score > _score_diff_threshold:
-            unnecessary_results.append(mutation)
-        logger.info(module_name=_name, msg="Effect of mutation residue number %s from chain %s (%s) into %s: "
-                                           "Energy difference: %.4f kcal/mol, Difference in average score from the "
-                                           "base case: %.4f"
-                                           "" % (mutation[2:-1], mutation[-1], _aa_dict_F[mutation[0]],
-                                                 _aa_dict_F[mutation[1]], mutation_energy, avg_score - base_avg_score))
-    data = OrderedDict(sorted(list(data.items()), key=lambda x: x[1][0]))   # sort by mutation energy
-    with open(os.path.join(work_dir, output_file), "w") as f:
-        f.write("%s,%s,%s,%s\n" % ("Mutation", "EnergyDiff", "AvgScore", "AvgScoreDiff"))
-        for mutation, values in list(data.items()):
-            f.write("%s,%.4f,%.4f,%.4f\n" % (mutation, values[0], values[1], values[2]))
-    return unnecessary_results
-
-
-def _cleanup(work_dir, mutation_list):
-    for mutation in mutation_list:
-        if isfile(join(work_dir, mutation, "A3D.csv")) and isfile(join(work_dir, mutation, "output.pdb")):
-            shutil.move(join(work_dir, mutation, "A3D.csv"), join(work_dir, "%s%s" % (mutation, ".csv")))
-            shutil.move(join(work_dir, mutation, "output.pdb"), join(work_dir, "%s%s" % (mutation, ".pdb")))
-            shutil.rmtree(join(work_dir, mutation))
-        else:
-            if isfile(join(work_dir, mutation, "Aggrescan.error")):
-                shutil.move(join(work_dir, mutation, "Aggrescan.error"), join(work_dir, "%s%s" % (mutation, ".error")))
-                shutil.rmtree(join(work_dir, mutation))
-            else:
-                with open(join(work_dir, "%s%s" %(mutation, ".error")), "w") as f:
-                    f.write("The mutation has failed and no error log was created during the simulation. "
-                            "This is unexpected and if you require further assistance please contact us or leave a bug "
-                            "report on our bitbucket at "
-                            "https://bitbucket.org/lcbio/aggrescan3d/issues?status=new&status=open")
-
-
-def _plots(work_dir):
-    make_auto_mut_plot(work_dir)
-
-
-# This is a copy from somewhere else, maybe should put it somewhere for imports
-_aa_dict_F = {'A': 'alanine', 'R': 'arginine', 'N': 'asparagine',
-              'D': 'aspartic acid', 'C': 'cysteine', 'E': 'glutamic acid',
-              'Q': 'glutamine', 'G': 'glycine', 'H': 'histidine',
-              'I': 'isoleucine', 'L': 'leucine', 'K': 'lysine',
-              'M': 'methionine', 'F': 'phenylalanine', 'P': 'proline',
-              'S': 'serine', 'T': 'threonine', 'W': 'tryptophan',
-              'Y': 'tyrosine', 'V': 'valine', 'X': 'unknown'}

aggrescan3d/aggrescan/data/buildModel.txt

@@ -1,3 +0,0 @@
-pdb=input_Repair.pdb
-command=BuildModel
-mutant-file=individual_list.txt

aggrescan3d/aggrescan/data/freesasa-2.0.1/INSTALL

@@ -1,370 +0,0 @@
-Installation Instructions
-*************************
-
-Copyright (C) 1994-1996, 1999-2002, 2004-2011 Free Software Foundation,
-Inc.
-
-   Copying and distribution of this file, with or without modification,
-are permitted in any medium without royalty provided the copyright
-notice and this notice are preserved.  This file is offered as-is,
-without warranty of any kind.
-
-Basic Installation
-==================
-
-   Briefly, the shell commands `./configure; make; make install' should
-configure, build, and install this package.  The following
-more-detailed instructions are generic; see the `README' file for
-instructions specific to this package.  Some packages provide this
-`INSTALL' file but do not implement all of the features documented
-below.  The lack of an optional feature in a given package is not
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-
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-
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-
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-     This target is generally not run by end users.
-
-Compilers and Options
-=====================
-
-   Some systems require unusual options for compilation or linking that
-the `configure' script does not know about.  Run `./configure --help'
-for details on some of the pertinent environment variables.
-
-   You can give `configure' initial values for configuration parameters
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-is an example:
-
-     ./configure CC=c99 CFLAGS=-g LIBS=-lposix
-
-   *Note Defining Variables::, for more details.
-
-Compiling For Multiple Architectures
-====================================
-
-   You can compile the package for more than one kind of computer at the
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-
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-
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-compiler but only a single `-arch' option to the preprocessor.  Like
-this:
-
-     ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
-                 CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \
-                 CPP="gcc -E" CXXCPP="g++ -E"
-
-   This is not guaranteed to produce working output in all cases, you
-may have to build one architecture at a time and combine the results
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-
-Installation Names
-==================
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-   By default, `make install' installs the package's commands under
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-it does better at avoiding recompilation issues, and works well even
-when some directory options were not specified in terms of `${prefix}'
-at `configure' time.
-
-Optional Features
-=================
-
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-Particular systems
-==================
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-Defining Variables
-==================
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-them in the `configure' command line, using `VAR=value'.  For example:
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-an Autoconf bug.  Until the bug is fixed you can use this workaround:
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-     CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash
-
-`configure' Invocation
-======================
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-   `configure' recognizes the following options to control how it
-operates.
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-     Print a summary of all of the options to `configure', and exit.
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-     `configure', and exit.  The `short' variant lists options used
-     only in the top level, while the `recursive' variant lists options
-     also present in any nested packages.
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-`-V'
-     Print the version of Autoconf used to generate the `configure'
-     script, and exit.
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-     traditionally `config.cache'.  FILE defaults to `/dev/null' to
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-     Run the configure checks, but stop before creating any output
-     files.
-
-`configure' also accepts some other, not widely useful, options.  Run
-`configure --help' for more details.
-

aggrescan3d/aggrescan/data/freesasa-2.0.1/Makefile

@@ -1,795 +0,0 @@
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aggrescan3d/aggrescan/data/freesasa-2.0.1/README.md

@@ -1,136 +0,0 @@
-FreeSASA
-========
-
-[![DOI](https://zenodo.org/badge/18467/mittinatten/freesasa.svg)](https://zenodo.org/badge/latestdoi/18467/mittinatten/freesasa)
-[![Build Status](https://travis-ci.org/mittinatten/freesasa.svg?branch=master)](https://travis-ci.org/mittinatten/freesasa)
-[![Coverage Status](https://coveralls.io/repos/github/mittinatten/freesasa/badge.svg?branch=master)](https://coveralls.io/github/mittinatten/freesasa?branch=master)
-
-C-library for calculating Solvent Accessible Surface Areas.
-
-License: MIT (see file LICENSE). Copyright: Simon Mitternacht 2013-2016.
-
-FreeSASA is a C library and command line tool for calculating Solvent
-Accessible Surface Area (SASA) of biomolecules. It is designed to be
-simple to use with defaults, but allows customization of all
-parameters of the calculation and provides a few different tools to
-analyze the results. Python bindings are also included in the
-repository.
-
-By default Lee & Richards' algorithm is used, but Shrake & Rupley's is
-also available. Both can be parameterized to arbitrary precision, and
-for high resolution versions of the algorithms, the calculations give
-identical results.
-
-FreeSASA assigns a radius and a class to each atom. The atomic radii
-are by default the _ProtOr_ radii defined by Tsai et
-al. ([JMB 1999, 290: 253](http://www.ncbi.nlm.nih.gov/pubmed/10388571))
-for standard amino acids and nucleic acids, and the van der Waals
-radius of the element for other atoms. Each atom is also classified as
-either polar or apolar.
-
-Users can provide their own atomic radii and classifications via
-configuration files. The input format for configuration files is
-described in the
-[online documentation](http://freesasa.github.io/doxygen/Config-file.html),
-and the `share/` directory contains some sample configurations,
-including one for the NACCESS parameters
-([Hubbard & Thornton 1993](http://www.bioinf.manchester.ac.uk/naccess/)).
-
-Version 2.0 adds some new features and breaks a few parts of the
-interface from 1.x (mainly the API), see CHANGELOG.md for detailed
-information.
-
-Building and installing
-------------------------
-
-FreeSASA can be compiled and installed using the following
-
-    ./configure
-    make && make install
-
-NB: If the source is downloaded from the git repository the
-configure-script needs to be set up first using `autoreconf -i`. Users
-who don't have autotools installed, can download a tarball that
-includes the autogenerated scripts from http://freesasa.github.io/ or
-from the latest
-[GitHub-release](https://github.com/mittinatten/freesasa/releases).
-
-The above commands build and install the command line tool `freesasa`
-(built in `src/`), the command
-
-    freesasa -h
-
-gives an overview of options. To run a calculation from PDB-file input
-using the defaults, simply type
-
-    freesasa <pdb-file>
-
-In addition, `make install` installs the header `freesasa.h` and the
-library `libfreesasa`. If the configure script is called with the
-option `--enable-python-bindings`, the Python module is also built and
-installed.
-
-The configuration can be changed with these options:
-* `--enable-python-bindings` builds Python bindings, requires Cython
-    0.21 or higher. On some platforms the C library needs to be
-    compiled with `CFLAGS=-fPIC` to allow it to be linked to the
-    Python module.
-* `--with-python=<python>` specifies which python binary to use
-* `--disable-json` build without support for JSON output.
-* `--disable-xml` build without support for XML output.
-* `--disable-threads` build without multithreaded calculations
-* `--enable-doxygen` activates building of Doxygen documentation
-
-For developers:
-* `--enable-check` enables unit-testing using the Check framework
-* `--enable-gcov` adds compiler flags for measuring coverage of tests
-    using gcov
-* `--enable-parser-generator` rebuild parser/lexer source from
-    Flex/Bison sources (the autogenerated code is included in the
-    repository, so no need to do this if you are not going to change
-    the parser).
-
-Documentation
--------------
-
-Enabling Doxygen builds a [full reference
-manual](http://freesasa.github.io/doxygen/), documenting both CLI and
-API in the folder `doc/html/doxygen/`, also available on the web at
-http://freesasa.github.io/.
-
-After building the package, calling
- 
-    freesasa -h
-    
-explains how the commandline tool can be used.
-
-Compatibility and dependencies
-------------------------------
-
-The program has been tested successfully with several versions of GNU
-C Compiler and Clang/LLVM. The library can be built using only
-standard C and GNU libraries. The standard build depends on
-[json-c](https://github.com/json-c/json-c) and
-[libxml2](http://xmlsoft.org/). These can be disabled by configuring
-with `--disable-json` and `--disable-xml` respectively.
-
-Developers who want to do testing need to install the Check unit
-testing framework. Building the full reference manual requires Doxygen
-(version > 1.8.8). Building the Python bindings requires
-Cython. Changing the selection parser and lexer requires Flex and
-Bison. These build options, which add extra dependencies, are disabled
-by default to simplify installation for users only interested in the
-command line tool and and/or C Library.
-
-Citing FreeSASA
----------------
-
-FreeSASA can be cited using the following publication
-
-* Simon Mitternacht (2016) FreeSASA: An open source C library for
-  solvent accessible surface area calculations. _F1000Research_
-  5:189. (doi:
-  [10.12688/f1000research.7931.1](http://dx.doi.org/10.12688/f1000research.7931.1))
-
-The [DOI numbers from Zenodo](https://zenodo.org/badge/latestdoi/18467/mittinatten/freesasa)
-can be used to cite a specific version of FreeSASA.

aggrescan3d/aggrescan/data/freesasa-2.0.1/aclocal.m4

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-dnl Copyright © 2012-2015 Dan Nicholson <[email protected]>
-dnl
-dnl This program is free software; you can redistribute it and/or modify
-dnl it under the terms of the GNU General Public License as published by
-dnl the Free Software Foundation; either version 2 of the License, or
-dnl (at your option) any later version.
-dnl
-dnl This program is distributed in the hope that it will be useful, but
-dnl WITHOUT ANY WARRANTY; without even the implied warranty of
-dnl MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-dnl General Public License for more details.
-dnl
-dnl You should have received a copy of the GNU General Public License
-dnl along with this program; if not, write to the Free Software
-dnl Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
-dnl 02111-1307, USA.
-dnl
-dnl As a special exception to the GNU General Public License, if you
-dnl distribute this file as part of a program that contains a
-dnl configuration script generated by Autoconf, you may include it under
-dnl the same distribution terms that you use for the rest of that
-dnl program.
-
-dnl PKG_PREREQ(MIN-VERSION)
-dnl -----------------------
-dnl Since: 0.29
-dnl
-dnl Verify that the version of the pkg-config macros are at least
-dnl MIN-VERSION. Unlike PKG_PROG_PKG_CONFIG, which checks the user's
-dnl installed version of pkg-config, this checks the developer's version
-dnl of pkg.m4 when generating configure.
-dnl
-dnl To ensure that this macro is defined, also add:
-dnl m4_ifndef([PKG_PREREQ],
-dnl     [m4_fatal([must install pkg-config 0.29 or later before running autoconf/autogen])])
-dnl
-dnl See the "Since" comment for each macro you use to see what version
-dnl of the macros you require.
-m4_defun([PKG_PREREQ],
-[m4_define([PKG_MACROS_VERSION], [0.29.1])
-m4_if(m4_version_compare(PKG_MACROS_VERSION, [$1]), -1,
-    [m4_fatal([pkg.m4 version $1 or higher is required but ]PKG_MACROS_VERSION[ found])])
-])dnl PKG_PREREQ
-
-dnl PKG_PROG_PKG_CONFIG([MIN-VERSION])
-dnl ----------------------------------
-dnl Since: 0.16
-dnl
-dnl Search for the pkg-config tool and set the PKG_CONFIG variable to
-dnl first found in the path. Checks that the version of pkg-config found
-dnl is at least MIN-VERSION. If MIN-VERSION is not specified, 0.9.0 is
-dnl used since that's the first version where most current features of
-dnl pkg-config existed.
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-m4_pattern_allow([^PKG_CONFIG(_(PATH|LIBDIR|SYSROOT_DIR|ALLOW_SYSTEM_(CFLAGS|LIBS)))?$])
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-
-if test "x$ac_cv_env_PKG_CONFIG_set" != "xset"; then
-	AC_PATH_TOOL([PKG_CONFIG], [pkg-config])
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-if test -n "$PKG_CONFIG"; then
-	_pkg_min_version=m4_default([$1], [0.9.0])
-	AC_MSG_CHECKING([pkg-config is at least version $_pkg_min_version])
-	if $PKG_CONFIG --atleast-pkgconfig-version $_pkg_min_version; then
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-])dnl PKG_PROG_PKG_CONFIG
-
-dnl PKG_CHECK_EXISTS(MODULES, [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND])
-dnl -------------------------------------------------------------------
-dnl Since: 0.18
-dnl
-dnl Check to see whether a particular set of modules exists. Similar to
-dnl PKG_CHECK_MODULES(), but does not set variables or print errors.
-dnl
-dnl Please remember that m4 expands AC_REQUIRE([PKG_PROG_PKG_CONFIG])
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-dnl _PKG_CONFIG([VARIABLE], [COMMAND], [MODULES])
-dnl ---------------------------------------------
-dnl Internal wrapper calling pkg-config via PKG_CONFIG and setting
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-])dnl _PKG_CONFIG
-
-dnl _PKG_SHORT_ERRORS_SUPPORTED
-dnl ---------------------------
-dnl Internal check to see if pkg-config supports short errors.
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-])dnl _PKG_SHORT_ERRORS_SUPPORTED
-
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-dnl PKG_CHECK_MODULES(VARIABLE-PREFIX, MODULES, [ACTION-IF-FOUND],
-dnl   [ACTION-IF-NOT-FOUND])
-dnl --------------------------------------------------------------
-dnl Since: 0.4.0
-dnl
-dnl Note that if there is a possibility the first call to
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-_PKG_TEXT
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-])dnl PKG_CHECK_MODULES
-
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-dnl PKG_CHECK_MODULES_STATIC(VARIABLE-PREFIX, MODULES, [ACTION-IF-FOUND],
-dnl   [ACTION-IF-NOT-FOUND])
-dnl ---------------------------------------------------------------------
-dnl Since: 0.29
-dnl
-dnl Checks for existence of MODULES and gathers its build flags with
-dnl static libraries enabled. Sets VARIABLE-PREFIX_CFLAGS from --cflags
-dnl and VARIABLE-PREFIX_LIBS from --libs.
-dnl
-dnl Note that if there is a possibility the first call to
-dnl PKG_CHECK_MODULES_STATIC might not happen, you should be sure to
-dnl include an explicit call to PKG_PROG_PKG_CONFIG in your
-dnl configure.ac.
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-PKG_CONFIG=$_save_PKG_CONFIG[]dnl
-])dnl PKG_CHECK_MODULES_STATIC
-
-
-dnl PKG_INSTALLDIR([DIRECTORY])
-dnl -------------------------
-dnl Since: 0.27
-dnl
-dnl Substitutes the variable pkgconfigdir as the location where a module
-dnl should install pkg-config .pc files. By default the directory is
-dnl $libdir/pkgconfig, but the default can be changed by passing
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-dnl PKG_NOARCH_INSTALLDIR([DIRECTORY])
-dnl --------------------------------
-dnl Since: 0.27
-dnl
-dnl Substitutes the variable noarch_pkgconfigdir as the location where a
-dnl module should install arch-independent pkg-config .pc files. By
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-dnl PKG_CHECK_VAR(VARIABLE, MODULE, CONFIG-VARIABLE,
-dnl [ACTION-IF-FOUND], [ACTION-IF-NOT-FOUND])
-dnl -------------------------------------------
-dnl Since: 0.28
-dnl
-dnl Retrieves the value of the pkg-config variable for the given module.
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-
-AS_VAR_IF([$1], [""], [$5], [$4])dnl
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-
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-@HAVE_CYTHON_TRUE@		@PYTHON@ setup.py clean --all;
-@HAVE_CYTHON_TRUE@	rm python/freesasa.so
-
-@HAVE_CYTHON_TRUE@all-local: $(python_bindings)
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:

aggrescan3d/aggrescan/data/freesasa-2.0.1/bindings/check-python

@@ -1,10 +0,0 @@
-#!/bin/bash
-
-if [ ! -e "/home/olek/agroscan/aggrescan3d/freesasa-2.0.1/bindings/python/data" ]; then
-    ln -s /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/tests/data /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/bindings/python/
-fi
-if [ ! -e "/home/olek/agroscan/aggrescan3d/freesasa-2.0.1/bindings/python/share" ]; then
-    ln -s /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/share /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/bindings/python/
-fi
-
- python/test.py

aggrescan3d/aggrescan/data/freesasa-2.0.1/bindings/check-python.in

@@ -1,10 +0,0 @@
-#!/bin/bash
-
-if [ ! -e "@abs_top_srcdir@/bindings/python/data" ]; then
-    ln -s @abs_top_srcdir@/tests/data @abs_top_srcdir@/bindings/python/
-fi
-if [ ! -e "@abs_top_srcdir@/bindings/python/share" ]; then
-    ln -s @abs_top_srcdir@/share @abs_top_srcdir@/bindings/python/
-fi
-
-@PYTHON@ python/test.py

aggrescan3d/aggrescan/data/freesasa-2.0.1/bindings/python/cfreesasa.pxd

@@ -1,175 +0,0 @@
-from libc.stdio cimport FILE
-
-cdef extern from "freesasa.h":
-    ctypedef enum freesasa_algorithm:
-        FREESASA_LEE_RICHARDS, FREESASA_SHRAKE_RUPLEY
-
-    ctypedef enum freesasa_verbosity:
-        FREESASA_V_NORMAL, FREESASA_V_NOWARNINGS, FREESASA_V_SILENT, FREESASA_V_DEBUG
-
-    ctypedef enum freesasa_atom_class:
-        FREESASA_ATOM_APOLAR, FREESASA_ATOM_POLAR, FREESASA_ATOM_UNKNOWN
-
-    cdef int FREESASA_SUCCESS
-    cdef int FREESASA_FAIL
-    cdef int FREESASA_WARN
-
-    cdef int FREESASA_INCLUDE_HETATM
-    cdef int FREESASA_INCLUDE_HYDROGEN
-    cdef int FREESASA_SEPARATE_CHAINS
-    cdef int FREESASA_SEPARATE_MODELS
-    cdef int FREESASA_JOIN_MODELS
-    cdef int FREESASA_HALT_AT_UNKNOWN
-    cdef int FREESASA_SKIP_UNKNOWN
-
-    cdef int FREESASA_MAX_SELECTION_NAME
-
-    ctypedef struct freesasa_parameters:
-        freesasa_algorithm alg
-        double probe_radius
-        int shrake_rupley_n_points
-        int lee_richards_n_slices
-        int n_threads
-
-    ctypedef struct freesasa_result:
-        double total
-        double *sasa
-        int n_atoms
-
-    ctypedef struct freesasa_nodearea:
-        const char *name
-        double total
-        double main_chain
-        double side_chain
-        double polar
-        double apolar
-        double unknown
-
-    ctypedef struct freesasa_classifier:
-        pass
-
-    ctypedef struct freesasa_structure:
-        pass
-
-    ctypedef struct freesasa_selection:
-        pass
-
-    cdef extern const freesasa_parameters freesasa_default_parameters
-    cdef extern const freesasa_classifier freesasa_default_classifier
-    cdef extern const freesasa_classifier freesasa_residue_classifier
-
-    freesasa_result* freesasa_calc_structure(const freesasa_structure *structure,
-                                             const freesasa_parameters *parameters)
-
-    freesasa_result* freesasa_calc_coord(const double *xyz,
-                                         const double *radii,
-                                         int n,
-                                         const freesasa_parameters *parameters)
-
-    void freesasa_result_free(freesasa_result *result)
-
-    freesasa_classifier* freesasa_classifier_from_file(FILE *file)
-
-    void freesasa_classifier_free(freesasa_classifier *classifier)
-
-    int freesasa_structure_chain_residues(const freesasa_structure *structure,
-                                          char chain,
-                                          int *first,
-                                          int *last)
-
-    double freesasa_classifier_radius(const freesasa_classifier *classifier,
-                                      const char *res_name,
-                                      const char *atom_name)
-
-    freesasa_atom_class freesasa_classifier_class(const freesasa_classifier *classifier,
-                                                  const char *res_name,
-                                                  const char *atom_name)
-
-    const char* freesasa_classifier_class2str(freesasa_atom_class the_class)
-
-    freesasa_selection * freesasa_selection_new(const char *command,
-                                                const freesasa_structure *structure,
-                                                const freesasa_result *result)
-
-    void freesasa_selection_free(freesasa_selection *selection)
-
-    const char * freesasa_selection_name(const freesasa_selection* selection)
-
-    const char * freesasa_selection_command(const freesasa_selection* selection)
-
-    double freesasa_selection_area(const freesasa_selection* selection)
-
-    int freesasa_selection_n_atoms(const freesasa_selection* selection)
-
-    int freesasa_write_pdb(FILE *output,
-                           freesasa_result *result,
-                           const freesasa_structure *structure)
-
-    int freesasa_per_residue_type(FILE *output,
-                                  freesasa_result *result,
-                                  const freesasa_structure *structure)
-
-    int freesasa_per_residue(FILE *output,
-                             freesasa_result *result,
-                             const freesasa_structure *structure)
-
-    int freesasa_set_verbosity(freesasa_verbosity v)
-
-    freesasa_verbosity freesasa_get_verbosity()
-
-    freesasa_structure* freesasa_structure_from_pdb(FILE *pdb,
-                                                    const freesasa_classifier* classifier,
-                                                    int options)
-
-    freesasa_structure** freesasa_structure_array(FILE *pdb,
-                                                  int *n,
-                                                  const freesasa_classifier* classifier,
-                                                  int options)
-
-    freesasa_structure* freesasa_structure_new()
-
-    int freesasa_structure_n(freesasa_structure *structure)
-
-    void freesasa_structure_free(freesasa_structure* structure)
-
-    const double* freesasa_structure_radius(const freesasa_structure *structure)
-
-    void freesasa_structure_set_radius(freesasa_structure *structure,
-                                       const double *radii)
-
-    
-    int freesasa_structure_add_atom(freesasa_structure *structure,
-                                    const char* atom_name,
-                                    const char* residue_name,
-                                    const char* residue_number,
-                                    char chain_label,
-                                    double x, double y, double z)
-
-    int freesasa_structure_add_atom_wopt(freesasa_structure *structure,
-                                         const char* atom_name,
-                                         const char* residue_name,
-                                         const char* residue_number,
-                                         char chain_label,
-                                         double x, double y, double z,
-                                         const freesasa_classifier *classifier,
-                                         int options)
-
-    const char* freesasa_structure_atom_name(const freesasa_structure *structure,
-                                             int i)
-
-    const char* freesasa_structure_atom_res_name(const freesasa_structure *structure,
-                                                 int i)
-
-    const char* freesasa_structure_atom_res_number(const freesasa_structure *structure,
-                                                   int i)
-
-    double freesasa_structure_atom_radius(const freesasa_structure *structure,
-                                          int i)
-
-    void freesasa_structure_atom_set_radius(const freesasa_structure *structure,
-                                            int i,
-                                            double radius)
-
-    char freesasa_structure_atom_chain(const freesasa_structure *structure, int i)
-
-    const double* freesasa_structure_coord_array(const freesasa_structure *structure)

aggrescan3d/aggrescan/data/freesasa-2.0.1/bindings/python/freesasa.pyx

@@ -1,784 +0,0 @@
-## @package freesasa
-# @author Simon Mitternacht
-# @copyright [MIT License](md_license.html)
-#
-# @brief FreeSASA Python interface.
-#
-# A minimal program would be something like
-#
-# ~~~{.py}
-#     structure = freesasa.Structure("1abc.pdb")
-#     result = freesasa.calc(structure)
-#     print "SASA = %f" % result.totalArea()
-# ~~~
-#
-# See documentation of the classes and functions for how to customize behavior.
-#
-
-from libc.stdio cimport FILE, fopen, fclose
-from libc.stdlib cimport free, realloc, malloc
-from libc.string cimport memcpy
-from cfreesasa cimport *
-
-## Used to specify the algorithm by Shrake & Rupley
-ShrakeRupley = 'ShrakeRupley'
-
-## Used to specify the algorithm by Lee & Richards
-LeeRichards = 'LeeRichards'
-
-## Used for classification
-polar = 'Polar'
-
-## Used for classification
-apolar = 'Apolar'
-
-## int: Suppress all warnings and errors (used by setVerbosity())
-silent = FREESASA_V_SILENT
-
-## int: Suppress all warnings but not errors (used by setVerbosity())
-nowarnings = FREESASA_V_NOWARNINGS
-
-## int: Normal verbosity (used by setVerbosity())
-normal = FREESASA_V_NORMAL
-
-## int: Print debug messages (used by setVerbosity())
-debug = FREESASA_V_DEBUG
-
-## The default values for calculation parameters
-defaultParameters = {
-     'algorithm'    : LeeRichards, 
-     'probe-radius' : freesasa_default_parameters.probe_radius,
-     'n-points'     : freesasa_default_parameters.shrake_rupley_n_points,
-     'n-slices'     : freesasa_default_parameters.lee_richards_n_slices,
-     'n-threads'    : freesasa_default_parameters.n_threads 
-}
-
-## Stores parameter values to be used by calculation.
-#   
-#  Wraps the C struct freesasa_parameters.
-cdef class Parameters:
-
-      cdef freesasa_parameters _c_param
-      ## Initializes Parameters object.
-      #      
-      #  @param param (dict) optional argument to specify parameter-values, modeled after
-      #            ::defaultParameters
-      #  @exception AssertionError invalid parameter values supplied
-      #  @see defaultParameters
-      def __init__(self,param=None):
-   
-            self._c_param = freesasa_default_parameters
-            if param != None:
-                  if 'algorithm' in param:    self.setAlgorithm(param['algorithm'])
-                  if 'probe-radius' in param: self.setProbeRadius(param['probe-radius'])
-                  if 'n-points' in param:     self.setNPoints(param['n-points'])
-                  if 'n-slices' in param:     self.setNSlices(param['n-slices'])
-                  if 'n-threads' in param:    self.setNThreads(param['n-threads'])
-                  unknownKeys = []
-                  for key in param:
-                        if not key in defaultParameters:
-                              unknownKeys.append(key)
-                  if len(unknownKeys) > 0:
-                        raise AssertionError('Key(s): ',unknownKeys,', unknown');
-
-      ## Set algorithm.
-      #
-      #  @param alg (str) algorithm name, only allowed values are ::ShrakeRupley and ::LeeRichards
-      #  @exception AssertionError unknown algorithm specified
-      def setAlgorithm(self,alg):
-            if alg == ShrakeRupley:
-                  self._c_param.alg = FREESASA_SHRAKE_RUPLEY
-            elif alg == LeeRichards:
-                  self._c_param.alg = FREESASA_LEE_RICHARDS
-            else:
-                  raise AssertionError("Algorithm '%s' is unknown" % alg)
-
-      ## Get algorithm.
-      #     
-      #  @return Name of algorithm
-      def algorithm(self):
-            if self._c_param.alg == FREESASA_SHRAKE_RUPLEY:
-                  return ShrakeRupley
-            if self._c_param.alg == FREESASA_LEE_RICHARDS:
-                  return LeeRichards
-            raise Exception("No algorithm specified, shouldn't be possible")
-
-      ## Set probe radius.
-      # @param r probe radius in Å (>= 0)
-      # @exception AssertionError r < 0
-      def setProbeRadius(self,r):
-            assert(r >= 0)
-            self._c_param.probe_radius = r
-
-      ## Get probe radius.
-      #  @return Probe radius in Å
-      def probeRadius(self):
-            return self._c_param.probe_radius
-
-      ## Set number of test points in Shrake & Rupley algorithm.
-      #  @param n (int) Number of points (> 0). 
-      #  @exception AssertionError n <= 0.
-      def setNPoints(self,n):
-            assert(n > 0)
-            self._c_param.shrake_rupley_n_points = n
-
-      ## Get number of test points in Shrake & Rupley algorithm.
-      #  @return Number of points.
-      def nPoints(self):
-            return self._c_param.shrake_rupley_n_points
-
-      ## Set the number of slices per atom in Lee & Richards algorithm.
-      #  @param n (int) Number of slices (> 0)
-      #  @exception AssertionError n <= 0
-      def setNSlices(self,n):
-            assert(n> 0)
-            self._c_param.lee_richards_n_slices = n
-
-      ## Get the number of slices per atom in Lee & Richards algorithm.
-      #  @return Number of slices.
-      def nSlices(self):
-            return self._c_param.lee_richards_n_slices
-
-      
-      ## Set the number of threads to use in calculations.
-      #  @param n (int) Number of points (> 0)
-      #  @exception AssertionError n <= 0
-      def setNThreads(self,n):
-            assert(n>0)
-            self._c_param.n_threads = n
-
-            
-      ## Get the number of threads to use in calculations.
-      #  @return Number of threads.
-      def nThreads(self):
-            return self._c_param.n_threads
-
-      # not pretty, but only way I've found to pass pointers around
-      def _get_address(self, size_t ptr2ptr):
-            cdef freesasa_parameters **p = <freesasa_parameters**> ptr2ptr
-            p[0] = &self._c_param
-
-## Stores results from SASA calculation.
-#  The type of object returned by calc(), not intended to be used
-#  outside of that context. 
-#
-#  Wraps the C struct freesasa_result.
-cdef class Result:
-      cdef freesasa_result* _c_result
-
-      ## The constructor
-      def __cinit__ (self):
-            self._c_result = NULL
-
-      ## The destructor
-      def __dealloc__(self):
-            if self._c_result is not NULL:
-                  freesasa_result_free(self._c_result)
-            
-      ## Number of atoms in the results
-      #  @return Number of atoms
-      def nAtoms(self):
-            if self._c_result is not NULL:
-                  return self._c_result.n_atoms
-            return 0
-
-      
-      ## Total SASA.
-      # @return The total area in Å^2.
-      # @exception AssertionError If no results have been associated
-      #              with the object
-      def totalArea(self):
-            assert(self._c_result is not NULL)
-            return self._c_result.total
-
-      ## SASA for a given atom.
-      #  @param i (int) index of atom.
-      #  @return SASA of atom i in Å^2.
-      #  @exception AssertionError If no results have been associated
-      #              with the object or if index is out of bounds
-      def atomArea(self,i):
-            assert(self._c_result is not NULL)
-            assert(i < self._c_result.n_atoms)
-            return self._c_result.sasa[i]
-
-      def _get_address(self, size_t ptr2ptr):
-            cdef freesasa_result **p = <freesasa_result**> ptr2ptr
-            p[0] = self._c_result
-
-      
-## Assigns class and radius to atom by residue and atom name.
-#
-#  Subclasses derived from Classifier can be used to define custom
-#  atomic radii and/or classes. Can also be initialized from a @ref
-#  Config-file "configuration file" with a custom classifier.
-#
-#  Wraps a C freesasa_classifier. If initialized without arguments the
-#  default classifier is used.
-#
-#  Derived classifiers should set the member purePython to True
-#
-#  Residue names should be of the format `"ALA"`,`"ARG"`, etc.
-#      
-#  Atom names should be of the format `"CA"`, `"N"`, etc. 
-#
-cdef class Classifier:
-      cdef freesasa_classifier* _c_classifier
-      purePython = False
-
-      ## Constructor.
-      #
-      #  If no file is provided the default classifier is used. 
-      #
-      #  @see @ref Config-file.
-      #      
-      #  @param fileName Name of file with classifier configuration.
-      #  @exception IOError   Problem opening/reading file
-      #  @exception Exception Problem parsing provided configuration or 
-      #                       initializing defaults
-      def __cinit__ (self,fileName=None):
-            cdef FILE *config
-            self._c_classifier = NULL
-            if fileName is not None:
-                  config = fopen(fileName,'r')
-                  if config is NULL:
-                        raise IOError("File '%s' could not be opened." % fileName)
-                  self._c_classifier = freesasa_classifier_from_file(config)
-                  fclose(config)
-                  if self._c_classifier is NULL:
-                        raise Exception("Error parsing configuration in '%s'." % fileName)
-            else:
-                  self._c_classifier = &freesasa_default_classifier
-      ## The destructor
-      def __dealloc__(self):
-            if self._c_classifier is not &freesasa_default_classifier:
-                  freesasa_classifier_free(self._c_classifier)
-
-
-      # This is used internally to determine if a Classifier wraps a C
-      # classifier or not (necessary when generating structures)
-      # @return Boolean
-      def _isCClassifier(self):
-            return not self.purePython
-
-      ## Class of atom.
-      #
-      #  Depending on the configuration these classes can be
-      #  anything, but typically they will be 'Polar' and 'Apolar'. 
-      #  Unrecognized atoms will get the class 'Unknown'. 
-      #
-      #  @param residueName (str) Residue name (`"ALA"`,`"ARG"`,...).
-      #  @param atomName (str) Atom name (`"CA"`,`"C"`,...).
-      #  @return A string describing the class
-      def classify(self,residueName,atomName):
-            classIndex = freesasa_classifier_class(self._c_classifier, residueName, atomName)
-            return freesasa_classifier_class2str(classIndex)
-
-      ## Radius of atom.
-      #
-      #  This allows the classifier to be used to calculate the atomic
-      #  radii used in calculations. Unknown atoms will get a negative
-      #  radius.
-      #
-      #  @param residueName (str) Residue name (`"ALA"`, `"ARG"`, ...).
-      #  @param atomName (str) Atom name (`"CA"`, `"C"`, ...).
-      #  @return The radius in Å.
-      def radius(self,residueName,atomName):
-            return freesasa_classifier_radius(self._c_classifier, residueName, atomName)
-
-      def _get_address(self, size_t ptr2ptr):
-            cdef freesasa_classifier **p = <freesasa_classifier**> ptr2ptr
-            p[0] = self._c_classifier
-
-## Represents a protein structure, including its atomic radii.
-#      
-#  Initialized from PDB-file. Calculates atomic radii using default
-#  classifier, or custom one provided as argument to initalizer
-#
-#  Wraps the C struct freesasa_structure.
-#
-#  Since it is intended to be a static structure the word 'get' is
-#  omitted in the getter-functions.
-cdef class Structure:
-      cdef freesasa_structure* _c_structure
-      ## By default ignore HETATM, Hydrogens, only use first model. For unknown atoms
-      # try to guess the radius, if this fails, assign radius 0 (to
-      # allow changing the radius later).
-      defaultOptions = {         'hetatm' : False,
-            'hydrogen' : False,
-            'join-models' : False,
-            'skip-unknown' : False,
-            'halt-at-unknown' : False
-            }
-
-      ## Constructor
-      #
-      #  If PDB file is provided, the structure will be constructed
-      #  based on the file. If not, this simply initializes an empty
-      #  structure and the other arguments are ignored. In this case 
-      #  atoms will have to be added manually using addAtom().
-      #
-      #  @param fileName (str) PDB file (if None empty structure generated).
-      #  @param classifier An optional Classifier to calculate atomic
-      #           radii, uses default if none provided
-      #  @param options specify which atoms and models to include
-      #  @exception IOError Problem opening/reading file.
-      #  @exception Exception Problem parsing PDB file or calculating 
-      #      atomic radii.
-      #  @exception Exception If option 'halt-at-unknown' selected and
-      #      unknown atom encountered.
-      def __init__(self,fileName=None,classifier=None,
-                   options = defaultOptions):
-
-            self._c_structure = NULL
-            cdef freesasa_classifier *c = NULL
-            if classifier is None:
-                  classifier = Classifier()
-            if classifier._isCClassifier():
-                  classifier._get_address(<size_t>&c)
-
-            if fileName is None:
-                  self._c_structure = freesasa_structure_new()
-                  return
-            cdef FILE *input
-            input = fopen(fileName,'r')
-            if input is NULL:
-                  raise IOError("File '%s' could not be opened." % fileName)
-            structure_options = Structure._get_structure_options(options)
-
-            if not classifier._isCClassifier(): # supress warnings
-                  setVerbosity(silent)
-
-            self._c_structure = freesasa_structure_from_pdb(input, c, structure_options)
-
-            if not classifier._isCClassifier():
-                  setVerbosity(normal)
-
-            fclose(input)
-
-            if self._c_structure is NULL:
-                  raise Exception("Error reading '%s'." % fileName)
-
-            # for pure Python classifiers we use the default
-            # classifier above to initialize the structure and then
-            # reassign radii using the provided classifier here
-            if (not classifier._isCClassifier()):
-                  self.setRadiiWithClassifier(classifier)
-
-
-      ## Add atom to structure.
-      #
-      # This function is meant to be used if the structure was not
-      # initialized from a PDB. Default radii will be assigned to each
-      # atom. This can be overriden by calling
-      # setRadiiWithClassifier() afterwards.
-      #
-      # There are no restraints on string lengths for the arguments, but
-      # the atom won't be added if the default classifier doesn't
-      # recognize the atom and also cannot deduce its element from the
-      # atom name.
-      #      
-      # @param atomName (str) atom name (e.g. `"CA"`)
-      # @param residueName (str) residue name (e.g. `"ALA"`)
-      # @param residueNumber (str or int) residue number (e.g. `'12'`)
-      #      or integer. Some PDBs have residue-numbers that aren't 
-      #      regular numbers. Therefore treated as a string primarily.
-      # @param chainLabel (str) 1-character string with chain label (e.g. 'A')
-      # @param x,y,z (float) coordinates
-      # 
-      # @exception Exception Residue-number invalid
-      def addAtom(self, atomName, residueName, residueNumber, chainLabel, x, y, z):
-            if (type(residueNumber) is str):
-                  resnum = residueNumber
-            elif (type(residueNumber) is int):
-                  resnum = "%d" % residueNumber
-            else:
-                  raise Exception("Residue-number invalid, must be either string or number")
-            cdef const char *label = chainLabel
-            ret = freesasa_structure_add_atom(self._c_structure, atomName,
-                                              residueName, resnum, label[0],
-                                              x, y, z)
-            assert(ret != FREESASA_FAIL)
-
-      ## Assign radii to atoms in structure using a classifier.
-      #
-      # @param classifier A classifier to use to calculate radii
-      # @exception AssertionError if structure not properly initialized
-      def setRadiiWithClassifier(self,classifier):
-            assert(self._c_structure is not NULL)
-            n = self.nAtoms()
-            r = []
-            for i in range(0,n):
-                  r.append(classifier.radius(self.residueName(i), self.atomName(i)))
-            self.setRadii(r)
-
-      ## Set atomic radii from an array
-      # @param radiusArray Array of atomic radii in Ångström, should 
-      #                    have nAtoms() elements.
-      # @exception AssertionError if radiusArray has wrong dimension, structure 
-      #                           not properly initialized, or if the array contains
-      #                           negative radii (not properly classified?) 
-      def setRadii(self,radiusArray):
-            assert(self._c_structure is not NULL)
-            n = self.nAtoms()
-            assert len(radiusArray) == n
-            cdef double *r = <double *>malloc(sizeof(double)*n)
-            assert(r is not NULL)
-            for i in range(0,n):
-                  r[i] = radiusArray[i]
-                  assert(r[i] >= 0)
-            freesasa_structure_set_radius(self._c_structure, r)
-
-      ## Number of atoms.
-      #
-      # @return  Number of atoms
-      # @exception AssertionError if not properly initialized
-      def nAtoms(self):
-            assert(self._c_structure is not NULL)
-            return freesasa_structure_n(self._c_structure)
-
-      ## Radius of atom.
-      # @param i (int) Index of atom.
-      # @return Radius in Å. 
-      # @exception AssertionError if index out of bounds, object not properly initalized.
-      def radius(self,i):
-            assert(i >= 0 and i < self.nAtoms())
-            assert(self._c_structure is not NULL)
-            cdef const double *r = freesasa_structure_radius(self._c_structure)
-            assert(r is not NULL)
-            return r[i]
-
-      ## Set radius for a given atom
-      # @param atomIndex Index of atom
-      # @param radius Value of radius
-      # @exception AssertionError if index out of bounds, radius
-      #            negative, or structure not properly initialized
-      def setRadius(self, atomIndex, radius):
-            assert(self._c_structure is not NULL)
-            assert(atomIndex >= 0 and atomIndex < self.nAtoms())
-            assert(radius >= 0)
-            freesasa_structure_atom_set_radius(self._c_structure, atomIndex, radius);
-      
-      ## Get atom name
-      # @param i (int) Atom index.
-      # @return Atom name as 4-character string.
-      # @exception AssertionError: if index out of range or Structure not properly initialized.
-      def atomName(self,i):
-            assert(i >= 0 and i < self.nAtoms())
-            assert(self._c_structure is not NULL)
-            return freesasa_structure_atom_name(self._c_structure,i);
-      
-      ## Get residue name of given atom.
-      # @param i (int) Atom index.
-      # @return Residue name as 3-character string.
-      # @exception AssertionError if index out of range or Structure not properly initialized
-      def residueName(self,i):
-            assert(i >= 0 and i < self.nAtoms())
-            assert(self._c_structure is not NULL)
-            return freesasa_structure_atom_res_name(self._c_structure,i)
-
-      ## Get residue number for given atom
-      # @param i (int) Atom index.
-      # @return Residue number as 4-character string
-      # @exception AssertionError if index out of range or Structure not properly initialized
-      def residueNumber(self,i):
-            assert(i >= 0 and i < self.nAtoms())
-            assert(self._c_structure is not NULL)
-            return freesasa_structure_atom_res_number(self._c_structure,i);
-
-      ## Get chain label for given atom.
-      # @param i (int) Atom index.
-      # @return Chain label as 1-character string
-      # @exception AssertionError if index out of range or Structure not properly initialized
-      def chainLabel(self,i):
-            assert(i >= 0 and i < self.nAtoms())
-            assert(self._c_structure is not NULL)
-            cdef char label[2]
-            label[0] = freesasa_structure_atom_chain(self._c_structure,i); 
-            label[1] = '\0'
-            return label
-
-      ## Get coordinates of given atom.
-      # @param i (int) Atom index.
-      # @return array of x, y, and z coordinates
-      # @exception AssertionError if index out of range or Structure not properly initialized
-      def coord(self, i):
-            assert(i >= 0 and i < self.nAtoms())
-            assert(self._c_structure is not NULL)
-            cdef const double *coord = freesasa_structure_coord_array(self._c_structure);
-            return [coord[3*i], coord[3*i+1], coord[3*i+2]]
-
-      @staticmethod
-      def _get_structure_options(param):
-            options = 0
-            
-            # check validity of options
-            knownOptions = {'hetatm','hydrogen','join-models','separate-models',
-                            'separate-chains','skip-unknown','halt-at-unknown'}
-            unknownOptions = []
-            for key in param:
-                  if not key in knownOptions:
-                        unknownOptions.append(key)
-            if len(unknownOptions) > 0:
-                  raise AssertionError("Option(s): ",unknownOptions," unknown.");
-
-            # calculate bitfield
-            if 'hetatm' in param and param['hetatm']:
-                  options |= FREESASA_INCLUDE_HETATM
-            if 'hydrogen' in param and param['hydrogen']:
-                  options |= FREESASA_INCLUDE_HYDROGEN
-            if 'join-models' in param and param['join-models']:
-                  options |= FREESASA_JOIN_MODELS
-            if 'separate-models' in param and param['separate-models']:
-                  options |= FREESASA_SEPARATE_MODELS
-            if 'separate-chains' in param and param['separate-chains']:
-                  options |= FREESASA_SEPARATE_CHAINS
-            if 'skip-unknown' in param and param['skip-unknown']:
-                  options |= FREESASA_SKIP_UNKNOWN
-            if 'halt-at-unknown' in param and param['halt-at-unknown']:
-                  options |= FREESASA_HALT_AT_UNKNOWN
-            return options
-
-      def _get_address(self, size_t ptr2ptr):
-            cdef freesasa_structure **p = <freesasa_structure**> ptr2ptr
-            p[0] = self._c_structure
-
-      def _set_address(self, size_t ptr2ptr):
-            cdef freesasa_structure **p = <freesasa_structure**> ptr2ptr
-            self._c_structure = p[0]
-
-      ## The destructor
-      def __dealloc__(self):
-            if self._c_structure is not NULL:
-                  freesasa_structure_free(self._c_structure)
-
-## Default options for structureArray.
-# Defined separately for Doxygen's sake.
-defaultStructureArrayOptions = {
-      'hetatm' : False, 
-      'hydrogen' : False,
-      'separate-chains' : True,
-      'separate-models' : False
-}
-
-## Create array of structures from PDB file.
-#
-# Split PDB file into several structures by either by treating
-# chains separately, by treating each MODEL as a separate
-# structure, or both.
-# 
-# @param fileName (str) The PDB file.
-# @param options (dict) Specification for how to read the PDB-file
-#  (see def value for options).
-# @param classifier: Classifier to assign atoms radii, default is used
-#   if none specified.
-# @exception AssertionError if fileName is None
-# @exception AssertionError if an option value is not recognized
-# @exception AssertionError if neither of the options 'separate-chains'
-#   and 'separate-models' are specified.
-# @exception IOError if can't open file
-# @exception Exception: if there are problems parsing the input
-# @return An array of Structures
-def structureArray(fileName,
-                   options = defaultStructureArrayOptions,
-                   classifier = None):
-      assert fileName is not None
-      # we need to have at least one of these
-      assert(('separate-chains' in options and options['separate-chains'] is True) 
-             or ('separate-models' in options and options['separate-models'] is True))
-      structure_options = Structure._get_structure_options(options)
-      cdef FILE *input
-      input = fopen(fileName,'r')
-      if input is NULL:
-            raise IOError("File '%s' could not be opened." % fileName)
-      cdef int n;
-      cdef freesasa_structure** sArray = freesasa_structure_array(input,&n,NULL,structure_options)
-      fclose(input)
-      if sArray is NULL:
-            raise Exception("Problems reading structures in '%s'." % fileName)
-      structures = []
-      for i in range(0,n):
-            structures.append(Structure())
-            structures[-1]._set_address(<size_t> &sArray[i])
-            if classifier is not None:
-                  structures[-1].setRadiiWithClassifier(classifier)
-      free(sArray)
-      return structures
-
-
-## Calculate SASA of Structure
-# @param structure Structure to be used
-# @param parameters Parameters to use (if not specified defaults are used)
-# @return A Result object
-# @exception Exception: something went wrong in calculation (see C library error messages)
-def calc(structure,parameters=None):
-      cdef const freesasa_parameters *p = NULL
-      cdef const freesasa_structure *s = NULL
-      if parameters is not None:  parameters._get_address(<size_t>&p)
-      structure._get_address(<size_t>&s)
-      result = Result()
-      result._c_result = <freesasa_result*> freesasa_calc_structure(s,p)
-      if result._c_result is NULL:
-            raise Exception("Error calculating SASA.")
-      return result
-
-## Calculate SASA for a set of coordinates and radii
-# @param coord list of size 3*N with atomic coordinates (x1, y1, z1,
-#   x2, y2, z2, ..., x_N, y_N, z_N'.
-# @param radii array of size N with atomic radii (r_1, r_2, ..., r_N)
-# @param Parameters to use (if not specified, defaults are used)
-# @exception AssertionError: mismatched array-sizes
-# @exception Exception: Out of memory
-# @exception Exception: something went wrong in calculation (see C library error messages)
-def calcCoord(coord, radii, parameters=None):
-      assert(len(coord) == 3*len(radii))
-
-      cdef const freesasa_parameters *p = NULL
-      cdef double *c = <double*> malloc(len(coord)*sizeof(double))
-      cdef double *r = <double*> malloc(len(radii)*sizeof(double))
-      if c is NULL or r is NULL:
-            raise Exception("Memory allocation error")
-
-      for i in xrange(len(coord)):
-            c[i] = coord[i]
-      for i in xrange(len(radii)):
-            r[i] = radii[i]
-
-      if parameters is not None: parameters._get_address(<size_t>&p)
-
-      result = Result()
-      result._c_result = <freesasa_result*> freesasa_calc_coord(c, r, len(radii), p)
-
-      if result._c_result is NULL:
-            raise Exception("Error calculating SASA.")
-
-      free(c)
-      free(r)
-
-      return result
-
-## Break SASA result down into classes.
-# @param result Result from sasa calculation.
-# @param structure Structure used in calculation.
-# @param classifier Classifier (if not specified default is used).
-# @return Dictionary with names of classes as keys and their SASA values as values.
-# @exception Exception: Problems with classification, see C library error messages 
-#  (or Python exceptions if run with derived classifier).
-def classifyResults(result,structure,classifier=None):
-      if classifier is None:
-            classifier = Classifier()
-      ret = dict()
-      for i in range(0,structure.nAtoms()):
-            name = classifier.classify(structure.residueName(i),structure.atomName(i))
-            if name not in ret:
-                  ret[name] = 0
-            ret[name] += result.atomArea(i)
-      return ret
-
-## Sum SASA result over a selection of atoms
-# @param commands A list of commands with selections using Pymol
-#   syntax, e.g. `"s1, resn ala+arg"` or `"s2, chain A and resi 1-5"` 
-#   (see @ref Selection).
-# @param structure A Structure.  
-# @param result Result from sasa calculation on structure.
-# @return Dictionary with names of selections (`"s1"`,`"s2"`,...) as 
-#   keys, and the corresponding SASA values as values.
-# @exception Exception: Parser failed (typically syntax error), see
-#   library error messages.
-def selectArea(commands, structure, result):
-      cdef freesasa_structure *s
-      cdef freesasa_result *r
-      cdef freesasa_selection *selection
-      structure._get_address(<size_t> &s)
-      result._get_address(<size_t> &r)
-      value = dict()
-      for cmd in commands:
-            selection = freesasa_selection_new(cmd, s, r)
-            if selection == NULL:
-                  raise Exception("Error parsing '%s'" % cmd)
-            value[freesasa_selection_name(selection)] = freesasa_selection_area(selection)
-            freesasa_selection_free(selection)
-      return value
-
-## Set global verbosity
-# @param verbosity Can have values freesasa.silent, freesasa.nowarnings or freesasa.normal
-# @exception AssertionError if verbosity has illegal value
-def setVerbosity(verbosity):
-      assert(verbosity in [silent, nowarnings, normal])
-      freesasa_set_verbosity(verbosity)
-
-
-## Get global verbosity
-# @return Verbosity (freesasa.silent, freesasa.nowarnings or freesasa.normal)
-def getVerbosity():
-      return freesasa_get_verbosity()
-
-## Create a freesasa structure from a Bio.PDB structure
-#
-#  @remark Experimental, not thorougly tested yet
-#
-#  @param bioPDBStructure a Bio.PDB structure
-#  @param classifier an optional classifier to specify atomic radii
-#  @param options Options supported are 'hetatm', 'skip-unknown' and 'halt-at-unknown'
-#  @return a freesasa.Structure
-#
-#  @exception Exception if option 'halt-at-unknown' is selected and
-#             unknown atoms are encountered. Passes on exceptions from
-#             Structure.addAtom() and
-#             Structure.setRadiiWithClassifier().
-def structureFromBioPDB(bioPDBStructure, classifier=None, options = Structure.defaultOptions):
-      structure = Structure()
-      if (classifier is None):
-            classifier = Classifier()
-      optbitfield = Structure._get_structure_options(options)
-
-      atoms = bioPDBStructure.get_atoms()
-
-      for a in atoms:
-            r = a.get_parent()
-            hetflag, resseq, icode = r.get_id()
-
-            if (hetflag is not ' ' and not (optbitfield & FREESASA_INCLUDE_HETATM)):
-                  continue
-
-            c = r.get_parent()
-            v = a.get_vector()
-
-            if (classifier.classify(r.get_resname(), a.get_fullname()) is 'Unknown'):
-                  if (optbitfield & FREESASA_SKIP_UNKNOWN):
-                        continue
-                  if (optbitfield & FREESASA_HALT_AT_UNKNOWN):
-                        raise Exception("Halting at unknown atom")
-
-            structure.addAtom(a.get_fullname(), r.get_resname(), resseq, c.get_id(),
-                              v[0], v[1], v[2])
-
-      structure.setRadiiWithClassifier(classifier)
-      return structure
-
-## Calc SASA from Bio.PDB structure
-#
-#  Usage 
-#
-#      result, sasa_classes = calcBioPDB(structure, ...)  
-#
-#  @remark Experimental, not thorougly tested yet
-#
-#  @param bioPDBStructure A Bio.PDB structure
-#  @param parameters A freesasa.Paremeters object
-#  @param classifier A freesasa.Classifier object
-#  @param options Options supported are 'hetatm', 'skip-unknown' and 'halt-at-unknown'
-#
-#  @return A freesasa.Result object and a dictionary with classes
-#         defined by the classifier and associated areas
-#
-#  @exception Exception if unknown atom is encountered and the option
-#             'halt-at-unknown' is active. Passes on exceptions from
-#             calc(), classifyResults() and structureFromBioPDB().
-def calcBioPDB(bioPDBStructure, parameters = Parameters(), 
-               classifier = None, options = Structure.defaultOptions):
-      structure = structureFromBioPDB(bioPDBStructure, classifier, options)
-      result = calc(structure, parameters)
-      sasa_classes = classifyResults(result, structure, classifier)
-      return result, sasa_classes
-      
-

aggrescan3d/aggrescan/data/freesasa-2.0.1/bindings/python/setup.py

@@ -1,27 +0,0 @@
-from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Build import cythonize
-
-lib = []
-lib.extend([]);
-lib.extend([]);
-
-extensions = [
-    Extension("*", ["*.pyx"],
-              include_dirs = ["../../src"],
-              language='c',
-              libraries=lib,
-              extra_objects = ["../../src/libfreesasa.a"],
-              extra_compile_args = ["-w"] 
-              )
-]
-
-setup(
-    name='FreeSASA',
-    description='Calculate solvent accessible surface areas of proteins',
-    version= '2.0.1',
-    author='Simon Mitternacht',
-    url='http://freesasa.github.io/',
-    license='MIT',
-    ext_modules = cythonize(extensions)
-)

aggrescan3d/aggrescan/data/freesasa-2.0.1/bindings/python/setup.py.in

@@ -1,27 +0,0 @@
-from distutils.core import setup
-from distutils.extension import Extension
-from Cython.Build import cythonize
-
-lib = [@JSONC_FOR_PY_BINDINGS@]
-lib.extend([@CHECK_FOR_PY_BINDINGS@]);
-lib.extend([@LIBXML_FOR_PY_BINDINGS@]);
-
-extensions = [
-    Extension("*", ["*.pyx"],
-              include_dirs = ["../../src"],
-              language='c',
-              libraries=lib,
-              extra_objects = ["../../src/libfreesasa.a"],
-              extra_compile_args = ["-w"] 
-              )
-]
-
-setup(
-    name='FreeSASA',
-    description='Calculate solvent accessible surface areas of proteins',
-    version= '@PACKAGE_VERSION@',
-    author='Simon Mitternacht',
-    url='http://freesasa.github.io/',
-    license='MIT',
-    ext_modules = cythonize(extensions)
-)

aggrescan3d/aggrescan/data/freesasa-2.0.1/bindings/python/test.py

@@ -1,322 +0,0 @@
-from freesasa import *
-import unittest
-import math
-import os
-from exceptions import Exception
-
-# this class tests using derived classes to create custom Classifiers
-class DerivedClassifier(Classifier):
-    purePython = True
-
-    def classify(self,residueName,atomName):
-        return 'bla'
-
-    def radius(self,residueName,atomName):
-        return 10
-
-class FreeSASATestCase(unittest.TestCase):
-    def testParameters(self):
-        d = defaultParameters
-        p = Parameters()
-        self.assertTrue(p.algorithm() == LeeRichards)
-        self.assertTrue(p.algorithm() == d['algorithm'])
-        self.assertTrue(p.probeRadius() == d['probe-radius'])
-        self.assertTrue(p.nPoints() == d['n-points'])
-        self.assertTrue(p.nSlices() == d['n-slices'])
-        self.assertTrue(p.nThreads() == d['n-threads'])
-        self.assertRaises(AssertionError,lambda: Parameters({'not-an-option' : 1}))
-        self.assertRaises(AssertionError,lambda: Parameters({'n-slices' : 50, 'not-an-option' : 1}))
-        self.assertRaises(AssertionError,lambda: Parameters({'not-an-option' : 50, 'also-not-an-option' : 1}))
-
-        p.setAlgorithm(ShrakeRupley)
-        self.assertTrue(p.algorithm() == ShrakeRupley)
-        p.setAlgorithm(LeeRichards)
-        self.assertTrue(p.algorithm() == LeeRichards)
-        self.assertRaises(AssertionError,lambda: p.setAlgorithm(-10))
-
-        p.setProbeRadius(1.5)
-        self.assertTrue(p.probeRadius() == 1.5)
-        self.assertRaises(AssertionError,lambda: p.setProbeRadius(-1))
-
-        p.setNPoints(20)
-        self.assertTrue(p.nPoints() == 20)
-        self.assertRaises(AssertionError,lambda: p.setNPoints(0))
-
-        p.setNSlices(10)
-        self.assertTrue(p.nSlices() == 10)
-        self.assertRaises(AssertionError,lambda: p.setNSlices(0))
-
-        p.setNThreads(2)
-        self.assertTrue(p.nThreads() == 2)
-        self.assertRaises(AssertionError, lambda: p.setNThreads(0))
-        
-    def testResult(self):
-        r = Result()
-        self.assertRaises(AssertionError,lambda: r.totalArea())
-        self.assertRaises(AssertionError,lambda: r.atomArea(0))
-
-    def testClassifier(self):
-        c = Classifier()
-        self.assertTrue(c._isCClassifier())
-        self.assertTrue(c.classify("ALA"," CB ") == apolar)
-        self.assertTrue(c.classify("ARG"," NH1") == polar)
-        self.assertTrue(c.radius("ALA"," CB ") == 1.88)
-
-        setVerbosity(silent)
-        self.assertRaises(Exception,lambda: Classifier("data/err.config"))
-        self.assertRaises(IOError,lambda: Classifier(""))
-        setVerbosity(normal)
-
-        c = Classifier("data/test.config")
-        self.assertTrue(c.classify("AA","aa") == "Polar")
-        self.assertTrue(c.classify("BB","bb") == "Apolar")
-        self.assertTrue(c.radius("AA","aa") == 1.0)
-        self.assertTrue(c.radius("BB","bb") == 2.0)
-
-        c = Classifier("share/oons.config")
-        self.assertTrue(c.radius("ALA"," CB ") == 2.00)
-
-        c = DerivedClassifier()
-        self.assertTrue(not c._isCClassifier())
-        self.assertTrue(c.radius("ALA"," CB ") == 10)
-        self.assertTrue(c.radius("ABCDEFG","HIJKLMNO") == 10)
-        self.assertTrue(c.classify("ABCDEFG","HIJKLMNO") == "bla")
-
-    def testStructure(self):
-        self.assertRaises(IOError,lambda: Structure("xyz#$%"))
-        setVerbosity(silent)
-        # test any file that's not a PDB file
-        self.assertRaises(Exception,lambda: Structure("data/err.config")) 
-        self.assertRaises(Exception,lambda: Structure("data/empty.pdb"))
-        self.assertRaises(Exception,lambda: Structure("data/empty_model.pdb"))
-        setVerbosity(normal)
-
-        s = Structure("data/1ubq.pdb")
-        self.assertTrue(s.nAtoms() == 602)
-        self.assertTrue(s.radius(1) == 1.88)
-        self.assertTrue(s.chainLabel(1) == 'A')
-        self.assertTrue(s.atomName(1) == ' CA ')
-        self.assertTrue(s.residueName(1) == 'MET')
-        self.assertTrue(s.residueNumber(1) == '   1')
-
-        s2 = Structure("data/1ubq.pdb",Classifier("share/oons.config"))
-        self.assertTrue(s.nAtoms() == 602)
-        self.assertTrue(math.fabs(s2.radius(1) - 2.0) < 1e-5)
-
-        s2 = Structure("data/1ubq.pdb",Classifier("share/protor.config"))
-        for i in range (0,601):
-            self.assertTrue(math.fabs(s.radius(i)- s2.radius(i)) < 1e-5)
-
-        self.assertRaises(Exception,lambda: Structure("data/1ubq.pdb","data/err.config"))
-
-        s = Structure()
-        s.addAtom(' CA ','ALA','   1','A',1,1,1)
-        self.assertTrue(s.nAtoms() == 1)
-        self.assertTrue(s.atomName(0) == ' CA ')
-        self.assertTrue(s.residueName(0) == 'ALA')
-        self.assertTrue(s.residueNumber(0) == '   1')
-        self.assertTrue(s.chainLabel(0) == 'A')
-        self.assertTrue(s.nAtoms() == 1)
-        x, y, z = s.coord(0)
-        self.assertTrue(x == 1 and y ==1 and z ==1)
-        s.addAtom(' CB ','ALA',2,'A',2,1,1)
-        self.assertTrue(s.nAtoms() == 2)
-        self.assertTrue(s.residueNumber(1) == '2')
-
-        self.assertRaises(AssertionError, lambda: s.atomName(3))
-        self.assertRaises(AssertionError, lambda: s.residueName(3))
-        self.assertRaises(AssertionError, lambda: s.residueNumber(3))
-        self.assertRaises(AssertionError, lambda: s.chainLabel(3))
-        self.assertRaises(AssertionError, lambda: s.coord(3))
-        self.assertRaises(AssertionError, lambda: s.radius(3))
-
-        s.setRadiiWithClassifier(Classifier())
-        self.assertTrue(s.radius(0) == 1.88)
-        self.assertTrue(s.radius(1) == 1.88)
-
-        s.setRadiiWithClassifier(DerivedClassifier())
-        self.assertTrue(s.radius(0) == s.radius(1) == 10.0)
-        
-        s.setRadii([1.0,3.0])
-        self.assertTrue(s.radius(0) == 1.0)
-        self.assertTrue(s.radius(1) == 3.0)
-
-        s.setRadius(0, 10.0)
-        self.assertTrue(s.radius(0) == 10.0);
-
-        self.assertRaises(AssertionError,lambda: s.setRadius(2,10));
-        self.assertRaises(AssertionError,lambda: s.setRadii([1]))
-        self.assertRaises(AssertionError,lambda: s.setRadii([1,2,3]))
-
-        self.assertRaises(AssertionError,lambda: s.atomName(2))
-        self.assertRaises(AssertionError,lambda: s.residueName(2))
-        self.assertRaises(AssertionError,lambda: s.residueNumber(2))
-        self.assertRaises(AssertionError,lambda: s.chainLabel(2))
-
-        setVerbosity(nowarnings)
-        s = Structure("data/1d3z.pdb",None,{'hydrogen' : True})
-        self.assertTrue(s.nAtoms() == 1231)
-
-        s = Structure("data/1d3z.pdb",None,{'hydrogen' : True, 'join-models' : True})
-        self.assertTrue(s.nAtoms() == 12310)
-
-        s = Structure("data/1ubq.pdb",None,{'hetatm' : True})
-        self.assertTrue(s.nAtoms() == 660)
-
-        s = Structure("data/1d3z.pdb",None,{'hydrogen' : True, 'skip-unknown' : True})
-        self.assertTrue(s.nAtoms() == 602)
-        
-        setVerbosity(silent)
-        self.assertRaises(Exception, lambda : Structure("data/1d3z.pdb",None,{'hydrogen' : True, 'halt-at-unknown' : True}))
-        setVerbosity(normal)
-
-    def testStructureArray(self):
-        # default separates chains, only uses first model (129 atoms per chain)
-        ss = structureArray("data/2jo4.pdb")
-        self.assertTrue(len(ss) == 4)
-        for s in ss:
-            self.assertTrue(s.nAtoms() == 129)
-
-        # include all models, separate chains, and include hydrogen and hetatm (286 atoms per chain)
-        setVerbosity(nowarnings)
-        ss = structureArray("data/2jo4.pdb",{'separate-models' : True,
-                                             'hydrogen' : True,
-                                             'hetatm' : True,
-                                             'separate-chains' : True})
-        self.assertTrue(len(ss) == 4*10)
-        for s in ss:
-            self.assertTrue(s.nAtoms() == 286)
-
-        # include all models, and include hydrogen and hetatm (286 atoms per chain)
-        ss = structureArray("data/2jo4.pdb",{'separate-models' : True,
-                                             'hydrogen' : True,
-                                             'hetatm' : True})
-        self.assertTrue(len(ss) == 10)
-        for s in ss:
-            self.assertTrue(s.nAtoms() == 286*4)
-        setVerbosity(normal)
-
-        # check that the structures initialized this way can be used for calculations
-        ss = structureArray("data/1ubq.pdb")
-        self.assertTrue(len(ss) == 1)
-        self.assertTrue(ss[0].nAtoms() == 602)
-        result = calc(ss[0],Parameters({'algorithm' : ShrakeRupley}))
-        self.assertTrue(math.fabs(result.totalArea() - 4834.716265) < 1e-5)
-
-        # Test exceptions
-        setVerbosity(silent)
-        self.assertRaises(AssertionError,lambda: structureArray(None))
-        self.assertRaises(IOError,lambda: structureArray(""))
-        self.assertRaises(Exception,lambda: structureArray("data/err.config"))
-        self.assertRaises(AssertionError,lambda: structureArray("data/2jo4.pdb",{'not-an-option' : True}))
-        self.assertRaises(AssertionError,
-                          lambda: structureArray("data/2jo4.pdb",
-                                                 {'not-an-option' : True, 'hydrogen' : True}))
-        self.assertRaises(AssertionError,
-                          lambda: structureArray("data/2jo4.pdb",
-                                                 {'hydrogen' : True}))
-        setVerbosity(normal)
-
-    def testCalc(self):
-        # test default settings
-        structure = Structure("data/1ubq.pdb")
-        result = calc(structure,Parameters({'algorithm' : ShrakeRupley}))
-        self.assertTrue(math.fabs(result.totalArea() - 4834.716265) < 1e-5)
-        sasa_classes = classifyResults(result,structure)
-        self.assertTrue(math.fabs(sasa_classes['Polar'] - 2515.821238) < 1e-5)
-        self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2318.895027) < 1e-5)
-
-        # test L&R
-        result = calc(structure,Parameters({'algorithm' : LeeRichards, 'n-slices' : 20}))
-        sasa_classes = classifyResults(result,structure)
-        self.assertTrue(math.fabs(result.totalArea() - 4804.055641) < 1e-5)
-        self.assertTrue(math.fabs(sasa_classes['Polar'] - 2504.217302) < 1e-5)
-        self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2299.838339) < 1e-5)
-
-        # test extending Classifier with derived class
-        sasa_classes = classifyResults(result,structure,DerivedClassifier())
-        self.assertTrue(math.fabs(sasa_classes['bla'] - 4804.055641) < 1e-5)
-        
-        ## test calculating with user-defined classifier ##
-        classifier = Classifier("share/oons.config")
-        # classifier passed to assign user-defined radii, could also have used setRadiiWithClassifier()
-        structure = Structure("data/1ubq.pdb",classifier) 
-        result = calc(structure,Parameters({'algorithm' : ShrakeRupley}))
-        self.assertTrue(math.fabs(result.totalArea() - 4779.5109924) < 1e-5)
-        sasa_classes = classifyResults(result,structure,classifier) # classifier passed to get user-classes
-        self.assertTrue(math.fabs(sasa_classes['Polar'] - 2236.9298941) < 1e-5)
-        self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2542.5810983) < 1e-5)
-
-    def testCalcCoord(self):
-        # one unit sphere
-        radii = [1]
-        coord = [0,0,0]
-        parameters = Parameters()
-        parameters.setNSlices(5000)
-        parameters.setProbeRadius(0)
-        result = calcCoord(coord, radii, parameters)
-        self.assertTrue(math.fabs(result.totalArea() - 4*math.pi) < 1e-3)
-
-        # two separate unit spheres
-        radii = [1,1]
-        coord = [0,0,0, 4,4,4]
-        result = calcCoord(coord, radii, parameters)
-        self.assertTrue(math.fabs(result.totalArea() - 2*4*math.pi) < 1e-3)
-
-        self.assertRaises(AssertionError,
-                          lambda: calcCoord(radii, radii))
-
-    def testSelectArea(self):
-        structure = Structure("data/1ubq.pdb")
-        result = calc(structure,Parameters({'algorithm' : ShrakeRupley}))
-        # will only test that this gets through to the C interface,
-        # extensive checking of the parser is done in the C unit tests
-        selections = selectArea(('s1, resn ala','s2, resi 1'),structure,result)
-        self.assertTrue(math.fabs(selections['s1'] - 118.35) < 0.1)
-        self.assertTrue(math.fabs(selections['s2'] - 50.77) < 0.1)
-
-    def testBioPDB(self):
-        try:
-            from Bio.PDB import PDBParser
-        except ImportError:
-            print("Can't import Bio.PDB, tests skipped")
-            pass
-        else:
-            parser = PDBParser()
-            bp_structure = parser.get_structure("Ubiquitin","data/1ubq.pdb")
-            s1 = structureFromBioPDB(bp_structure)
-            s2 = Structure("data/1ubq.pdb")
-            self.assertTrue(s1.nAtoms() == s2.nAtoms())
-
-            for i in range(0, s2.nAtoms()):
-                self.assertTrue(s1.radius(i) == s2.radius(i))
-                # there can be tiny errors here
-                self.assertTrue(math.fabs(s1.coord(i)[0] - s2.coord(i)[0]) < 1e-5)
-                self.assertTrue(math.fabs(s1.coord(i)[1] - s2.coord(i)[1]) < 1e-5)
-                self.assertTrue(math.fabs(s1.coord(i)[2] - s2.coord(i)[2]) < 1e-5)
-
-            # because Bio.PDB structures will have slightly different
-            # coordinates (due to rounding errors) we set the
-            # tolerance as high as 1e-3
-            result = calc(s1, Parameters({'algorithm' : LeeRichards, 'n-slices' : 20}))
-            print(result.totalArea())
-            self.assertTrue(math.fabs(result.totalArea() - 4804.055641) < 1e-3)
-            sasa_classes = classifyResults(result, s1)
-            self.assertTrue(math.fabs(sasa_classes['Polar'] - 2504.217302) < 1e-3)
-            self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2299.838339) < 1e-3)
-
-            result, sasa_classes = calcBioPDB(bp_structure, Parameters({'algorithm' : ShrakeRupley}))
-            self.assertTrue(math.fabs(result.totalArea() - 4834.716265) < 1e-3)
-            self.assertTrue(math.fabs(sasa_classes['Polar'] - 2515.821238) < 1e-3)
-            self.assertTrue(math.fabs(sasa_classes['Apolar'] - 2318.895027) < 1e-3)
-            print(result.totalArea())
-
-
-if __name__ == '__main__':
-    # make sure we're in the right directory (if script is called from
-    # outside the directory)
-    abspath = os.path.abspath(__file__)
-    dirname = os.path.dirname(abspath)
-    os.chdir(dirname)
-    unittest.main()
-

aggrescan3d/aggrescan/data/freesasa-2.0.1/compile

@@ -1,347 +0,0 @@
-#! /bin/sh
-# Wrapper for compilers which do not understand '-c -o'.
-
-scriptversion=2012-10-14.11; # UTC
-
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
-# Written by Tom Tromey <[email protected]>.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# This file is maintained in Automake, please report
-# bugs to <[email protected]> or send patches to
-# <[email protected]>.
-
-nl='
-'
-
-# We need space, tab and new line, in precisely that order.  Quoting is
-# there to prevent tools from complaining about whitespace usage.
-IFS=" ""	$nl"
-
-file_conv=
-
-# func_file_conv build_file lazy
-# Convert a $build file to $host form and store it in $file
-# Currently only supports Windows hosts. If the determined conversion
-# type is listed in (the comma separated) LAZY, no conversion will
-# take place.
-func_file_conv ()
-{
-  file=$1
-  case $file in
-    / | /[!/]*) # absolute file, and not a UNC file
-      if test -z "$file_conv"; then
-	# lazily determine how to convert abs files
-	case `uname -s` in
-	  MINGW*)
-	    file_conv=mingw
-	    ;;
-	  CYGWIN*)
-	    file_conv=cygwin
-	    ;;
-	  *)
-	    file_conv=wine
-	    ;;
-	esac
-      fi
-      case $file_conv/,$2, in
-	*,$file_conv,*)
-	  ;;
-	mingw/*)
-	  file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'`
-	  ;;
-	cygwin/*)
-	  file=`cygpath -m "$file" || echo "$file"`
-	  ;;
-	wine/*)
-	  file=`winepath -w "$file" || echo "$file"`
-	  ;;
-      esac
-      ;;
-  esac
-}
-
-# func_cl_dashL linkdir
-# Make cl look for libraries in LINKDIR
-func_cl_dashL ()
-{
-  func_file_conv "$1"
-  if test -z "$lib_path"; then
-    lib_path=$file
-  else
-    lib_path="$lib_path;$file"
-  fi
-  linker_opts="$linker_opts -LIBPATH:$file"
-}
-
-# func_cl_dashl library
-# Do a library search-path lookup for cl
-func_cl_dashl ()
-{
-  lib=$1
-  found=no
-  save_IFS=$IFS
-  IFS=';'
-  for dir in $lib_path $LIB
-  do
-    IFS=$save_IFS
-    if $shared && test -f "$dir/$lib.dll.lib"; then
-      found=yes
-      lib=$dir/$lib.dll.lib
-      break
-    fi
-    if test -f "$dir/$lib.lib"; then
-      found=yes
-      lib=$dir/$lib.lib
-      break
-    fi
-    if test -f "$dir/lib$lib.a"; then
-      found=yes
-      lib=$dir/lib$lib.a
-      break
-    fi
-  done
-  IFS=$save_IFS
-
-  if test "$found" != yes; then
-    lib=$lib.lib
-  fi
-}
-
-# func_cl_wrapper cl arg...
-# Adjust compile command to suit cl
-func_cl_wrapper ()
-{
-  # Assume a capable shell
-  lib_path=
-  shared=:
-  linker_opts=
-  for arg
-  do
-    if test -n "$eat"; then
-      eat=
-    else
-      case $1 in
-	-o)
-	  # configure might choose to run compile as 'compile cc -o foo foo.c'.
-	  eat=1
-	  case $2 in
-	    *.o | *.[oO][bB][jJ])
-	      func_file_conv "$2"
-	      set x "$@" -Fo"$file"
-	      shift
-	      ;;
-	    *)
-	      func_file_conv "$2"
-	      set x "$@" -Fe"$file"
-	      shift
-	      ;;
-	  esac
-	  ;;
-	-I)
-	  eat=1
-	  func_file_conv "$2" mingw
-	  set x "$@" -I"$file"
-	  shift
-	  ;;
-	-I*)
-	  func_file_conv "${1#-I}" mingw
-	  set x "$@" -I"$file"
-	  shift
-	  ;;
-	-l)
-	  eat=1
-	  func_cl_dashl "$2"
-	  set x "$@" "$lib"
-	  shift
-	  ;;
-	-l*)
-	  func_cl_dashl "${1#-l}"
-	  set x "$@" "$lib"
-	  shift
-	  ;;
-	-L)
-	  eat=1
-	  func_cl_dashL "$2"
-	  ;;
-	-L*)
-	  func_cl_dashL "${1#-L}"
-	  ;;
-	-static)
-	  shared=false
-	  ;;
-	-Wl,*)
-	  arg=${1#-Wl,}
-	  save_ifs="$IFS"; IFS=','
-	  for flag in $arg; do
-	    IFS="$save_ifs"
-	    linker_opts="$linker_opts $flag"
-	  done
-	  IFS="$save_ifs"
-	  ;;
-	-Xlinker)
-	  eat=1
-	  linker_opts="$linker_opts $2"
-	  ;;
-	-*)
-	  set x "$@" "$1"
-	  shift
-	  ;;
-	*.cc | *.CC | *.cxx | *.CXX | *.[cC]++)
-	  func_file_conv "$1"
-	  set x "$@" -Tp"$file"
-	  shift
-	  ;;
-	*.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO])
-	  func_file_conv "$1" mingw
-	  set x "$@" "$file"
-	  shift
-	  ;;
-	*)
-	  set x "$@" "$1"
-	  shift
-	  ;;
-      esac
-    fi
-    shift
-  done
-  if test -n "$linker_opts"; then
-    linker_opts="-link$linker_opts"
-  fi
-  exec "$@" $linker_opts
-  exit 1
-}
-
-eat=
-
-case $1 in
-  '')
-     echo "$0: No command.  Try '$0 --help' for more information." 1>&2
-     exit 1;
-     ;;
-  -h | --h*)
-    cat <<\EOF
-Usage: compile [--help] [--version] PROGRAM [ARGS]
-
-Wrapper for compilers which do not understand '-c -o'.
-Remove '-o dest.o' from ARGS, run PROGRAM with the remaining
-arguments, and rename the output as expected.
-
-If you are trying to build a whole package this is not the
-right script to run: please start by reading the file 'INSTALL'.
-
-Report bugs to <[email protected]>.
-EOF
-    exit $?
-    ;;
-  -v | --v*)
-    echo "compile $scriptversion"
-    exit $?
-    ;;
-  cl | *[/\\]cl | cl.exe | *[/\\]cl.exe )
-    func_cl_wrapper "$@"      # Doesn't return...
-    ;;
-esac
-
-ofile=
-cfile=
-
-for arg
-do
-  if test -n "$eat"; then
-    eat=
-  else
-    case $1 in
-      -o)
-	# configure might choose to run compile as 'compile cc -o foo foo.c'.
-	# So we strip '-o arg' only if arg is an object.
-	eat=1
-	case $2 in
-	  *.o | *.obj)
-	    ofile=$2
-	    ;;
-	  *)
-	    set x "$@" -o "$2"
-	    shift
-	    ;;
-	esac
-	;;
-      *.c)
-	cfile=$1
-	set x "$@" "$1"
-	shift
-	;;
-      *)
-	set x "$@" "$1"
-	shift
-	;;
-    esac
-  fi
-  shift
-done
-
-if test -z "$ofile" || test -z "$cfile"; then
-  # If no '-o' option was seen then we might have been invoked from a
-  # pattern rule where we don't need one.  That is ok -- this is a
-  # normal compilation that the losing compiler can handle.  If no
-  # '.c' file was seen then we are probably linking.  That is also
-  # ok.
-  exec "$@"
-fi
-
-# Name of file we expect compiler to create.
-cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'`
-
-# Create the lock directory.
-# Note: use '[/\\:.-]' here to ensure that we don't use the same name
-# that we are using for the .o file.  Also, base the name on the expected
-# object file name, since that is what matters with a parallel build.
-lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d
-while true; do
-  if mkdir "$lockdir" >/dev/null 2>&1; then
-    break
-  fi
-  sleep 1
-done
-# FIXME: race condition here if user kills between mkdir and trap.
-trap "rmdir '$lockdir'; exit 1" 1 2 15
-
-# Run the compile.
-"$@"
-ret=$?
-
-if test -f "$cofile"; then
-  test "$cofile" = "$ofile" || mv "$cofile" "$ofile"
-elif test -f "${cofile}bj"; then
-  test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile"
-fi
-
-rmdir "$lockdir"
-exit $ret
-
-# Local Variables:
-# mode: shell-script
-# sh-indentation: 2
-# eval: (add-hook 'write-file-hooks 'time-stamp)
-# time-stamp-start: "scriptversion="
-# time-stamp-format: "%:y-%02m-%02d.%02H"
-# time-stamp-time-zone: "UTC"
-# time-stamp-end: "; # UTC"
-# End:

aggrescan3d/aggrescan/data/freesasa-2.0.1/config.h

@@ -1,244 +0,0 @@
-/* config.h.  Generated from config.h.in by configure.  */
-/* config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* Define to one of `_getb67', `GETB67', `getb67' for Cray-2 and Cray-YMP
-   systems. This function is required for `alloca.c' support on those systems.
-   */
-/* #undef CRAY_STACKSEG_END */
-
-/* Define to 1 if using `alloca.c'. */
-/* #undef C_ALLOCA */
-
-/* XML namespace */
-#define FREESASA_XMLNS "http://freesasa.github.io/"
-
-/* Define to 1 if you have `alloca', as a function or macro. */
-#define HAVE_ALLOCA 1
-
-/* Define to 1 if you have <alloca.h> and it should be used (not on Ultrix).
-   */
-#define HAVE_ALLOCA_H 1
-
-/* Define to 1 if you have the <dlfcn.h> header file. */
-#define HAVE_DLFCN_H 1
-
-/* Define to 1 if you have the `getline' function. */
-#define HAVE_GETLINE 1
-
-/* Define to 1 if you have the `getopt_long' function. */
-#define HAVE_GETOPT_LONG 1
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#define HAVE_INTTYPES_H 1
-
-/* Define to 1 if you have the `check' library (-lcheck). */
-/* #undef HAVE_LIBCHECK */
-
-/* Define to 1 if you have the `dl' library (-ldl). */
-#define HAVE_LIBDL 1
-
-/* Define to 1 if you have the `gcov' library (-lgcov). */
-/* #undef HAVE_LIBGCOV */
-
-/* Define to 1 if you have the <libintl.h> header file. */
-#define HAVE_LIBINTL_H 1
-
-/* Define to 1 if you have the `m' library (-lm). */
-#define HAVE_LIBM 1
-
-/* Define to 1 if you have the `pthread' library (-lpthread). */
-#define HAVE_LIBPTHREAD 1
-
-/* Define to 1 if you have the `rt' library (-lrt). */
-/* #undef HAVE_LIBRT */
-
-/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
-   to 0 otherwise. */
-#define HAVE_MALLOC 1
-
-/* Define to 1 if you have the <malloc.h> header file. */
-#define HAVE_MALLOC_H 1
-
-/* Define to 1 if you have the <memory.h> header file. */
-#define HAVE_MEMORY_H 1
-
-/* Define to 1 if you have the `memset' function. */
-#define HAVE_MEMSET 1
-
-/* Define to 1 if you have the `mkdir' function. */
-#define HAVE_MKDIR 1
-
-/* Define to 1 if your system has a GNU libc compatible `realloc' function,
-   and to 0 otherwise. */
-#define HAVE_REALLOC 1
-
-/* Define to 1 if you have the `sqrt' function. */
-#define HAVE_SQRT 1
-
-/* Define to 1 if you have the <stddef.h> header file. */
-#define HAVE_STDDEF_H 1
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#define HAVE_STDINT_H 1
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#define HAVE_STDLIB_H 1
-
-/* Define to 1 if you have the `strchr' function. */
-#define HAVE_STRCHR 1
-
-/* Define to 1 if you have the `strdup' function. */
-#define HAVE_STRDUP 1
-
-/* Define to 1 if you have the `strerror' function. */
-#define HAVE_STRERROR 1
-
-/* Define to 1 if you have the <strings.h> header file. */
-#define HAVE_STRINGS_H 1
-
-/* Define to 1 if you have the <string.h> header file. */
-#define HAVE_STRING_H 1
-
-/* Define to 1 if you have the `strncasecmp' function. */
-#define HAVE_STRNCASECMP 1
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#define HAVE_SYS_STAT_H 1
-
-/* Define to 1 if you have the <sys/time.h> header file. */
-#define HAVE_SYS_TIME_H 1
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#define HAVE_SYS_TYPES_H 1
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#define HAVE_UNISTD_H 1
-
-/* Project homepage */
-#define HOMEPAGE "<http://freesasa.github.io>"
-
-/* Name of package */
-#define PACKAGE "freesasa"
-
-/* Define to the address where bug reports for this package should be sent. */
-#define PACKAGE_BUGREPORT ""
-
-/* Define to the full name of this package. */
-#define PACKAGE_NAME "FreeSASA"
-
-/* Define to the full name and version of this package. */
-#define PACKAGE_STRING "FreeSASA 2.0.1"
-
-/* Define to the one symbol short name of this package. */
-#define PACKAGE_TARNAME "freesasa"
-
-/* Define to the home page for this package. */
-#define PACKAGE_URL ""
-
-/* Define to the version of this package. */
-#define PACKAGE_VERSION "2.0.1"
-
-/* Bug report string */
-#define REPORTBUG "Report bugs to <https://github.com/mittinatten/freesasa/issues>"
-
-/* If using the C implementation of alloca, define if you know the
-   direction of stack growth for your system; otherwise it will be
-   automatically deduced at runtime.
-	STACK_DIRECTION > 0 => grows toward higher addresses
-	STACK_DIRECTION < 0 => grows toward lower addresses
-	STACK_DIRECTION = 0 => direction of growth unknown */
-/* #undef STACK_DIRECTION */
-
-/* Define to 1 if you have the ANSI C header files. */
-#define STDC_HEADERS 1
-
-/* Build with Check unit testing framework */
-#define USE_CHECK 0
-
-/* Define if JSON should be included */
-#define USE_JSON 0
-
-/* Define if threads should be used. */
-#define USE_THREADS 1
-
-/* Define if XML should be included. */
-#define USE_XML 0
-
-/* Version number of package */
-#define VERSION "2.0.1"
-
-/* Define to 1 if `lex' declares `yytext' as a `char *' by default, not a
-   `char[]'. */
-/* #undef YYTEXT_POINTER */
-
-/* Define for Solaris 2.5.1 so the uint32_t typedef from <sys/synch.h>,
-   <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
-   #define below would cause a syntax error. */
-/* #undef _UINT32_T */
-
-/* Define for Solaris 2.5.1 so the uint64_t typedef from <sys/synch.h>,
-   <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
-   #define below would cause a syntax error. */
-/* #undef _UINT64_T */
-
-/* Define for Solaris 2.5.1 so the uint8_t typedef from <sys/synch.h>,
-   <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
-   #define below would cause a syntax error. */
-/* #undef _UINT8_T */
-
-/* Define to `__inline__' or `__inline' if that's what the C compiler
-   calls it, or to nothing if 'inline' is not supported under any name.  */
-#ifndef __cplusplus
-/* #undef inline */
-#endif
-
-/* Define to the type of a signed integer type of width exactly 16 bits if
-   such a type exists and the standard includes do not define it. */
-/* #undef int16_t */
-
-/* Define to the type of a signed integer type of width exactly 32 bits if
-   such a type exists and the standard includes do not define it. */
-/* #undef int32_t */
-
-/* Define to the type of a signed integer type of width exactly 8 bits if such
-   a type exists and the standard includes do not define it. */
-/* #undef int8_t */
-
-/* Define to rpl_malloc if the replacement function should be used. */
-/* #undef malloc */
-
-/* Define to rpl_realloc if the replacement function should be used. */
-/* #undef realloc */
-
-/* Define to the equivalent of the C99 'restrict' keyword, or to
-   nothing if this is not supported.  Do not define if restrict is
-   supported directly.  */
-#define restrict __restrict
-/* Work around a bug in Sun C++: it does not support _Restrict or
-   __restrict__, even though the corresponding Sun C compiler ends up with
-   "#define restrict _Restrict" or "#define restrict __restrict__" in the
-   previous line.  Perhaps some future version of Sun C++ will work with
-   restrict; if so, hopefully it defines __RESTRICT like Sun C does.  */
-#if defined __SUNPRO_CC && !defined __RESTRICT
-# define _Restrict
-# define __restrict__
-#endif
-
-/* Define to `unsigned int' if <sys/types.h> does not define. */
-/* #undef size_t */
-
-/* Define to the type of an unsigned integer type of width exactly 16 bits if
-   such a type exists and the standard includes do not define it. */
-/* #undef uint16_t */
-
-/* Define to the type of an unsigned integer type of width exactly 32 bits if
-   such a type exists and the standard includes do not define it. */
-/* #undef uint32_t */
-
-/* Define to the type of an unsigned integer type of width exactly 64 bits if
-   such a type exists and the standard includes do not define it. */
-/* #undef uint64_t */
-
-/* Define to the type of an unsigned integer type of width exactly 8 bits if
-   such a type exists and the standard includes do not define it. */
-/* #undef uint8_t */

aggrescan3d/aggrescan/data/freesasa-2.0.1/config.h.in

@@ -1,243 +0,0 @@
-/* config.h.in.  Generated from configure.ac by autoheader.  */
-
-/* Define to one of `_getb67', `GETB67', `getb67' for Cray-2 and Cray-YMP
-   systems. This function is required for `alloca.c' support on those systems.
-   */
-#undef CRAY_STACKSEG_END
-
-/* Define to 1 if using `alloca.c'. */
-#undef C_ALLOCA
-
-/* XML namespace */
-#undef FREESASA_XMLNS
-
-/* Define to 1 if you have `alloca', as a function or macro. */
-#undef HAVE_ALLOCA
-
-/* Define to 1 if you have <alloca.h> and it should be used (not on Ultrix).
-   */
-#undef HAVE_ALLOCA_H
-
-/* Define to 1 if you have the <dlfcn.h> header file. */
-#undef HAVE_DLFCN_H
-
-/* Define to 1 if you have the `getline' function. */
-#undef HAVE_GETLINE
-
-/* Define to 1 if you have the `getopt_long' function. */
-#undef HAVE_GETOPT_LONG
-
-/* Define to 1 if you have the <inttypes.h> header file. */
-#undef HAVE_INTTYPES_H
-
-/* Define to 1 if you have the `check' library (-lcheck). */
-#undef HAVE_LIBCHECK
-
-/* Define to 1 if you have the `dl' library (-ldl). */
-#undef HAVE_LIBDL
-
-/* Define to 1 if you have the `gcov' library (-lgcov). */
-#undef HAVE_LIBGCOV
-
-/* Define to 1 if you have the <libintl.h> header file. */
-#undef HAVE_LIBINTL_H
-
-/* Define to 1 if you have the `m' library (-lm). */
-#undef HAVE_LIBM
-
-/* Define to 1 if you have the `pthread' library (-lpthread). */
-#undef HAVE_LIBPTHREAD
-
-/* Define to 1 if you have the `rt' library (-lrt). */
-#undef HAVE_LIBRT
-
-/* Define to 1 if your system has a GNU libc compatible `malloc' function, and
-   to 0 otherwise. */
-#undef HAVE_MALLOC
-
-/* Define to 1 if you have the <malloc.h> header file. */
-#undef HAVE_MALLOC_H
-
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
-/* Define to 1 if you have the `memset' function. */
-#undef HAVE_MEMSET
-
-/* Define to 1 if you have the `mkdir' function. */
-#undef HAVE_MKDIR
-
-/* Define to 1 if your system has a GNU libc compatible `realloc' function,
-   and to 0 otherwise. */
-#undef HAVE_REALLOC
-
-/* Define to 1 if you have the `sqrt' function. */
-#undef HAVE_SQRT
-
-/* Define to 1 if you have the <stddef.h> header file. */
-#undef HAVE_STDDEF_H
-
-/* Define to 1 if you have the <stdint.h> header file. */
-#undef HAVE_STDINT_H
-
-/* Define to 1 if you have the <stdlib.h> header file. */
-#undef HAVE_STDLIB_H
-
-/* Define to 1 if you have the `strchr' function. */
-#undef HAVE_STRCHR
-
-/* Define to 1 if you have the `strdup' function. */
-#undef HAVE_STRDUP
-
-/* Define to 1 if you have the `strerror' function. */
-#undef HAVE_STRERROR
-
-/* Define to 1 if you have the <strings.h> header file. */
-#undef HAVE_STRINGS_H
-
-/* Define to 1 if you have the <string.h> header file. */
-#undef HAVE_STRING_H
-
-/* Define to 1 if you have the `strncasecmp' function. */
-#undef HAVE_STRNCASECMP
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#undef HAVE_SYS_STAT_H
-
-/* Define to 1 if you have the <sys/time.h> header file. */
-#undef HAVE_SYS_TIME_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#undef HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the <unistd.h> header file. */
-#undef HAVE_UNISTD_H
-
-/* Project homepage */
-#undef HOMEPAGE
-
-/* Name of package */
-#undef PACKAGE
-
-/* Define to the address where bug reports for this package should be sent. */
-#undef PACKAGE_BUGREPORT
-
-/* Define to the full name of this package. */
-#undef PACKAGE_NAME
-
-/* Define to the full name and version of this package. */
-#undef PACKAGE_STRING
-
-/* Define to the one symbol short name of this package. */
-#undef PACKAGE_TARNAME
-
-/* Define to the home page for this package. */
-#undef PACKAGE_URL
-
-/* Define to the version of this package. */
-#undef PACKAGE_VERSION
-
-/* Bug report string */
-#undef REPORTBUG
-
-/* If using the C implementation of alloca, define if you know the
-   direction of stack growth for your system; otherwise it will be
-   automatically deduced at runtime.
-	STACK_DIRECTION > 0 => grows toward higher addresses
-	STACK_DIRECTION < 0 => grows toward lower addresses
-	STACK_DIRECTION = 0 => direction of growth unknown */
-#undef STACK_DIRECTION
-
-/* Define to 1 if you have the ANSI C header files. */
-#undef STDC_HEADERS
-
-/* Build with Check unit testing framework */
-#undef USE_CHECK
-
-/* Define if JSON should be included */
-#undef USE_JSON
-
-/* Define if threads should be used. */
-#undef USE_THREADS
-
-/* Define if XML should be included. */
-#undef USE_XML
-
-/* Version number of package */
-#undef VERSION
-
-/* Define to 1 if `lex' declares `yytext' as a `char *' by default, not a
-   `char[]'. */
-#undef YYTEXT_POINTER
-
-/* Define for Solaris 2.5.1 so the uint32_t typedef from <sys/synch.h>,
-   <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
-   #define below would cause a syntax error. */
-#undef _UINT32_T
-
-/* Define for Solaris 2.5.1 so the uint64_t typedef from <sys/synch.h>,
-   <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
-   #define below would cause a syntax error. */
-#undef _UINT64_T
-
-/* Define for Solaris 2.5.1 so the uint8_t typedef from <sys/synch.h>,
-   <pthread.h>, or <semaphore.h> is not used. If the typedef were allowed, the
-   #define below would cause a syntax error. */
-#undef _UINT8_T
-
-/* Define to `__inline__' or `__inline' if that's what the C compiler
-   calls it, or to nothing if 'inline' is not supported under any name.  */
-#ifndef __cplusplus
-#undef inline
-#endif
-
-/* Define to the type of a signed integer type of width exactly 16 bits if
-   such a type exists and the standard includes do not define it. */
-#undef int16_t
-
-/* Define to the type of a signed integer type of width exactly 32 bits if
-   such a type exists and the standard includes do not define it. */
-#undef int32_t
-
-/* Define to the type of a signed integer type of width exactly 8 bits if such
-   a type exists and the standard includes do not define it. */
-#undef int8_t
-
-/* Define to rpl_malloc if the replacement function should be used. */
-#undef malloc
-
-/* Define to rpl_realloc if the replacement function should be used. */
-#undef realloc
-
-/* Define to the equivalent of the C99 'restrict' keyword, or to
-   nothing if this is not supported.  Do not define if restrict is
-   supported directly.  */
-#undef restrict
-/* Work around a bug in Sun C++: it does not support _Restrict or
-   __restrict__, even though the corresponding Sun C compiler ends up with
-   "#define restrict _Restrict" or "#define restrict __restrict__" in the
-   previous line.  Perhaps some future version of Sun C++ will work with
-   restrict; if so, hopefully it defines __RESTRICT like Sun C does.  */
-#if defined __SUNPRO_CC && !defined __RESTRICT
-# define _Restrict
-# define __restrict__
-#endif
-
-/* Define to `unsigned int' if <sys/types.h> does not define. */
-#undef size_t
-
-/* Define to the type of an unsigned integer type of width exactly 16 bits if
-   such a type exists and the standard includes do not define it. */
-#undef uint16_t
-
-/* Define to the type of an unsigned integer type of width exactly 32 bits if
-   such a type exists and the standard includes do not define it. */
-#undef uint32_t
-
-/* Define to the type of an unsigned integer type of width exactly 64 bits if
-   such a type exists and the standard includes do not define it. */
-#undef uint64_t
-
-/* Define to the type of an unsigned integer type of width exactly 8 bits if
-   such a type exists and the standard includes do not define it. */
-#undef uint8_t

aggrescan3d/aggrescan/data/freesasa-2.0.1/config.log

@@ -1,1108 +0,0 @@
-This file contains any messages produced by compilers while
-running configure, to aid debugging if configure makes a mistake.
-
-It was created by FreeSASA configure 2.0.1, which was
-generated by GNU Autoconf 2.69.  Invocation command line was
-
-  $ ./configure --disable-xml --disable-json
-
-## --------- ##
-## Platform. ##
-## --------- ##
-
-hostname = chlamydia
-uname -m = x86_64
-uname -r = 4.4.0-96-generic
-uname -s = Linux
-uname -v = #119-Ubuntu SMP Tue Sep 12 14:59:54 UTC 2017
-
-/usr/bin/uname -p = unknown
-/bin/uname -X     = unknown
-
-/bin/arch              = unknown
-/usr/bin/arch -k       = unknown
-/usr/convex/getsysinfo = unknown
-/usr/bin/hostinfo      = unknown
-/bin/machine           = unknown
-/usr/bin/oslevel       = unknown
-/bin/universe          = unknown
-
-PATH: /home/olek/anaconda2/bin
-PATH: home/olek/pycharm-community-2017.2/bin
-PATH: /home/olek/bin
-PATH: /home/olek/.local/bin
-PATH: /usr/local/sbin
-PATH: /usr/local/bin
-PATH: /usr/sbin
-PATH: /usr/bin
-PATH: /sbin
-PATH: /bin
-PATH: /usr/games
-PATH: /usr/local/games
-PATH: /snap/bin
-
-
-## ----------- ##
-## Core tests. ##
-## ----------- ##
-
-configure:2450: checking for a BSD-compatible install
-configure:2518: result: /usr/bin/install -c
-configure:2529: checking whether build environment is sane
-configure:2584: result: yes
-configure:2735: checking for a thread-safe mkdir -p
-configure:2774: result: /bin/mkdir -p
-configure:2781: checking for gawk
-configure:2797: found /usr/bin/gawk
-configure:2808: result: gawk
-configure:2819: checking whether make sets $(MAKE)
-configure:2841: result: yes
-configure:2870: checking whether make supports nested variables
-configure:2887: result: yes
-configure:3159: checking for gcc
-configure:3175: found /usr/bin/gcc
-configure:3186: result: gcc
-configure:3415: checking for C compiler version
-configure:3424: gcc --version >&5
-gcc (Ubuntu 5.4.0-6ubuntu1~16.04.4) 5.4.0 20160609
-Copyright (C) 2015 Free Software Foundation, Inc.
-This is free software; see the source for copying conditions.  There is NO
-warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
-configure:3435: $? = 0
-configure:3424: gcc -v >&5
-Using built-in specs.
-COLLECT_GCC=gcc
-COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/5/lto-wrapper
-Target: x86_64-linux-gnu
-Configured with: ../src/configure -v --with-pkgversion='Ubuntu 5.4.0-6ubuntu1~16.04.4' --with-bugurl=file:///usr/share/doc/gcc-5/README.Bugs --enable-languages=c,ada,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-5 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-libmpx --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-5-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-5-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-5-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
-Thread model: posix
-gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.4) 
-configure:3435: $? = 0
-configure:3424: gcc -V >&5
-gcc: error: unrecognized command line option '-V'
-gcc: fatal error: no input files
-compilation terminated.
-configure:3435: $? = 1
-configure:3424: gcc -qversion >&5
-gcc: error: unrecognized command line option '-qversion'
-gcc: fatal error: no input files
-compilation terminated.
-configure:3435: $? = 1
-configure:3455: checking whether the C compiler works
-configure:3477: gcc    conftest.c  >&5
-configure:3481: $? = 0
-configure:3529: result: yes
-configure:3532: checking for C compiler default output file name
-configure:3534: result: a.out
-configure:3540: checking for suffix of executables
-configure:3547: gcc -o conftest    conftest.c  >&5
-configure:3551: $? = 0
-configure:3573: result: 
-configure:3595: checking whether we are cross compiling
-configure:3603: gcc -o conftest    conftest.c  >&5
-configure:3607: $? = 0
-configure:3614: ./conftest
-configure:3618: $? = 0
-configure:3633: result: no
-configure:3638: checking for suffix of object files
-configure:3660: gcc -c   conftest.c >&5
-configure:3664: $? = 0
-configure:3685: result: o
-configure:3689: checking whether we are using the GNU C compiler
-configure:3708: gcc -c   conftest.c >&5
-configure:3708: $? = 0
-configure:3717: result: yes
-configure:3726: checking whether gcc accepts -g
-configure:3746: gcc -c -g  conftest.c >&5
-configure:3746: $? = 0
-configure:3787: result: yes
-configure:3804: checking for gcc option to accept ISO C89
-configure:3867: gcc  -c -g -O2  conftest.c >&5
-configure:3867: $? = 0
-configure:3880: result: none needed
-configure:3905: checking whether gcc understands -c and -o together
-configure:3927: gcc -c conftest.c -o conftest2.o
-configure:3930: $? = 0
-configure:3927: gcc -c conftest.c -o conftest2.o
-configure:3930: $? = 0
-configure:3942: result: yes
-configure:3970: checking for style of include used by make
-configure:3998: result: GNU
-configure:4024: checking dependency style of gcc
-configure:4135: result: gcc3
-configure:4193: checking for ranlib
-configure:4209: found /usr/bin/ranlib
-configure:4220: result: ranlib
-configure:4246: checking for sqrt in -lm
-configure:4271: gcc -o conftest -g -O2   conftest.c -lm   >&5
-conftest.c:21:6: warning: conflicting types for built-in function 'sqrt'
- char sqrt ();
-      ^
-configure:4271: $? = 0
-configure:4280: result: yes
-configure:4291: checking for dlsym in -ldl
-configure:4316: gcc -o conftest -g -O2   conftest.c -ldl  -lm  >&5
-configure:4316: $? = 0
-configure:4325: result: yes
-configure:4343: checking how to run the C preprocessor
-configure:4374: gcc -E  conftest.c
-configure:4374: $? = 0
-configure:4388: gcc -E  conftest.c
-conftest.c:16:28: fatal error: ac_nonexistent.h: No such file or directory
-compilation terminated.
-configure:4388: $? = 1
-configure: failed program was:
-| /* confdefs.h */
-| #define PACKAGE_NAME "FreeSASA"
-| #define PACKAGE_TARNAME "freesasa"
-| #define PACKAGE_VERSION "2.0.1"
-| #define PACKAGE_STRING "FreeSASA 2.0.1"
-| #define PACKAGE_BUGREPORT ""
-| #define PACKAGE_URL ""
-| #define PACKAGE "freesasa"
-| #define VERSION "2.0.1"
-| #define REPORTBUG "Report bugs to <https://github.com/mittinatten/freesasa/issues>"
-| #define HOMEPAGE "<http://freesasa.github.io>"
-| #define FREESASA_XMLNS "http://freesasa.github.io/"
-| #define HAVE_LIBM 1
-| #define HAVE_LIBDL 1
-| /* end confdefs.h.  */
-| #include <ac_nonexistent.h>
-configure:4413: result: gcc -E
-configure:4433: gcc -E  conftest.c
-configure:4433: $? = 0
-configure:4447: gcc -E  conftest.c
-conftest.c:16:28: fatal error: ac_nonexistent.h: No such file or directory
-compilation terminated.
-configure:4447: $? = 1
-configure: failed program was:
-| /* confdefs.h */
-| #define PACKAGE_NAME "FreeSASA"
-| #define PACKAGE_TARNAME "freesasa"
-| #define PACKAGE_VERSION "2.0.1"
-| #define PACKAGE_STRING "FreeSASA 2.0.1"
-| #define PACKAGE_BUGREPORT ""
-| #define PACKAGE_URL ""
-| #define PACKAGE "freesasa"
-| #define VERSION "2.0.1"
-| #define REPORTBUG "Report bugs to <https://github.com/mittinatten/freesasa/issues>"
-| #define HOMEPAGE "<http://freesasa.github.io>"
-| #define FREESASA_XMLNS "http://freesasa.github.io/"
-| #define HAVE_LIBM 1
-| #define HAVE_LIBDL 1
-| /* end confdefs.h.  */
-| #include <ac_nonexistent.h>
-configure:4476: checking for grep that handles long lines and -e
-configure:4534: result: /bin/grep
-configure:4539: checking for egrep
-configure:4601: result: /bin/grep -E
-configure:4606: checking for ANSI C header files
-configure:4626: gcc -c -g -O2  conftest.c >&5
-configure:4626: $? = 0
-configure:4699: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:4699: $? = 0
-configure:4699: ./conftest
-configure:4699: $? = 0
-configure:4710: result: yes
-configure:4723: checking for sys/types.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4723: checking for sys/stat.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4723: checking for stdlib.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4723: checking for string.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4723: checking for memory.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4723: checking for strings.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4723: checking for inttypes.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4723: checking for stdint.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4723: checking for unistd.h
-configure:4723: gcc -c -g -O2  conftest.c >&5
-configure:4723: $? = 0
-configure:4723: result: yes
-configure:4735: checking for size_t
-configure:4735: gcc -c -g -O2  conftest.c >&5
-configure:4735: $? = 0
-configure:4735: gcc -c -g -O2  conftest.c >&5
-conftest.c: In function 'main':
-conftest.c:62:21: error: expected expression before ')' token
- if (sizeof ((size_t)))
-                     ^
-configure:4735: $? = 1
-configure: failed program was:
-| /* confdefs.h */
-| #define PACKAGE_NAME "FreeSASA"
-| #define PACKAGE_TARNAME "freesasa"
-| #define PACKAGE_VERSION "2.0.1"
-| #define PACKAGE_STRING "FreeSASA 2.0.1"
-| #define PACKAGE_BUGREPORT ""
-| #define PACKAGE_URL ""
-| #define PACKAGE "freesasa"
-| #define VERSION "2.0.1"
-| #define REPORTBUG "Report bugs to <https://github.com/mittinatten/freesasa/issues>"
-| #define HOMEPAGE "<http://freesasa.github.io>"
-| #define FREESASA_XMLNS "http://freesasa.github.io/"
-| #define HAVE_LIBM 1
-| #define HAVE_LIBDL 1
-| #define STDC_HEADERS 1
-| #define HAVE_SYS_TYPES_H 1
-| #define HAVE_SYS_STAT_H 1
-| #define HAVE_STDLIB_H 1
-| #define HAVE_STRING_H 1
-| #define HAVE_MEMORY_H 1
-| #define HAVE_STRINGS_H 1
-| #define HAVE_INTTYPES_H 1
-| #define HAVE_STDINT_H 1
-| #define HAVE_UNISTD_H 1
-| /* end confdefs.h.  */
-| #include <stdio.h>
-| #ifdef HAVE_SYS_TYPES_H
-| # include <sys/types.h>
-| #endif
-| #ifdef HAVE_SYS_STAT_H
-| # include <sys/stat.h>
-| #endif
-| #ifdef STDC_HEADERS
-| # include <stdlib.h>
-| # include <stddef.h>
-| #else
-| # ifdef HAVE_STDLIB_H
-| #  include <stdlib.h>
-| # endif
-| #endif
-| #ifdef HAVE_STRING_H
-| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
-| #  include <memory.h>
-| # endif
-| # include <string.h>
-| #endif
-| #ifdef HAVE_STRINGS_H
-| # include <strings.h>
-| #endif
-| #ifdef HAVE_INTTYPES_H
-| # include <inttypes.h>
-| #endif
-| #ifdef HAVE_STDINT_H
-| # include <stdint.h>
-| #endif
-| #ifdef HAVE_UNISTD_H
-| # include <unistd.h>
-| #endif
-| int
-| main ()
-| {
-| if (sizeof ((size_t)))
-| 	    return 0;
-|   ;
-|   return 0;
-| }
-configure:4735: result: yes
-configure:4748: checking for working alloca.h
-configure:4765: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:4765: $? = 0
-configure:4773: result: yes
-configure:4781: checking for alloca
-configure:4818: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:4818: $? = 0
-configure:4826: result: yes
-configure:4935: checking for inttypes.h
-configure:4935: result: yes
-configure:4935: checking libintl.h usability
-configure:4935: gcc -c -g -O2  conftest.c >&5
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking libintl.h presence
-configure:4935: gcc -E  conftest.c
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking for libintl.h
-configure:4935: result: yes
-configure:4935: checking malloc.h usability
-configure:4935: gcc -c -g -O2  conftest.c >&5
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking malloc.h presence
-configure:4935: gcc -E  conftest.c
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking for malloc.h
-configure:4935: result: yes
-configure:4935: checking stddef.h usability
-configure:4935: gcc -c -g -O2  conftest.c >&5
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking stddef.h presence
-configure:4935: gcc -E  conftest.c
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking for stddef.h
-configure:4935: result: yes
-configure:4935: checking for stdlib.h
-configure:4935: result: yes
-configure:4935: checking for string.h
-configure:4935: result: yes
-configure:4935: checking for strings.h
-configure:4935: result: yes
-configure:4935: checking sys/time.h usability
-configure:4935: gcc -c -g -O2  conftest.c >&5
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking sys/time.h presence
-configure:4935: gcc -E  conftest.c
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking for sys/time.h
-configure:4935: result: yes
-configure:4935: checking for unistd.h
-configure:4935: result: yes
-configure:4935: checking dlfcn.h usability
-configure:4935: gcc -c -g -O2  conftest.c >&5
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking dlfcn.h presence
-configure:4935: gcc -E  conftest.c
-configure:4935: $? = 0
-configure:4935: result: yes
-configure:4935: checking for dlfcn.h
-configure:4935: result: yes
-configure:4947: checking for inline
-configure:4963: gcc -c -g -O2  conftest.c >&5
-configure:4963: $? = 0
-configure:4971: result: inline
-configure:4989: checking for size_t
-configure:4989: result: yes
-configure:5000: checking for C/C++ restrict keyword
-configure:5025: gcc -c -g -O2  conftest.c >&5
-configure:5025: $? = 0
-configure:5033: result: __restrict
-configure:5046: checking for int16_t
-configure:5046: gcc -c -g -O2  conftest.c >&5
-configure:5046: $? = 0
-configure:5046: gcc -c -g -O2  conftest.c >&5
-conftest.c: In function 'main':
-conftest.c:76:12: error: size of array 'test_array' is negative
- static int test_array [1 - 2 * !((int16_t) (((((int16_t) 1 << N) << N) - 1) * 2 + 1)
-            ^
-configure:5046: $? = 1
-configure: failed program was:
-| /* confdefs.h */
-| #define PACKAGE_NAME "FreeSASA"
-| #define PACKAGE_TARNAME "freesasa"
-| #define PACKAGE_VERSION "2.0.1"
-| #define PACKAGE_STRING "FreeSASA 2.0.1"
-| #define PACKAGE_BUGREPORT ""
-| #define PACKAGE_URL ""
-| #define PACKAGE "freesasa"
-| #define VERSION "2.0.1"
-| #define REPORTBUG "Report bugs to <https://github.com/mittinatten/freesasa/issues>"
-| #define HOMEPAGE "<http://freesasa.github.io>"
-| #define FREESASA_XMLNS "http://freesasa.github.io/"
-| #define HAVE_LIBM 1
-| #define HAVE_LIBDL 1
-| #define STDC_HEADERS 1
-| #define HAVE_SYS_TYPES_H 1
-| #define HAVE_SYS_STAT_H 1
-| #define HAVE_STDLIB_H 1
-| #define HAVE_STRING_H 1
-| #define HAVE_MEMORY_H 1
-| #define HAVE_STRINGS_H 1
-| #define HAVE_INTTYPES_H 1
-| #define HAVE_STDINT_H 1
-| #define HAVE_UNISTD_H 1
-| #define HAVE_ALLOCA_H 1
-| #define HAVE_ALLOCA 1
-| #define HAVE_INTTYPES_H 1
-| #define HAVE_LIBINTL_H 1
-| #define HAVE_MALLOC_H 1
-| #define HAVE_STDDEF_H 1
-| #define HAVE_STDLIB_H 1
-| #define HAVE_STRING_H 1
-| #define HAVE_STRINGS_H 1
-| #define HAVE_SYS_TIME_H 1
-| #define HAVE_UNISTD_H 1
-| #define HAVE_DLFCN_H 1
-| #define restrict __restrict
-| /* end confdefs.h.  */
-| #include <stdio.h>
-| #ifdef HAVE_SYS_TYPES_H
-| # include <sys/types.h>
-| #endif
-| #ifdef HAVE_SYS_STAT_H
-| # include <sys/stat.h>
-| #endif
-| #ifdef STDC_HEADERS
-| # include <stdlib.h>
-| # include <stddef.h>
-| #else
-| # ifdef HAVE_STDLIB_H
-| #  include <stdlib.h>
-| # endif
-| #endif
-| #ifdef HAVE_STRING_H
-| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
-| #  include <memory.h>
-| # endif
-| # include <string.h>
-| #endif
-| #ifdef HAVE_STRINGS_H
-| # include <strings.h>
-| #endif
-| #ifdef HAVE_INTTYPES_H
-| # include <inttypes.h>
-| #endif
-| #ifdef HAVE_STDINT_H
-| # include <stdint.h>
-| #endif
-| #ifdef HAVE_UNISTD_H
-| # include <unistd.h>
-| #endif
-| 	        enum { N = 16 / 2 - 1 };
-| int
-| main ()
-| {
-| static int test_array [1 - 2 * !((int16_t) (((((int16_t) 1 << N) << N) - 1) * 2 + 1)
-| 		 < (int16_t) (((((int16_t) 1 << N) << N) - 1) * 2 + 2))];
-| test_array [0] = 0;
-| return test_array [0];
-| 
-|   ;
-|   return 0;
-| }
-configure:5046: result: yes
-configure:5057: checking for int32_t
-configure:5057: gcc -c -g -O2  conftest.c >&5
-configure:5057: $? = 0
-configure:5057: gcc -c -g -O2  conftest.c >&5
-conftest.c: In function 'main':
-conftest.c:77:53: warning: integer overflow in expression [-Woverflow]
-    < (int32_t) (((((int32_t) 1 << N) << N) - 1) * 2 + 2))];
-                                                     ^
-conftest.c:76:12: error: storage size of 'test_array' isn't constant
- static int test_array [1 - 2 * !((int32_t) (((((int32_t) 1 << N) << N) - 1) * 2 + 1)
-            ^
-configure:5057: $? = 1
-configure: failed program was:
-| /* confdefs.h */
-| #define PACKAGE_NAME "FreeSASA"
-| #define PACKAGE_TARNAME "freesasa"
-| #define PACKAGE_VERSION "2.0.1"
-| #define PACKAGE_STRING "FreeSASA 2.0.1"
-| #define PACKAGE_BUGREPORT ""
-| #define PACKAGE_URL ""
-| #define PACKAGE "freesasa"
-| #define VERSION "2.0.1"
-| #define REPORTBUG "Report bugs to <https://github.com/mittinatten/freesasa/issues>"
-| #define HOMEPAGE "<http://freesasa.github.io>"
-| #define FREESASA_XMLNS "http://freesasa.github.io/"
-| #define HAVE_LIBM 1
-| #define HAVE_LIBDL 1
-| #define STDC_HEADERS 1
-| #define HAVE_SYS_TYPES_H 1
-| #define HAVE_SYS_STAT_H 1
-| #define HAVE_STDLIB_H 1
-| #define HAVE_STRING_H 1
-| #define HAVE_MEMORY_H 1
-| #define HAVE_STRINGS_H 1
-| #define HAVE_INTTYPES_H 1
-| #define HAVE_STDINT_H 1
-| #define HAVE_UNISTD_H 1
-| #define HAVE_ALLOCA_H 1
-| #define HAVE_ALLOCA 1
-| #define HAVE_INTTYPES_H 1
-| #define HAVE_LIBINTL_H 1
-| #define HAVE_MALLOC_H 1
-| #define HAVE_STDDEF_H 1
-| #define HAVE_STDLIB_H 1
-| #define HAVE_STRING_H 1
-| #define HAVE_STRINGS_H 1
-| #define HAVE_SYS_TIME_H 1
-| #define HAVE_UNISTD_H 1
-| #define HAVE_DLFCN_H 1
-| #define restrict __restrict
-| /* end confdefs.h.  */
-| #include <stdio.h>
-| #ifdef HAVE_SYS_TYPES_H
-| # include <sys/types.h>
-| #endif
-| #ifdef HAVE_SYS_STAT_H
-| # include <sys/stat.h>
-| #endif
-| #ifdef STDC_HEADERS
-| # include <stdlib.h>
-| # include <stddef.h>
-| #else
-| # ifdef HAVE_STDLIB_H
-| #  include <stdlib.h>
-| # endif
-| #endif
-| #ifdef HAVE_STRING_H
-| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
-| #  include <memory.h>
-| # endif
-| # include <string.h>
-| #endif
-| #ifdef HAVE_STRINGS_H
-| # include <strings.h>
-| #endif
-| #ifdef HAVE_INTTYPES_H
-| # include <inttypes.h>
-| #endif
-| #ifdef HAVE_STDINT_H
-| # include <stdint.h>
-| #endif
-| #ifdef HAVE_UNISTD_H
-| # include <unistd.h>
-| #endif
-| 	        enum { N = 32 / 2 - 1 };
-| int
-| main ()
-| {
-| static int test_array [1 - 2 * !((int32_t) (((((int32_t) 1 << N) << N) - 1) * 2 + 1)
-| 		 < (int32_t) (((((int32_t) 1 << N) << N) - 1) * 2 + 2))];
-| test_array [0] = 0;
-| return test_array [0];
-| 
-|   ;
-|   return 0;
-| }
-configure:5057: result: yes
-configure:5068: checking for int8_t
-configure:5068: gcc -c -g -O2  conftest.c >&5
-configure:5068: $? = 0
-configure:5068: gcc -c -g -O2  conftest.c >&5
-conftest.c: In function 'main':
-conftest.c:76:12: error: size of array 'test_array' is negative
- static int test_array [1 - 2 * !((int8_t) (((((int8_t) 1 << N) << N) - 1) * 2 + 1)
-            ^
-configure:5068: $? = 1
-configure: failed program was:
-| /* confdefs.h */
-| #define PACKAGE_NAME "FreeSASA"
-| #define PACKAGE_TARNAME "freesasa"
-| #define PACKAGE_VERSION "2.0.1"
-| #define PACKAGE_STRING "FreeSASA 2.0.1"
-| #define PACKAGE_BUGREPORT ""
-| #define PACKAGE_URL ""
-| #define PACKAGE "freesasa"
-| #define VERSION "2.0.1"
-| #define REPORTBUG "Report bugs to <https://github.com/mittinatten/freesasa/issues>"
-| #define HOMEPAGE "<http://freesasa.github.io>"
-| #define FREESASA_XMLNS "http://freesasa.github.io/"
-| #define HAVE_LIBM 1
-| #define HAVE_LIBDL 1
-| #define STDC_HEADERS 1
-| #define HAVE_SYS_TYPES_H 1
-| #define HAVE_SYS_STAT_H 1
-| #define HAVE_STDLIB_H 1
-| #define HAVE_STRING_H 1
-| #define HAVE_MEMORY_H 1
-| #define HAVE_STRINGS_H 1
-| #define HAVE_INTTYPES_H 1
-| #define HAVE_STDINT_H 1
-| #define HAVE_UNISTD_H 1
-| #define HAVE_ALLOCA_H 1
-| #define HAVE_ALLOCA 1
-| #define HAVE_INTTYPES_H 1
-| #define HAVE_LIBINTL_H 1
-| #define HAVE_MALLOC_H 1
-| #define HAVE_STDDEF_H 1
-| #define HAVE_STDLIB_H 1
-| #define HAVE_STRING_H 1
-| #define HAVE_STRINGS_H 1
-| #define HAVE_SYS_TIME_H 1
-| #define HAVE_UNISTD_H 1
-| #define HAVE_DLFCN_H 1
-| #define restrict __restrict
-| /* end confdefs.h.  */
-| #include <stdio.h>
-| #ifdef HAVE_SYS_TYPES_H
-| # include <sys/types.h>
-| #endif
-| #ifdef HAVE_SYS_STAT_H
-| # include <sys/stat.h>
-| #endif
-| #ifdef STDC_HEADERS
-| # include <stdlib.h>
-| # include <stddef.h>
-| #else
-| # ifdef HAVE_STDLIB_H
-| #  include <stdlib.h>
-| # endif
-| #endif
-| #ifdef HAVE_STRING_H
-| # if !defined STDC_HEADERS && defined HAVE_MEMORY_H
-| #  include <memory.h>
-| # endif
-| # include <string.h>
-| #endif
-| #ifdef HAVE_STRINGS_H
-| # include <strings.h>
-| #endif
-| #ifdef HAVE_INTTYPES_H
-| # include <inttypes.h>
-| #endif
-| #ifdef HAVE_STDINT_H
-| # include <stdint.h>
-| #endif
-| #ifdef HAVE_UNISTD_H
-| # include <unistd.h>
-| #endif
-| 	        enum { N = 8 / 2 - 1 };
-| int
-| main ()
-| {
-| static int test_array [1 - 2 * !((int8_t) (((((int8_t) 1 << N) << N) - 1) * 2 + 1)
-| 		 < (int8_t) (((((int8_t) 1 << N) << N) - 1) * 2 + 2))];
-| test_array [0] = 0;
-| return test_array [0];
-| 
-|   ;
-|   return 0;
-| }
-configure:5068: result: yes
-configure:5079: checking for uint16_t
-configure:5079: gcc -c -g -O2  conftest.c >&5
-configure:5079: $? = 0
-configure:5079: result: yes
-configure:5091: checking for uint32_t
-configure:5091: gcc -c -g -O2  conftest.c >&5
-configure:5091: $? = 0
-configure:5091: result: yes
-configure:5105: checking for uint64_t
-configure:5105: gcc -c -g -O2  conftest.c >&5
-configure:5105: $? = 0
-configure:5105: result: yes
-configure:5119: checking for uint8_t
-configure:5119: gcc -c -g -O2  conftest.c >&5
-configure:5119: $? = 0
-configure:5119: result: yes
-configure:5135: checking for gcc option to accept ISO C99
-configure:5284: gcc  -c -g -O2  conftest.c >&5
-configure:5284: $? = 0
-configure:5297: result: none needed
-configure:5312: checking for inline
-configure:5336: result: inline
-configure:5358: checking for stdlib.h
-configure:5358: result: yes
-configure:5368: checking for GNU libc compatible malloc
-configure:5392: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:5392: $? = 0
-configure:5392: ./conftest
-configure:5392: $? = 0
-configure:5402: result: yes
-configure:5425: checking for stdlib.h
-configure:5425: result: yes
-configure:5435: checking for GNU libc compatible realloc
-configure:5459: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:5459: $? = 0
-configure:5459: ./conftest
-configure:5459: $? = 0
-configure:5469: result: yes
-configure:5493: checking for memset
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-conftest.c:66:6: warning: conflicting types for built-in function 'memset'
- char memset ();
-      ^
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5493: checking for mkdir
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5493: checking for sqrt
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-conftest.c:68:6: warning: conflicting types for built-in function 'sqrt'
- char sqrt ();
-      ^
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5493: checking for strchr
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-conftest.c:69:6: warning: conflicting types for built-in function 'strchr'
- char strchr ();
-      ^
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5493: checking for strdup
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-conftest.c:70:6: warning: conflicting types for built-in function 'strdup'
- char strdup ();
-      ^
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5493: checking for strerror
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5493: checking for strncasecmp
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-conftest.c:72:6: warning: conflicting types for built-in function 'strncasecmp'
- char strncasecmp ();
-      ^
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5493: checking for getopt_long
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5493: checking for getline
-configure:5493: gcc -o conftest -g -O2   conftest.c -ldl -lm  >&5
-configure:5493: $? = 0
-configure:5493: result: yes
-configure:5518: checking for pthread_create in -lpthread
-configure:5543: gcc -o conftest -g -O2   conftest.c -lpthread  -ldl -lm  >&5
-configure:5543: $? = 0
-configure:5552: result: yes
-configure:5563: checking pthread.h usability
-configure:5563: gcc -c -g -O2  conftest.c >&5
-configure:5563: $? = 0
-configure:5563: result: yes
-configure:5563: checking pthread.h presence
-configure:5563: gcc -E  conftest.c
-configure:5563: $? = 0
-configure:5563: result: yes
-configure:5563: checking for pthread.h
-configure:5563: result: yes
-configure:5860: Building without support for XML output.
-configure:5985: Building without support for JSON output.
-configure:6789: checking that generated files are newer than configure
-configure:6795: result: done
-configure:6894: creating ./config.status
-
-## ---------------------- ##
-## Running config.status. ##
-## ---------------------- ##
-
-This file was extended by FreeSASA config.status 2.0.1, which was
-generated by GNU Autoconf 2.69.  Invocation command line was
-
-  CONFIG_FILES    = 
-  CONFIG_HEADERS  = 
-  CONFIG_LINKS    = 
-  CONFIG_COMMANDS = 
-  $ ./config.status 
-
-on chlamydia
-
-config.status:938: creating Makefile
-config.status:938: creating src/Makefile
-config.status:938: creating doc/Makefile
-config.status:938: creating doc/Doxyfile
-config.status:938: creating tests/Makefile
-config.status:938: creating bindings/Makefile
-config.status:938: creating share/Makefile
-config.status:938: creating bindings/python/setup.py
-config.status:938: creating tests/test-cli
-config.status:938: creating bindings/check-python
-config.status:938: creating config.h
-config.status:1167: executing depfiles commands
-
-## ---------------- ##
-## Cache variables. ##
-## ---------------- ##
-
-ac_cv_c_compiler_gnu=yes
-ac_cv_c_inline=inline
-ac_cv_c_int16_t=yes
-ac_cv_c_int32_t=yes
-ac_cv_c_int8_t=yes
-ac_cv_c_restrict=__restrict
-ac_cv_c_uint16_t=yes
-ac_cv_c_uint32_t=yes
-ac_cv_c_uint64_t=yes
-ac_cv_c_uint8_t=yes
-ac_cv_env_CC_set=
-ac_cv_env_CC_value=
-ac_cv_env_CFLAGS_set=
-ac_cv_env_CFLAGS_value=
-ac_cv_env_CPPFLAGS_set=
-ac_cv_env_CPPFLAGS_value=
-ac_cv_env_CPP_set=
-ac_cv_env_CPP_value=
-ac_cv_env_LDFLAGS_set=
-ac_cv_env_LDFLAGS_value=
-ac_cv_env_LIBS_set=
-ac_cv_env_LIBS_value=
-ac_cv_env_PKG_CONFIG_LIBDIR_set=
-ac_cv_env_PKG_CONFIG_LIBDIR_value=
-ac_cv_env_PKG_CONFIG_PATH_set=
-ac_cv_env_PKG_CONFIG_PATH_value=
-ac_cv_env_PKG_CONFIG_set=
-ac_cv_env_PKG_CONFIG_value=
-ac_cv_env_build_alias_set=
-ac_cv_env_build_alias_value=
-ac_cv_env_host_alias_set=
-ac_cv_env_host_alias_value=
-ac_cv_env_libxml2_CFLAGS_set=
-ac_cv_env_libxml2_CFLAGS_value=
-ac_cv_env_libxml2_LIBS_set=
-ac_cv_env_libxml2_LIBS_value=
-ac_cv_env_target_alias_set=
-ac_cv_env_target_alias_value=
-ac_cv_func_alloca_works=yes
-ac_cv_func_getline=yes
-ac_cv_func_getopt_long=yes
-ac_cv_func_malloc_0_nonnull=yes
-ac_cv_func_memset=yes
-ac_cv_func_mkdir=yes
-ac_cv_func_realloc_0_nonnull=yes
-ac_cv_func_sqrt=yes
-ac_cv_func_strchr=yes
-ac_cv_func_strdup=yes
-ac_cv_func_strerror=yes
-ac_cv_func_strncasecmp=yes
-ac_cv_header_dlfcn_h=yes
-ac_cv_header_inttypes_h=yes
-ac_cv_header_libintl_h=yes
-ac_cv_header_malloc_h=yes
-ac_cv_header_memory_h=yes
-ac_cv_header_pthread_h=yes
-ac_cv_header_stdc=yes
-ac_cv_header_stddef_h=yes
-ac_cv_header_stdint_h=yes
-ac_cv_header_stdlib_h=yes
-ac_cv_header_string_h=yes
-ac_cv_header_strings_h=yes
-ac_cv_header_sys_stat_h=yes
-ac_cv_header_sys_time_h=yes
-ac_cv_header_sys_types_h=yes
-ac_cv_header_unistd_h=yes
-ac_cv_lib_dl_dlsym=yes
-ac_cv_lib_m_sqrt=yes
-ac_cv_lib_pthread_pthread_create=yes
-ac_cv_objext=o
-ac_cv_path_EGREP='/bin/grep -E'
-ac_cv_path_GREP=/bin/grep
-ac_cv_path_install='/usr/bin/install -c'
-ac_cv_path_mkdir=/bin/mkdir
-ac_cv_prog_AWK=gawk
-ac_cv_prog_CPP='gcc -E'
-ac_cv_prog_ac_ct_CC=gcc
-ac_cv_prog_ac_ct_RANLIB=ranlib
-ac_cv_prog_cc_c89=
-ac_cv_prog_cc_c99=
-ac_cv_prog_cc_g=yes
-ac_cv_prog_make_make_set=yes
-ac_cv_type_size_t=yes
-ac_cv_working_alloca_h=yes
-am_cv_CC_dependencies_compiler_type=gcc3
-am_cv_make_support_nested_variables=yes
-am_cv_prog_cc_c_o=yes
-
-## ----------------- ##
-## Output variables. ##
-## ----------------- ##
-
-ACLOCAL='${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/missing aclocal-1.15'
-ALLOCA=''
-AMDEPBACKSLASH='\'
-AMDEP_FALSE='#'
-AMDEP_TRUE=''
-AMTAR='$${TAR-tar}'
-AM_BACKSLASH='\'
-AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
-AM_DEFAULT_VERBOSITY='1'
-AM_V='$(V)'
-AUTOCONF='${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/missing autoconf'
-AUTOHEADER='${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/missing autoheader'
-AUTOMAKE='${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/missing automake-1.15'
-AWK='gawk'
-BUILD_DOC_FALSE=''
-BUILD_DOC_TRUE='#'
-CC='gcc'
-CCDEPMODE='depmode=gcc3'
-CFLAGS='-g -O2'
-CHECK_FOR_PY_BINDINGS=''
-COND_GCOV_FALSE=''
-COND_GCOV_TRUE='#'
-CPP='gcc -E'
-CPPFLAGS=''
-CYGPATH_W='echo'
-CYTHON=''
-DEFS='-DHAVE_CONFIG_H'
-DEPDIR='.deps'
-DOXYGEN=''
-ECHO_C=''
-ECHO_N='-n'
-ECHO_T=''
-EGREP='/bin/grep -E'
-EXEEXT=''
-GENERATE_PARSER_FALSE=''
-GENERATE_PARSER_TRUE='#'
-GREP='/bin/grep'
-HAVE_CYTHON_FALSE=''
-HAVE_CYTHON_TRUE='#'
-HAVE_DOXYGEN_FALSE=''
-HAVE_DOXYGEN_TRUE='#'
-INSTALL_DATA='${INSTALL} -m 644'
-INSTALL_PROGRAM='${INSTALL}'
-INSTALL_SCRIPT='${INSTALL}'
-INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
-JSONC_FOR_PY_BINDINGS=''
-JSONLINT=''
-LDFLAGS=''
-LEX=''
-LEXLIB=''
-LEX_OUTPUT_ROOT=''
-LIBOBJS=''
-LIBS='-lpthread -ldl -lm '
-LIBXML_FOR_PY_BINDINGS=''
-LTLIBOBJS=''
-MAKEINFO='${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/missing makeinfo'
-MKDIR_P='/bin/mkdir -p'
-OBJEXT='o'
-PACKAGE='freesasa'
-PACKAGE_BUGREPORT=''
-PACKAGE_NAME='FreeSASA'
-PACKAGE_STRING='FreeSASA 2.0.1'
-PACKAGE_TARNAME='freesasa'
-PACKAGE_URL=''
-PACKAGE_VERSION='2.0.1'
-PATH_SEPARATOR=':'
-PKG_CONFIG=''
-PKG_CONFIG_LIBDIR=''
-PKG_CONFIG_PATH=''
-PYTHON=''
-RANLIB='ranlib'
-RUN_CLI_TESTS_FALSE='#'
-RUN_CLI_TESTS_TRUE=''
-SET_MAKE=''
-SHELL='/bin/bash'
-STRIP=''
-USE_CHECK_FALSE=''
-USE_CHECK_TRUE='#'
-USE_JSON=''
-USE_JSON_FALSE=''
-USE_JSON_TRUE='#'
-USE_THREADS_FALSE='#'
-USE_THREADS_TRUE=''
-USE_XML=''
-USE_XML_FALSE=''
-USE_XML_TRUE='#'
-VERSION='2.0.1'
-XMLLINT=''
-YACC=''
-ac_ct_CC='gcc'
-am__EXEEXT_FALSE=''
-am__EXEEXT_TRUE='#'
-am__fastdepCC_FALSE='#'
-am__fastdepCC_TRUE=''
-am__include='include'
-am__isrc=''
-am__leading_dot='.'
-am__nodep='_no'
-am__quote=''
-am__tar='$${TAR-tar} chof - "$$tardir"'
-am__untar='$${TAR-tar} xf -'
-bindir='${exec_prefix}/bin'
-build_alias=''
-datadir='${datarootdir}'
-datarootdir='${prefix}/share'
-docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
-dvidir='${docdir}'
-exec_prefix='${prefix}'
-host_alias=''
-htmldir='${docdir}'
-includedir='${prefix}/include'
-infodir='${datarootdir}/info'
-install_sh='${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/install-sh'
-libdir='${exec_prefix}/lib'
-libexecdir='${exec_prefix}/libexec'
-libxml2_CFLAGS=''
-libxml2_LIBS=''
-localedir='${datarootdir}/locale'
-localstatedir='${prefix}/var'
-mandir='${datarootdir}/man'
-mkdir_p='$(MKDIR_P)'
-oldincludedir='/usr/include'
-pdfdir='${docdir}'
-prefix='/usr/local'
-program_transform_name='s,x,x,'
-psdir='${docdir}'
-sbindir='${exec_prefix}/sbin'
-sharedstatedir='${prefix}/com'
-sysconfdir='${prefix}/etc'
-target_alias=''
-
-## ----------- ##
-## confdefs.h. ##
-## ----------- ##
-
-/* confdefs.h */
-#define PACKAGE_NAME "FreeSASA"
-#define PACKAGE_TARNAME "freesasa"
-#define PACKAGE_VERSION "2.0.1"
-#define PACKAGE_STRING "FreeSASA 2.0.1"
-#define PACKAGE_BUGREPORT ""
-#define PACKAGE_URL ""
-#define PACKAGE "freesasa"
-#define VERSION "2.0.1"
-#define REPORTBUG "Report bugs to <https://github.com/mittinatten/freesasa/issues>"
-#define HOMEPAGE "<http://freesasa.github.io>"
-#define FREESASA_XMLNS "http://freesasa.github.io/"
-#define HAVE_LIBM 1
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-#define STDC_HEADERS 1
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-#define HAVE_INTTYPES_H 1
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-#define HAVE_UNISTD_H 1
-#define HAVE_ALLOCA_H 1
-#define HAVE_ALLOCA 1
-#define HAVE_INTTYPES_H 1
-#define HAVE_LIBINTL_H 1
-#define HAVE_MALLOC_H 1
-#define HAVE_STDDEF_H 1
-#define HAVE_STDLIB_H 1
-#define HAVE_STRING_H 1
-#define HAVE_STRINGS_H 1
-#define HAVE_SYS_TIME_H 1
-#define HAVE_UNISTD_H 1
-#define HAVE_DLFCN_H 1
-#define restrict __restrict
-#define HAVE_STDLIB_H 1
-#define HAVE_MALLOC 1
-#define HAVE_STDLIB_H 1
-#define HAVE_REALLOC 1
-#define HAVE_MEMSET 1
-#define HAVE_MKDIR 1
-#define HAVE_SQRT 1
-#define HAVE_STRCHR 1
-#define HAVE_STRDUP 1
-#define HAVE_STRERROR 1
-#define HAVE_STRNCASECMP 1
-#define HAVE_GETOPT_LONG 1
-#define HAVE_GETLINE 1
-#define HAVE_LIBPTHREAD 1
-#define USE_THREADS 1
-#define USE_XML 0
-#define USE_JSON 0
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-configure: exit 0

aggrescan3d/aggrescan/data/freesasa-2.0.1/config.status

@@ -1,1274 +0,0 @@
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-DUALCASE=1; export DUALCASE # for MKS sh
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-PS1='$ '
-PS2='> '
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-# NLS nuisances.
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-export LC_ALL
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-# CDPATH.
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-# as_fn_error STATUS ERROR [LINENO LOG_FD]
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-# as_fn_executable_p FILE
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-exec 6>&1
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-ac_cs_usage="\
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-ac_cs_config="'--disable-xml' '--disable-json'"
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-    "bindings/Makefile") CONFIG_FILES="$CONFIG_FILES bindings/Makefile" ;;
-    "share/Makefile") CONFIG_FILES="$CONFIG_FILES share/Makefile" ;;
-    "bindings/python/setup.py") CONFIG_FILES="$CONFIG_FILES bindings/python/setup.py" ;;
-    "tests/test-cli") CONFIG_FILES="$CONFIG_FILES tests/test-cli" ;;
-    "bindings/check-python") CONFIG_FILES="$CONFIG_FILES bindings/check-python" ;;
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-  test "${CONFIG_FILES+set}" = set || CONFIG_FILES=$config_files
-  test "${CONFIG_HEADERS+set}" = set || CONFIG_HEADERS=$config_headers
-  test "${CONFIG_COMMANDS+set}" = set || CONFIG_COMMANDS=$config_commands
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-
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-# Set up the scripts for CONFIG_FILES section.
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-S["libxml2_LIBS"]=""
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-S["USE_XML_FALSE"]=""
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-S["LIBOBJS"]=""
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-S["DEPDIR"]=".deps"
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-S["CC"]="gcc"
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-S["AUTOMAKE"]="${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/missing automake-1.15"
-S["AUTOCONF"]="${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/missing autoconf"
-S["ACLOCAL"]="${SHELL} /home/olek/agroscan/aggrescan3d/freesasa-2.0.1/missing aclocal-1.15"
-S["VERSION"]="2.0.1"
-S["PACKAGE"]="freesasa"
-S["CYGPATH_W"]="echo"
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-S["INSTALL_DATA"]="${INSTALL} -m 644"
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-S["sharedstatedir"]="${prefix}/com"
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-S["exec_prefix"]="${prefix}"
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-S["PACKAGE_BUGREPORT"]=""
-S["PACKAGE_STRING"]="FreeSASA 2.0.1"
-S["PACKAGE_VERSION"]="2.0.1"
-S["PACKAGE_TARNAME"]="freesasa"
-S["PACKAGE_NAME"]="FreeSASA"
-S["PATH_SEPARATOR"]=":"
-S["SHELL"]="/bin/bash"
-_ACAWK
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-  FS = ""
-
-}
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-  line = $ 0
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-  substed = 0
-  len = length(field[1])
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-    key = field[i]
-    keylen = length(key)
-    if (S_is_set[key]) {
-      value = S[key]
-      line = substr(line, 1, len) "" value "" substr(line, len + keylen + 3)
-      len += length(value) + length(field[++i])
-      substed = 1
-    } else
-      len += 1 + keylen
-  }
-
-  print line
-}
-
-_ACAWK
-if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then
-  sed "s/$ac_cr\$//; s/$ac_cr/$ac_cs_awk_cr/g"
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-  cat
-fi < "$ac_tmp/subs1.awk" > "$ac_tmp/subs.awk" \
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-D["PACKAGE_VERSION"]=" \"2.0.1\""
-D["PACKAGE_STRING"]=" \"FreeSASA 2.0.1\""
-D["PACKAGE_BUGREPORT"]=" \"\""
-D["PACKAGE_URL"]=" \"\""
-D["PACKAGE"]=" \"freesasa\""
-D["VERSION"]=" \"2.0.1\""
-D["REPORTBUG"]=" \"Report bugs to <https://github.com/mittinatten/freesasa/issues>\""
-D["HOMEPAGE"]=" \"<http://freesasa.github.io>\""
-D["FREESASA_XMLNS"]=" \"http://freesasa.github.io/\""
-D["HAVE_LIBM"]=" 1"
-D["HAVE_LIBDL"]=" 1"
-D["STDC_HEADERS"]=" 1"
-D["HAVE_SYS_TYPES_H"]=" 1"
-D["HAVE_SYS_STAT_H"]=" 1"
-D["HAVE_STDLIB_H"]=" 1"
-D["HAVE_STRING_H"]=" 1"
-D["HAVE_MEMORY_H"]=" 1"
-D["HAVE_STRINGS_H"]=" 1"
-D["HAVE_INTTYPES_H"]=" 1"
-D["HAVE_STDINT_H"]=" 1"
-D["HAVE_UNISTD_H"]=" 1"
-D["HAVE_ALLOCA_H"]=" 1"
-D["HAVE_ALLOCA"]=" 1"
-D["HAVE_INTTYPES_H"]=" 1"
-D["HAVE_LIBINTL_H"]=" 1"
-D["HAVE_MALLOC_H"]=" 1"
-D["HAVE_STDDEF_H"]=" 1"
-D["HAVE_STDLIB_H"]=" 1"
-D["HAVE_STRING_H"]=" 1"
-D["HAVE_STRINGS_H"]=" 1"
-D["HAVE_SYS_TIME_H"]=" 1"
-D["HAVE_UNISTD_H"]=" 1"
-D["HAVE_DLFCN_H"]=" 1"
-D["restrict"]=" __restrict"
-D["HAVE_STDLIB_H"]=" 1"
-D["HAVE_MALLOC"]=" 1"
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-D["HAVE_SQRT"]=" 1"
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-D["HAVE_GETLINE"]=" 1"
-D["HAVE_LIBPTHREAD"]=" 1"
-D["USE_THREADS"]=" 1"
-D["USE_XML"]=" 0"
-D["USE_JSON"]=" 0"
-D["USE_CHECK"]=" 0"
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-  FS = ""
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-    mac1 = arg[2]
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-  prefix = substr(line, 1, index(line, defundef) - 1)
-  if (D_is_set[macro]) {
-    # Preserve the white space surrounding the "#".
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-    next
-  } else {
-    # Replace #undef with comments.  This is necessary, for example,
-    # in the case of _POSIX_SOURCE, which is predefined and required
-    # on some systems where configure will not decide to define it.
-    if (defundef == "undef") {
-      print "/*", prefix defundef, macro, "*/"
-      next
-    }
-  }
-}
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-
-
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-	   case $ac_f in
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-	   *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";;
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-esac
-ac_sed_extra="/^[	 ]*VPATH[	 ]*=[	 ]*/{
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-s/:@srcdir@:/:/g
-s/^:*//
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-    # $(DEPDIR) in their names.  We invoke sed twice because it is the
-    # simplest approach to changing $(DEPDIR) to its actual value in the
-    # expansion.
-    for file in `sed -n "
-      s/^$am__include $am__quote\(.*(DEPDIR).*\)$am__quote"'$/\1/p' <"$mf" | \
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-$as_echo X"$file" |
-    sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{
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-      as_dir=$dirpart/$fdir; as_fn_mkdir_p
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-      echo '# dummy' > "$dirpart/$file"
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-    "tests/test-cli":F) chmod +x tests/test-cli ;;
-    "bindings/check-python":F) chmod +x bindings/check-python ;;
-
-  esac
-done # for ac_tag
-
-
-as_fn_exit 0

aggrescan3d/aggrescan/data/freesasa-2.0.1/configure.ac

@@ -1,216 +0,0 @@
-#                                               -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-AC_PREREQ([2.68])
-AC_INIT([FreeSASA], [2.0.1])
-AM_INIT_AUTOMAKE([foreign])
-AC_CONFIG_SRCDIR([config.h.in])
-AC_CONFIG_HEADERS([config.h])
-m4_include([m4/ax_compare_version.m4])
-AC_DEFINE([REPORTBUG], ["Report bugs to <https://github.com/mittinatten/freesasa/issues>"], [Bug report string])
-AC_DEFINE([HOMEPAGE], ["<http://freesasa.github.io>"], [Project homepage])
-AC_DEFINE([FREESASA_XMLNS], ["http://freesasa.github.io/"], [XML namespace])
-
-# Checks for programs.
-AC_PROG_CC
-AC_PROG_RANLIB
-AC_PROG_INSTALL
-
-# Checks for libraries.
-AC_CHECK_LIB([m], [sqrt])
-AC_CHECK_LIB([dl], [dlsym])
-
-# Checks for header files.
-AC_FUNC_ALLOCA
-AC_CHECK_HEADERS([inttypes.h libintl.h malloc.h stddef.h stdlib.h string.h strings.h sys/time.h unistd.h dlfcn.h])
-
-# Checks for typedefs, structures, and compiler characteristics.
-AC_C_INLINE
-AC_TYPE_SIZE_T
-AC_C_RESTRICT
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-AC_TYPE_INT8_T
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-AC_TYPE_UINT64_T
-AC_TYPE_UINT8_T
-
-# use C99
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-AC_C_INLINE
-
-# Checks for library functions.
-AC_FUNC_MALLOC
-AC_FUNC_REALLOC
-AC_CHECK_FUNCS([memset mkdir sqrt strchr strdup strerror strncasecmp getopt_long getline])
-
-AC_CONFIG_FILES([Makefile src/Makefile doc/Makefile doc/Doxyfile
-                 tests/Makefile bindings/Makefile share/Makefile
-                 bindings/python/setup.py])
-AC_CONFIG_FILES([tests/test-cli], [chmod +x tests/test-cli])
-AC_CONFIG_FILES([bindings/check-python], [chmod +x bindings/check-python])
-
-# Optionally disable thread support
-AC_ARG_ENABLE([threads],
-  AS_HELP_STRING([--disable-threads],
-    [Build without support for multiple threads]))
-
-if test "x$enable_threads" != "xno"; then
-  AC_CHECK_LIB([pthread], [pthread_create])
-  AC_CHECK_HEADER([pthread.h])
-fi
-if test "$ac_cv_header_pthread_h" != yes || \
-   test "$ac_cv_lib_pthread_pthread_create" != yes; then
-  AC_DEFINE([USE_THREADS], [0], [])
-  AM_CONDITIONAL([USE_THREADS], false)
-  echo "Building without thread support"
-else
-  AC_DEFINE([USE_THREADS], [1], [Define if threads should be used.])
-  AM_CONDITIONAL([USE_THREADS], true)
-fi
-
-# disable XML
-AC_ARG_ENABLE([xml],
-  AS_HELP_STRING([--disable-xml],
-     [Build without support for XML output]))
-
-AC_DEFINE([USE_XML], [0], [Define if XML should be included.])
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-AC_SUBST([LIBXML_FOR_PY_BINDINGS], [])
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-if test "x$enable_xml" != "xno" ; then
-  AC_CHECK_PROG([XMLLINT],[xmllint],[xmllint],[]) 
-  PKG_CHECK_MODULES([libxml2], [libxml-2.0],
-    [AC_DEFINE([USE_XML], [1])
-     AC_SUBST([LIBXML_FOR_PY_BINDINGS], ['"xml2"'])
-     AC_SUBST([USE_XML], [yes])
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-# Disable json-c
-AC_ARG_ENABLE([json],
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-AC_DEFINE([USE_JSON], [0], [Define if JSON should be included])
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-AM_CONDITIONAL([USE_JSON], false)
-
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-  AC_CHECK_LIB([json-c], [json_object_get],
-     [AC_CHECK_HEADER([json-c/json_object.h],
-        [AC_DEFINE([USE_JSON], [1])
-         AC_SUBST([JSONC_FOR_PY_BINDINGS], ['"json-c"'])
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-
-AC_OUTPUT

aggrescan3d/aggrescan/data/freesasa-2.0.1/depcomp

@@ -1,791 +0,0 @@
-#! /bin/sh
-# depcomp - compile a program generating dependencies as side-effects
-
-scriptversion=2013-05-30.07; # UTC
-
-# Copyright (C) 1999-2013 Free Software Foundation, Inc.
-
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2, or (at your option)
-# any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-# As a special exception to the GNU General Public License, if you
-# distribute this file as part of a program that contains a
-# configuration script generated by Autoconf, you may include it under
-# the same distribution terms that you use for the rest of that program.
-
-# Originally written by Alexandre Oliva <[email protected]>.
-
-case $1 in
-  '')
-    echo "$0: No command.  Try '$0 --help' for more information." 1>&2
-    exit 1;
-    ;;
-  -h | --h*)
-    cat <<\EOF
-Usage: depcomp [--help] [--version] PROGRAM [ARGS]
-
-Run PROGRAMS ARGS to compile a file, generating dependencies
-as side-effects.
-
-Environment variables:
-  depmode     Dependency tracking mode.
-  source      Source file read by 'PROGRAMS ARGS'.
-  object      Object file output by 'PROGRAMS ARGS'.
-  DEPDIR      directory where to store dependencies.
-  depfile     Dependency file to output.
-  tmpdepfile  Temporary file to use when outputting dependencies.
-  libtool     Whether libtool is used (yes/no).
-
-Report bugs to <[email protected]>.
-EOF
-    exit $?
-    ;;
-  -v | --v*)
-    echo "depcomp $scriptversion"
-    exit $?
-    ;;
-esac
-
-# Get the directory component of the given path, and save it in the
-# global variables '$dir'.  Note that this directory component will
-# be either empty or ending with a '/' character.  This is deliberate.
-set_dir_from ()
-{
-  case $1 in
-    */*) dir=`echo "$1" | sed -e 's|/[^/]*$|/|'`;;
-      *) dir=;;
-  esac
-}
-
-# Get the suffix-stripped basename of the given path, and save it the
-# global variable '$base'.
-set_base_from ()
-{
-  base=`echo "$1" | sed -e 's|^.*/||' -e 's/\.[^.]*$//'`
-}
-
-# If no dependency file was actually created by the compiler invocation,
-# we still have to create a dummy depfile, to avoid errors with the
-# Makefile "include basename.Plo" scheme.
-make_dummy_depfile ()
-{
-  echo "#dummy" > "$depfile"
-}
-
-# Factor out some common post-processing of the generated depfile.
-# Requires the auxiliary global variable '$tmpdepfile' to be set.
-aix_post_process_depfile ()
-{
-  # If the compiler actually managed to produce a dependency file,
-  # post-process it.
-  if test -f "$tmpdepfile"; then
-    # Each line is of the form 'foo.o: dependency.h'.
-    # Do two passes, one to just change these to
-    #   $object: dependency.h
-    # and one to simply output
-    #   dependency.h:
-    # which is needed to avoid the deleted-header problem.
-    { sed -e "s,^.*\.[$lower]*:,$object:," < "$tmpdepfile"
-      sed -e "s,^.*\.[$lower]*:[$tab ]*,," -e 's,$,:,' < "$tmpdepfile"
-    } > "$depfile"
-    rm -f "$tmpdepfile"
-  else
-    make_dummy_depfile
-  fi
-}
-
-# A tabulation character.
-tab='	'
-# A newline character.
-nl='
-'
-# Character ranges might be problematic outside the C locale.
-# These definitions help.
-upper=ABCDEFGHIJKLMNOPQRSTUVWXYZ
-lower=abcdefghijklmnopqrstuvwxyz
-digits=0123456789
-alpha=${upper}${lower}
-
-if test -z "$depmode" || test -z "$source" || test -z "$object"; then
-  echo "depcomp: Variables source, object and depmode must be set" 1>&2
-  exit 1
-fi
-
-# Dependencies for sub/bar.o or sub/bar.obj go into sub/.deps/bar.Po.
-depfile=${depfile-`echo "$object" |
-  sed 's|[^\\/]*$|'${DEPDIR-.deps}'/&|;s|\.\([^.]*\)$|.P\1|;s|Pobj$|Po|'`}
-tmpdepfile=${tmpdepfile-`echo "$depfile" | sed 's/\.\([^.]*\)$/.T\1/'`}
-
-rm -f "$tmpdepfile"
-
-# Avoid interferences from the environment.
-gccflag= dashmflag=
-
-# Some modes work just like other modes, but use different flags.  We
-# parameterize here, but still list the modes in the big case below,
-# to make depend.m4 easier to write.  Note that we *cannot* use a case
-# here, because this file can only contain one case statement.
-if test "$depmode" = hp; then
-  # HP compiler uses -M and no extra arg.
-  gccflag=-M
-  depmode=gcc
-fi
-
-if test "$depmode" = dashXmstdout; then
-  # This is just like dashmstdout with a different argument.
-  dashmflag=-xM
-  depmode=dashmstdout
-fi
-
-cygpath_u="cygpath -u -f -"
-if test "$depmode" = msvcmsys; then
-  # This is just like msvisualcpp but w/o cygpath translation.
-  # Just convert the backslash-escaped backslashes to single forward
-  # slashes to satisfy depend.m4
-  cygpath_u='sed s,\\\\,/,g'
-  depmode=msvisualcpp
-fi
-
-if test "$depmode" = msvc7msys; then
-  # This is just like msvc7 but w/o cygpath translation.
-  # Just convert the backslash-escaped backslashes to single forward
-  # slashes to satisfy depend.m4
-  cygpath_u='sed s,\\\\,/,g'
-  depmode=msvc7
-fi
-
-if test "$depmode" = xlc; then
-  # IBM C/C++ Compilers xlc/xlC can output gcc-like dependency information.
-  gccflag=-qmakedep=gcc,-MF
-  depmode=gcc
-fi
-
-case "$depmode" in
-gcc3)
-## gcc 3 implements dependency tracking that does exactly what
-## we want.  Yay!  Note: for some reason libtool 1.4 doesn't like
-## it if -MD -MP comes after the -MF stuff.  Hmm.
-## Unfortunately, FreeBSD c89 acceptance of flags depends upon
-## the command line argument order; so add the flags where they
-## appear in depend2.am.  Note that the slowdown incurred here
-## affects only configure: in makefiles, %FASTDEP% shortcuts this.
-  for arg
-  do
-    case $arg in
-    -c) set fnord "$@" -MT "$object" -MD -MP -MF "$tmpdepfile" "$arg" ;;
-    *)  set fnord "$@" "$arg" ;;
-    esac
-    shift # fnord
-    shift # $arg
-  done
-  "$@"
-  stat=$?
-  if test $stat -ne 0; then
-    rm -f "$tmpdepfile"
-    exit $stat
-  fi
-  mv "$tmpdepfile" "$depfile"
-  ;;
-
-gcc)
-## Note that this doesn't just cater to obsosete pre-3.x GCC compilers.
-## but also to in-use compilers like IMB xlc/xlC and the HP C compiler.
-## (see the conditional assignment to $gccflag above).
-## There are various ways to get dependency output from gcc.  Here's
-## why we pick this rather obscure method:
-## - Don't want to use -MD because we'd like the dependencies to end
-##   up in a subdir.  Having to rename by hand is ugly.
-##   (We might end up doing this anyway to support other compilers.)
-## - The DEPENDENCIES_OUTPUT environment variable makes gcc act like
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-hp)
-  # This case exists only to let depend.m4 do its work.  It works by
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-sgi)
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-xlc)
-  # This case exists only to let depend.m4 do its work.  It works by
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-    tmpdepfile2=$base.u
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-    tmpdepfile1=$dir$base.u
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-
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-  aix_post_process_depfile
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-tcc)
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-  rm -f "$tmpdepfile"
-  ;;
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-  # Portland's C compiler understands '-MD'.
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-  # For projects that build the same source file twice into different object
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-  ;;
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-cpp)
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-  # Remove the call to Libtool.
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-  # Remove the call to Libtool.
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-# End:

aggrescan3d/aggrescan/data/freesasa-2.0.1/doc/Doxyfile

@@ -1,1741 +0,0 @@
-# Doxyfile 1.7.6.1
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project.
-#
-# All text after a hash (#) is considered a comment and will be ignored.
-# The format is:
-#       TAG = value [value, ...]
-# For lists items can also be appended using:
-#       TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ").
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# This tag specifies the encoding used for all characters in the config file
-# that follow. The default is UTF-8 which is also the encoding used for all
-# text before the first occurrence of this tag. Doxygen uses libiconv (or the
-# iconv built into libc) for the transcoding. See
-# http://www.gnu.org/software/libiconv for the list of possible encodings.
-
-DOXYFILE_ENCODING      = UTF-8
-
-# The PROJECT_NAME tag is a single word (or sequence of words) that should
-# identify the project. Note that if you do not use Doxywizard you need
-# to put quotes around the project name if it contains spaces.
-
-PROJECT_NAME           = FreeSASA
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
-
-PROJECT_NUMBER         = 2.0.1
-
-# Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer
-# a quick idea about the purpose of the project. Keep the description short.
-
-PROJECT_BRIEF          = "Open source SASA calculations"
-
-# With the PROJECT_LOGO tag one can specify an logo or icon that is
-# included in the documentation. The maximum height of the logo should not
-# exceed 55 pixels and the maximum width should not exceed 200 pixels.
-# Doxygen will copy the logo to the output directory.
-
-PROJECT_LOGO           =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
-OUTPUT_DIRECTORY       = html/doxygen
-
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
-
-CREATE_SUBDIRS         = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
-# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
-# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
-
-OUTPUT_LANGUAGE        = English
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
-
-BRIEF_MEMBER_DESC      = YES
-
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
-# brief descriptions will be completely suppressed.
-
-REPEAT_BRIEF           = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
-
-ABBREVIATE_BRIEF       =
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
-# description.
-
-ALWAYS_DETAILED_SEC    = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-
-INLINE_INHERITED_MEMB  = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
-
-FULL_PATH_NAMES        = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
-
-STRIP_FROM_PATH        =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
-
-STRIP_FROM_INC_PATH    =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful if your file system
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
-SHORT_NAMES            = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like regular Qt-style comments
-# (thus requiring an explicit @brief command for a brief description.)
-
-JAVADOC_AUTOBRIEF      = YES
-
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
-# interpret the first line (until the first dot) of a Qt-style
-# comment as the brief description. If set to NO, the comments
-# will behave just like regular Qt-style comments (thus requiring
-# an explicit \brief command for a brief description.)
-
-QT_AUTOBRIEF           = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
-
-INHERIT_DOCS           = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
-
-SEPARATE_MEMBER_PAGES  = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
-TAB_SIZE               = 4
-
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
-
-ALIASES                =
-
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding
-# "class=itcl::class" will allow you to use the command class in the
-# itcl::class meaning.
-
-TCL_SUBST              =
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
-
-OPTIMIZE_OUTPUT_FOR_C  = YES
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for
-# Java. For instance, namespaces will be presented as packages, qualified
-# scopes will look different, etc.
-
-OPTIMIZE_OUTPUT_JAVA   = NO
-
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources only. Doxygen will then generate output that is more tailored for
-# Fortran.
-
-OPTIMIZE_FOR_FORTRAN   = NO
-
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for
-# VHDL.
-
-OPTIMIZE_OUTPUT_VHDL   = NO
-
-# Doxygen selects the parser to use depending on the extension of the files it
-# parses. With this tag you can assign which parser to use for a given extension.
-# Doxygen has a built-in mapping, but you can override or extend it using this
-# tag. The format is ext=language, where ext is a file extension, and language
-# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
-# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
-# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
-# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
-# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
-
-EXTENSION_MAPPING      = pyx=Python
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-# to include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also makes the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-
-BUILTIN_STL_SUPPORT    = NO
-
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
-# enable parsing support.
-
-CPP_CLI_SUPPORT        = NO
-
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
-# Doxygen will parse them like normal C++ but will assume all classes use public
-# instead of private inheritance when no explicit protection keyword is present.
-
-SIP_SUPPORT            = NO
-
-# For Microsoft's IDL there are propget and propput attributes to indicate getter
-# and setter methods for a property. Setting this option to YES (the default)
-# will make doxygen replace the get and set methods by a property in the
-# documentation. This will only work if the methods are indeed getting or
-# setting a simple type. If this is not the case, or you want to show the
-# methods anyway, you should set this option to NO.
-
-IDL_PROPERTY_SUPPORT   = NO
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
-# all members of a group must be documented explicitly.
-
-DISTRIBUTE_GROUP_DOC   = NO
-
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
-
-SUBGROUPING            = YES
-
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
-# unions are shown inside the group in which they are included (e.g. using
-# @ingroup) instead of on a separate page (for HTML and Man pages) or
-# section (for LaTeX and RTF).
-
-INLINE_GROUPED_CLASSES = NO
-
-# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
-# unions with only public data fields will be shown inline in the documentation
-# of the scope in which they are defined (i.e. file, namespace, or group
-# documentation), provided this scope is documented. If set to NO (the default),
-# structs, classes, and unions are shown on a separate page (for HTML and Man
-# pages) or section (for LaTeX and RTF).
-
-INLINE_SIMPLE_STRUCTS  = NO
-
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
-# is documented as struct, union, or enum with the name of the typedef. So
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-# with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically
-# be useful for C code in case the coding convention dictates that all compound
-# types are typedef'ed and only the typedef is referenced, never the tag name.
-
-TYPEDEF_HIDES_STRUCT   = YES
-
-
-# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
-# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
-# their name and scope. Since this can be an expensive process and often the
-# same symbol appear multiple times in the code, doxygen keeps a cache of
-# pre-resolved symbols. If the cache is too small doxygen will become slower.
-# If the cache is too large, memory is wasted. The cache size is given by this
-# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
-
-LOOKUP_CACHE_SIZE      = 0
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL            = NO
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
-
-EXTRACT_PRIVATE        = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
-
-EXTRACT_STATIC         = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES  = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS  = NO
-
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespaces are hidden.
-
-EXTRACT_ANON_NSPACES   = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS     = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES     = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS  = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
-
-HIDE_IN_BODY_DOCS      = NO
-
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
-
-INTERNAL_DOCS          = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-
-CASE_SENSE_NAMES       = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
-
-HIDE_SCOPE_NAMES       = NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
-
-SHOW_INCLUDE_FILES     = YES
-
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
-# will list include files with double quotes in the documentation
-# rather than with sharp brackets.
-
-FORCE_LOCAL_INCLUDES   = NO
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
-
-INLINE_INFO            = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
-
-SORT_MEMBER_DOCS       = NO
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
-
-SORT_BRIEF_DOCS        = NO
-
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
-# will sort the (brief and detailed) documentation of class members so that
-# constructors and destructors are listed first. If set to NO (the default)
-# the constructors will appear in the respective orders defined by
-# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
-# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
-# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
-
-SORT_MEMBERS_CTORS_1ST = NO
-
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
-# hierarchy of group names into alphabetical order. If set to NO (the default)
-# the group names will appear in their defined order.
-
-SORT_GROUP_NAMES       = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
-
-SORT_BY_SCOPE_NAME     = NO
-
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
-# do proper type resolution of all parameters of a function it will reject a
-# match between the prototype and the implementation of a member function even
-# if there is only one candidate or it is obvious which candidate to choose
-# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
-# will still accept a match between prototype and implementation in such cases.
-
-STRICT_PROTO_MATCHING  = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
-
-GENERATE_TODOLIST      = YES
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
-
-GENERATE_TESTLIST      = YES
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
-
-GENERATE_BUGLIST       = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
-
-ENABLED_SECTIONS       =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or macro consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and macros in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
-
-MAX_INITIALIZER_LINES  = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
-# list will mention the files that were used to generate the documentation.
-
-SHOW_USED_FILES        = YES
-
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
-# This will remove the Files entry from the Quick Index and from the
-# Folder Tree View (if specified). The default is YES.
-
-SHOW_FILES             = YES
-
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
-# Namespaces page.
-# This will remove the Namespaces entry from the Quick Index
-# and from the Folder Tree View (if specified). The default is YES.
-
-SHOW_NAMESPACES        = YES
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from
-# the version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
-
-FILE_VERSION_FILTER    =
-
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
-# by doxygen. The layout file controls the global structure of the generated
-# output files in an output format independent way. The create the layout file
-# that represents doxygen's defaults, run doxygen with the -l option.
-# You can optionally specify a file name after the option, if omitted
-# DoxygenLayout.xml will be used as the name of the layout file.
-
-LAYOUT_FILE            =
-
-# The CITE_BIB_FILES tag can be used to specify one or more bib files
-# containing the references data. This must be a list of .bib files. The
-# .bib extension is automatically appended if omitted. Using this command
-# requires the bibtex tool to be installed. See also
-# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
-# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
-# feature you need bibtex and perl available in the search path.
-
-CITE_BIB_FILES         =
-
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
-
-QUIET                  = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
-
-WARNINGS               = YES
-
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
-
-WARN_IF_UNDOCUMENTED   = YES
-
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
-
-WARN_IF_DOC_ERROR      = YES
-
-# The WARN_NO_PARAMDOC option can be enabled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
-
-WARN_NO_PARAMDOC       = YES
-
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
-
-WARN_FORMAT            = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
-
-WARN_LOGFILE           =
-
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
-
-INPUT                  = ../src/freesasa.h ../src/example.c
-INPUT                  += doxy_main.md 
-INPUT                  += README.md license.md
-INPUT                  += ../bindings/python/freesasa.pyx
-USE_MDFILE_AS_MAINPAGE = doxy_main.md
-
-# This tag can be used to specify the character encoding of the source files
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
-# also the default input encoding. Doxygen uses libiconv (or the iconv built
-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
-# the list of possible encodings.
-
-INPUT_ENCODING         = UTF-8
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
-# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
-# *.f90 *.f *.for *.vhd *.vhdl
-
-FILE_PATTERNS          = 
-
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
-
-RECURSIVE              = NO
-
-# The EXCLUDE tag can be used to specify files and/or directories that should be
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-# Note that relative paths are relative to the directory from which doxygen is
-# run.
-
-EXCLUDE                =
-
-# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
-# directories that are symbolic links (a Unix file system feature) are excluded
-# from the input.
-
-EXCLUDE_SYMLINKS       = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS       =
-
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-# (namespaces, classes, functions, etc.) that should be excluded from the
-# output. The symbol name can be a fully qualified name, a word, or if the
-# wildcard * is used, a substring. Examples: ANamespace, AClass,
-# AClass::ANamespace, ANamespace::*Test
-
-EXCLUDE_SYMBOLS        =
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
-
-EXAMPLE_PATH           =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
-
-EXAMPLE_PATTERNS       =
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
-
-EXAMPLE_RECURSIVE      = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
-
-IMAGE_PATH             =
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output.
-# If FILTER_PATTERNS is specified, this tag will be
-# ignored.
-
-INPUT_FILTER           =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis.
-# Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match.
-# The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty or if
-# non of the patterns match the file name, INPUT_FILTER is applied.
-
-FILTER_PATTERNS        =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
-
-FILTER_SOURCE_FILES    = NO
-
-# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
-# and it is also possible to disable source filtering for a specific pattern
-# using *.ext= (so without naming a filter). This option only has effect when
-# FILTER_SOURCE_FILES is enabled.
-
-FILTER_SOURCE_PATTERNS =
-
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
-
-SOURCE_BROWSER         = YES
-
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
-
-INLINE_SOURCES         = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C and C++ comments will always remain visible.
-
-STRIP_CODE_COMMENTS    = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES
-# then for each documented function all documented
-# functions referencing it will be listed.
-
-REFERENCED_BY_RELATION = NO
-
-# If the REFERENCES_RELATION tag is set to YES
-# then for each documented function all documented entities
-# called/used by that function will be listed.
-
-REFERENCES_RELATION    = NO
-
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code.
-# Otherwise they will link to the documentation.
-
-REFERENCES_LINK_SOURCE = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
-
-USE_HTAGS              = NO
-
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
-
-VERBATIM_HEADERS       = YES
-
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
-
-ALPHABETICAL_INDEX     = YES
-
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
-
-COLS_IN_ALPHA_INDEX    = 5
-
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
-
-IGNORE_PREFIX          =
-
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
-
-GENERATE_HTML          = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
-
-HTML_OUTPUT            = .
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
-
-HTML_FILE_EXTENSION    = .html
-
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header. Note that when using a custom header you are responsible
-#  for the proper inclusion of any scripts and style sheets that doxygen
-# needs, which is dependent on the configuration options used.
-# It is advised to generate a default header using "doxygen -w html
-# header.html footer.html stylesheet.css YourConfigFile" and then modify
-# that header. Note that the header is subject to change so you typically
-# have to redo this when upgrading to a newer version of doxygen or when
-# changing the value of configuration settings such as GENERATE_TREEVIEW!
-
-HTML_HEADER            = doxygen-header.html
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
-
-HTML_FOOTER            = doxygen-footer.html
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# style sheet in the HTML output directory as well, or it will be erased!
-
-HTML_STYLESHEET        =
-
-# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
-# other source files which should be copied to the HTML output directory. Note
-# that these files will be copied to the base HTML output directory. Use the
-# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that
-# the files will be copied as-is; there are no commands or markers available.
-
-HTML_EXTRA_FILES       =
-
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
-# Doxygen will adjust the colors in the style sheet and background images
-# according to this color. Hue is specified as an angle on a colorwheel,
-# see http://en.wikipedia.org/wiki/Hue for more information.
-# For instance the value 0 represents red, 60 is yellow, 120 is green,
-# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
-# The allowed range is 0 to 359.
-
-HTML_COLORSTYLE_HUE    = 220
-
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
-# the colors in the HTML output. For a value of 0 the output will use
-# grayscales only. A value of 255 will produce the most vivid colors.
-
-HTML_COLORSTYLE_SAT    = 100
-
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
-# the luminance component of the colors in the HTML output. Values below
-# 100 gradually make the output lighter, whereas values above 100 make
-# the output darker. The value divided by 100 is the actual gamma applied,
-# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
-# and 100 does not change the gamma.
-
-HTML_COLORSTYLE_GAMMA  = 80
-
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting
-# this to NO can help when comparing the output of multiple runs.
-
-HTML_TIMESTAMP         = YES
-
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-# documentation will contain sections that can be hidden and shown after the
-# page has loaded. For this to work a browser that supports
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
-
-HTML_DYNAMIC_SECTIONS  = NO
-
-# If the GENERATE_DOCSET tag is set to YES, additional index files
-# will be generated that can be used as input for Apple's Xcode 3
-# integrated development environment, introduced with OSX 10.5 (Leopard).
-# To create a documentation set, doxygen will generate a Makefile in the
-# HTML output directory. Running make will produce the docset in that
-# directory and running "make install" will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
-# it at startup.
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
-# for more information.
-
-GENERATE_DOCSET        = NO
-
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
-# feed. A documentation feed provides an umbrella under which multiple
-# documentation sets from a single provider (such as a company or product suite)
-# can be grouped.
-
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
-# should uniquely identify the documentation set bundle. This should be a
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
-# will append .docset to the name.
-
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
-# the documentation publisher. This should be a reverse domain-name style
-# string, e.g. com.mycompany.MyDocSet.documentation.
-
-DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
-
-# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
-
-DOCSET_PUBLISHER_NAME  = Publisher
-
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
-# of the generated HTML documentation.
-
-GENERATE_HTMLHELP      = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
-# written to the html output directory.
-
-CHM_FILE               =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
-
-HHC_LOCATION           =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
-
-GENERATE_CHI           = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file
-# content.
-
-CHM_INDEX_ENCODING     =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
-
-BINARY_TOC             = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
-
-TOC_EXPAND             = NO
-
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
-# that can be used as input for Qt's qhelpgenerator to generate a
-# Qt Compressed Help (.qch) of the generated HTML documentation.
-
-GENERATE_QHP           = NO
-
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
-# be used to specify the file name of the resulting .qch file.
-# The path specified is relative to the HTML output folder.
-
-QCH_FILE               =
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#namespace
-
-QHP_NAMESPACE          = org.doxygen.Project
-
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#virtual-folders
-
-QHP_VIRTUAL_FOLDER     = doc
-
-# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
-# add. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#custom-filters
-
-QHP_CUST_FILTER_NAME   =
-
-# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
-# custom filter to add. For more information please see
-# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
-# Qt Help Project / Custom Filters</a>.
-
-QHP_CUST_FILTER_ATTRS  =
-
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-# project's
-# filter section matches.
-# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
-# Qt Help Project / Filter Attributes</a>.
-
-QHP_SECT_FILTER_ATTRS  =
-
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
-# be used to specify the location of Qt's qhelpgenerator.
-# If non-empty doxygen will try to run qhelpgenerator on the generated
-# .qhp file.
-
-QHG_LOCATION           =
-
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
-#  will be generated, which together with the HTML files, form an Eclipse help
-# plugin. To install this plugin and make it available under the help contents
-# menu in Eclipse, the contents of the directory containing the HTML and XML
-# files needs to be copied into the plugins directory of eclipse. The name of
-# the directory within the plugins directory should be the same as
-# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
-# the help appears.
-
-GENERATE_ECLIPSEHELP   = NO
-
-# A unique identifier for the eclipse help plugin. When installing the plugin
-# the directory name containing the HTML and XML files should also have
-# this name.
-
-ECLIPSE_DOC_ID         = org.doxygen.Project
-
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
-# at top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it. Since the tabs have the same information as the
-# navigation tree you can set this option to NO if you already set
-# GENERATE_TREEVIEW to YES.
-
-DISABLE_INDEX          = NO
-
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information.
-# If the tag value is set to YES, a side panel will be generated
-# containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
-# Windows users are probably better off using the HTML help feature.
-# Since the tree basically has the same information as the tab index you
-# could consider to set DISABLE_INDEX to NO when enabling this option.
-
-GENERATE_TREEVIEW      = NO
-
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
-# (range [0,1..20]) that doxygen will group on one line in the generated HTML
-# documentation. Note that a value of 0 will completely suppress the enum
-# values from appearing in the overview section.
-
-ENUM_VALUES_PER_LINE   = 4
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
-
-TREEVIEW_WIDTH         = 250
-
-# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
-# links to external symbols imported via tag files in a separate window.
-
-EXT_LINKS_IN_WINDOW    = NO
-
-# Use this tag to change the font size of Latex formulas included
-# as images in the HTML documentation. The default is 10. Note that
-# when you change the font size after a successful doxygen run you need
-# to manually remove any form_*.png images from the HTML output directory
-# to force them to be regenerated.
-
-FORMULA_FONTSIZE       = 10
-
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are
-# not supported properly for IE 6.0, but are supported on all modern browsers.
-# Note that when changing this option you need to delete any form_*.png files
-# in the HTML output before the changes have effect.
-
-FORMULA_TRANSPARENT    = YES
-
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
-# (see http://www.mathjax.org) which uses client side Javascript for the
-# rendering instead of using prerendered bitmaps. Use this if you do not
-# have LaTeX installed or if you want to formulas look prettier in the HTML
-# output. When enabled you also need to install MathJax separately and
-# configure the path to it using the MATHJAX_RELPATH option.
-
-USE_MATHJAX            = YES
-
-# When MathJax is enabled you need to specify the location relative to the
-# HTML output directory using the MATHJAX_RELPATH option. The destination
-# directory should contain the MathJax.js script. For instance, if the mathjax
-# directory is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the
-# mathjax.org site, so you can quickly see the result without installing
-# MathJax, but it is strongly recommended to install a local copy of MathJax
-# before deployment.
-
-MATHJAX_RELPATH        = https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML
-
-# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
-# names that should be enabled during MathJax rendering.
-
-MATHJAX_EXTENSIONS     =
-
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box
-# for the HTML output. The underlying search engine uses javascript
-# and DHTML and should work on any modern browser. Note that when using
-# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
-# (GENERATE_DOCSET) there is already a search function so this one should
-# typically be disabled. For large projects the javascript based search engine
-# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
-
-SEARCHENGINE           = YES
-
-# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a PHP enabled web server instead of at the web client
-# using Javascript. Doxygen will generate the search PHP script and index
-# file to put on the web server. The advantage of the server
-# based approach is that it scales better to large projects and allows
-# full text search. The disadvantages are that it is more difficult to setup
-# and does not have live searching capabilities.
-
-SERVER_BASED_SEARCH    = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
-
-GENERATE_LATEX         = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
-
-LATEX_OUTPUT           = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-# Note that when enabling USE_PDFLATEX this option is only used for
-# generating bitmaps for formulas in the HTML output, but not in the
-# Makefile that is written to the output directory.
-
-LATEX_CMD_NAME         = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
-
-MAKEINDEX_CMD_NAME     = makeindex
-
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_LATEX          = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, letter, legal and
-# executive. If left blank a4wide will be used.
-
-PAPER_TYPE             = a4
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
-
-EXTRA_PACKAGES         =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
-
-LATEX_HEADER           =
-
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
-# the generated latex document. The footer should contain everything after
-# the last chapter. If it is left blank doxygen will generate a
-# standard footer. Notice: only use this tag if you know what you are doing!
-
-LATEX_FOOTER           =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
-
-PDF_HYPERLINKS         = YES
-
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
-# higher quality PDF documentation.
-
-USE_PDFLATEX           = YES
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
-
-LATEX_BATCHMODE        = NO
-
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
-
-LATEX_HIDE_INDICES     = NO
-
-# If LATEX_SOURCE_CODE is set to YES then doxygen will include
-# source code with syntax highlighting in the LaTeX output.
-# Note that which sources are shown also depends on other settings
-# such as SOURCE_BROWSER.
-
-LATEX_SOURCE_CODE      = NO
-
-# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
-# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
-# http://en.wikipedia.org/wiki/BibTeX for more info.
-
-LATEX_BIB_STYLE        = plain
-
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
-
-GENERATE_RTF           = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
-
-RTF_OUTPUT             = rtf
-
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_RTF            = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
-
-RTF_HYPERLINKS         = NO
-
-# Load style sheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
-
-RTF_STYLESHEET_FILE    =
-
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
-
-RTF_EXTENSIONS_FILE    =
-
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
-
-GENERATE_MAN           = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
-
-MAN_OUTPUT             = man
-
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
-
-MAN_EXTENSION          = .3
-
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
-
-MAN_LINKS              = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
-
-GENERATE_XML           = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
-
-XML_OUTPUT             = xml
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
-
-XML_PROGRAMLISTING     = YES
-
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
-
-GENERATE_AUTOGEN_DEF   = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
-
-GENERATE_PERLMOD       = NO
-
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
-
-PERLMOD_LATEX          = NO
-
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader.
-# This is useful
-# if you want to understand what is going on.
-# On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
-
-PERLMOD_PRETTY         = YES
-
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
-
-PERLMOD_MAKEVAR_PREFIX =
-
-#---------------------------------------------------------------------------
-# Configuration options related to the preprocessor
-#---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
-
-ENABLE_PREPROCESSING   = YES
-
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
-
-MACRO_EXPANSION        = NO
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
-
-EXPAND_ONLY_PREDEF     = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# pointed to by INCLUDE_PATH will be searched when a #include is found.
-
-SEARCH_INCLUDES        = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
-
-INCLUDE_PATH           =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
-
-INCLUDE_FILE_PATTERNS  =
-
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
-
-PREDEFINED             =
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition that
-# overrules the definition found in the source code.
-
-EXPAND_AS_DEFINED      =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all references to function-like macros
-# that are alone on a line, have an all uppercase name, and do not end with a
-# semicolon, because these will confuse the parser if not removed.
-
-SKIP_FUNCTION_MACROS   = YES
-
-#---------------------------------------------------------------------------
-# Configuration::additions related to external references
-#---------------------------------------------------------------------------
-
-# The TAGFILES option can be used to specify one or more tagfiles.
-# Optionally an initial location of the external documentation
-# can be added for each tagfile. The format of a tag file without
-# this location is as follows:
-#
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-#
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
-# URLs. If a location is present for each tag, the installdox tool
-# does not have to be run to correct the links.
-# Note that each tag file must have a unique name
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen
-# is run, you must also specify the path to the tagfile here.
-
-TAGFILES               =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
-
-GENERATE_TAGFILE       =
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
-
-ALLEXTERNALS           = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
-
-EXTERNAL_GROUPS        = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
-
-PERL_PATH              = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option also works with HAVE_DOT disabled, but it is recommended to
-# install and use dot, since it yields more powerful graphs.
-
-CLASS_DIAGRAMS         = YES
-
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see
-# http://www.mcternan.me.uk/mscgen/) to produce the chart and insert it in the
-# documentation. The MSCGEN_PATH tag allows you to specify the directory where
-# the mscgen tool resides. If left empty the tool is assumed to be found in the
-# default search path.
-
-MSCGEN_PATH            =
-
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
-
-HIDE_UNDOC_RELATIONS   = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
-
-HAVE_DOT               = NO
-
-# The DOT_NUM_THREADS specifies the number of dot invocations doxygen is
-# allowed to run in parallel. When set to 0 (the default) doxygen will
-# base this on the number of processors available in the system. You can set it
-# explicitly to a value larger than 0 to get control over the balance
-# between CPU load and processing speed.
-
-DOT_NUM_THREADS        = 0
-
-# By default doxygen will use the Helvetica font for all dot files that
-# doxygen generates. When you want a differently looking font you can specify
-# the font name using DOT_FONTNAME. You need to make sure dot is able to find
-# the font, which can be done by putting it in a standard location or by setting
-# the DOTFONTPATH environment variable or by setting DOT_FONTPATH to the
-# directory containing the font.
-
-DOT_FONTNAME           = Helvetica
-
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
-# The default size is 10pt.
-
-DOT_FONTSIZE           = 10
-
-# By default doxygen will tell dot to use the Helvetica font.
-# If you specify a different font using DOT_FONTNAME you can use DOT_FONTPATH to
-# set the path where dot can find it.
-
-DOT_FONTPATH           =
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# CLASS_DIAGRAMS tag to NO.
-
-CLASS_GRAPH            = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
-
-COLLABORATION_GRAPH    = YES
-
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
-
-GROUP_GRAPHS           = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-
-UML_LOOK               = NO
-
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
-
-TEMPLATE_RELATIONS     = NO
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
-
-INCLUDE_GRAPH          = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
-
-INCLUDED_BY_GRAPH      = YES
-
-# If the CALL_GRAPH and HAVE_DOT options are set to YES then
-# doxygen will generate a call dependency graph for every global function
-# or class method. Note that enabling this option will significantly increase
-# the time of a run. So in most cases it will be better to enable call graphs
-# for selected functions only using the \callgraph command.
-
-CALL_GRAPH             = NO
-
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
-# doxygen will generate a caller dependency graph for every global function
-# or class method. Note that enabling this option will significantly increase
-# the time of a run. So in most cases it will be better to enable caller
-# graphs for selected functions only using the \callergraph command.
-
-CALLER_GRAPH           = NO
-
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will generate a graphical hierarchy of all classes instead of a textual one.
-
-GRAPHICAL_HIERARCHY    = YES
-
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
-
-DIRECTORY_GRAPH        = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are svg, png, jpg, or gif.
-# If left blank png will be used. If you choose svg you need to set
-# HTML_FILE_EXTENSION to xhtml in order to make the SVG files
-# visible in IE 9+ (other browsers do not have this requirement).
-
-DOT_IMAGE_FORMAT       = png
-
-# If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
-# enable generation of interactive SVG images that allow zooming and panning.
-# Note that this requires a modern browser other than Internet Explorer.
-# Tested and working are Firefox, Chrome, Safari, and Opera. For IE 9+ you
-# need to set HTML_FILE_EXTENSION to xhtml in order to make the SVG files
-# visible. Older versions of IE do not have SVG support.
-
-INTERACTIVE_SVG        = NO
-
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found in the path.
-
-DOT_PATH               =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
-
-DOTFILE_DIRS           =
-
-# The MSCFILE_DIRS tag can be used to specify one or more directories that
-# contain msc files that are included in the documentation (see the
-# \mscfile command).
-
-MSCFILE_DIRS           =
-
-# The DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
-# nodes that will be shown in the graph. If the number of nodes in a graph
-# becomes larger than this value, doxygen will truncate the graph, which is
-# visualized by representing a node as a red box. Note that doxygen if the
-# number of direct children of the root node in a graph is already larger than
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
-
-DOT_GRAPH_MAX_NODES    = 50
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes
-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that the size of a graph can be further restricted by
-# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
-
-MAX_DOT_GRAPH_DEPTH    = 0
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not
-# seem to support this out of the box. Warning: Depending on the platform used,
-# enabling this option may lead to badly anti-aliased labels on the edges of
-# a graph (i.e. they become hard to read).
-
-DOT_TRANSPARENT        = NO
-
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10)
-# support this, this feature is disabled by default.
-
-DOT_MULTI_TARGETS      = YES
-
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# arrows in the dot generated graphs.
-
-GENERATE_LEGEND        = YES
-
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
-
-DOT_CLEANUP            = YES

aggrescan3d/aggrescan/data/freesasa-2.0.1/doc/Doxyfile.in

@@ -1,1741 +0,0 @@
-# Doxyfile 1.7.6.1
-
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project.
-#
-# All text after a hash (#) is considered a comment and will be ignored.
-# The format is:
-#       TAG = value [value, ...]
-# For lists items can also be appended using:
-#       TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ").
-
-#---------------------------------------------------------------------------
-# Project related configuration options
-#---------------------------------------------------------------------------
-
-# This tag specifies the encoding used for all characters in the config file
-# that follow. The default is UTF-8 which is also the encoding used for all
-# text before the first occurrence of this tag. Doxygen uses libiconv (or the
-# iconv built into libc) for the transcoding. See
-# http://www.gnu.org/software/libiconv for the list of possible encodings.
-
-DOXYFILE_ENCODING      = UTF-8
-
-# The PROJECT_NAME tag is a single word (or sequence of words) that should
-# identify the project. Note that if you do not use Doxywizard you need
-# to put quotes around the project name if it contains spaces.
-
-PROJECT_NAME           = @PACKAGE_NAME@
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
-
-PROJECT_NUMBER         = @PACKAGE_VERSION@
-
-# Using the PROJECT_BRIEF tag one can provide an optional one line description
-# for a project that appears at the top of each page and should give viewer
-# a quick idea about the purpose of the project. Keep the description short.
-
-PROJECT_BRIEF          = "Open source SASA calculations"
-
-# With the PROJECT_LOGO tag one can specify an logo or icon that is
-# included in the documentation. The maximum height of the logo should not
-# exceed 55 pixels and the maximum width should not exceed 200 pixels.
-# Doxygen will copy the logo to the output directory.
-
-PROJECT_LOGO           =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
-OUTPUT_DIRECTORY       = html/doxygen
-
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
-
-CREATE_SUBDIRS         = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
-# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
-# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
-# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrillic, Slovak,
-# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
-
-OUTPUT_LANGUAGE        = English
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
-
-BRIEF_MEMBER_DESC      = YES
-
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
-# brief descriptions will be completely suppressed.
-
-REPEAT_BRIEF           = YES
-
-# This tag implements a quasi-intelligent brief description abbreviator
-# that is used to form the text in various listings. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
-
-ABBREVIATE_BRIEF       =
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
-# description.
-
-ALWAYS_DETAILED_SEC    = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-
-INLINE_INHERITED_MEMB  = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
-
-FULL_PATH_NAMES        = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
-
-STRIP_FROM_PATH        =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
-
-STRIP_FROM_INC_PATH    =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (but less readable) file names. This can be useful if your file system
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
-SHORT_NAMES            = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like regular Qt-style comments
-# (thus requiring an explicit @brief command for a brief description.)
-
-JAVADOC_AUTOBRIEF      = YES
-
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
-# interpret the first line (until the first dot) of a Qt-style
-# comment as the brief description. If set to NO, the comments
-# will behave just like regular Qt-style comments (thus requiring
-# an explicit \brief command for a brief description.)
-
-QT_AUTOBRIEF           = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
-# description. Set this tag to YES if you prefer the old behaviour instead.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
-
-INHERIT_DOCS           = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
-
-SEPARATE_MEMBER_PAGES  = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
-TAB_SIZE               = 4
-
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
-
-ALIASES                =
-
-# This tag can be used to specify a number of word-keyword mappings (TCL only).
-# A mapping has the form "name=value". For example adding
-# "class=itcl::class" will allow you to use the command class in the
-# itcl::class meaning.
-
-TCL_SUBST              =
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
-
-OPTIMIZE_OUTPUT_FOR_C  = YES
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for
-# Java. For instance, namespaces will be presented as packages, qualified
-# scopes will look different, etc.
-
-OPTIMIZE_OUTPUT_JAVA   = NO
-
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources only. Doxygen will then generate output that is more tailored for
-# Fortran.
-
-OPTIMIZE_FOR_FORTRAN   = NO
-
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for
-# VHDL.
-
-OPTIMIZE_OUTPUT_VHDL   = NO
-
-# Doxygen selects the parser to use depending on the extension of the files it
-# parses. With this tag you can assign which parser to use for a given extension.
-# Doxygen has a built-in mapping, but you can override or extend it using this
-# tag. The format is ext=language, where ext is a file extension, and language
-# is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
-# C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
-# doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
-# (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
-# you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
-
-EXTENSION_MAPPING      = pyx=Python
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-# to include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also makes the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-
-BUILTIN_STL_SUPPORT    = NO
-
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
-# enable parsing support.
-
-CPP_CLI_SUPPORT        = NO
-
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
-# Doxygen will parse them like normal C++ but will assume all classes use public
-# instead of private inheritance when no explicit protection keyword is present.
-
-SIP_SUPPORT            = NO
-
-# For Microsoft's IDL there are propget and propput attributes to indicate getter
-# and setter methods for a property. Setting this option to YES (the default)
-# will make doxygen replace the get and set methods by a property in the
-# documentation. This will only work if the methods are indeed getting or
-# setting a simple type. If this is not the case, or you want to show the
-# methods anyway, you should set this option to NO.
-
-IDL_PROPERTY_SUPPORT   = NO
-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
-# all members of a group must be documented explicitly.
-
-DISTRIBUTE_GROUP_DOC   = NO
-
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
-
-SUBGROUPING            = YES
-
-# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and
-# unions are shown inside the group in which they are included (e.g. using
-# @ingroup) instead of on a separate page (for HTML and Man pages) or
-# section (for LaTeX and RTF).
-
-INLINE_GROUPED_CLASSES = NO
-
-# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and
-# unions with only public data fields will be shown inline in the documentation
-# of the scope in which they are defined (i.e. file, namespace, or group
-# documentation), provided this scope is documented. If set to NO (the default),
-# structs, classes, and unions are shown on a separate page (for HTML and Man
-# pages) or section (for LaTeX and RTF).
-
-INLINE_SIMPLE_STRUCTS  = NO
-
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
-# is documented as struct, union, or enum with the name of the typedef. So
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-# with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically
-# be useful for C code in case the coding convention dictates that all compound
-# types are typedef'ed and only the typedef is referenced, never the tag name.
-
-TYPEDEF_HIDES_STRUCT   = YES
-
-
-# Similar to the SYMBOL_CACHE_SIZE the size of the symbol lookup cache can be
-# set using LOOKUP_CACHE_SIZE. This cache is used to resolve symbols given
-# their name and scope. Since this can be an expensive process and often the
-# same symbol appear multiple times in the code, doxygen keeps a cache of
-# pre-resolved symbols. If the cache is too small doxygen will become slower.
-# If the cache is too large, memory is wasted. The cache size is given by this
-# formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols.
-
-LOOKUP_CACHE_SIZE      = 0
-
-#---------------------------------------------------------------------------
-# Build related configuration options
-#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
-EXTRACT_ALL            = NO
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
-
-EXTRACT_PRIVATE        = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
-
-EXTRACT_STATIC         = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
-EXTRACT_LOCAL_CLASSES  = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
-EXTRACT_LOCAL_METHODS  = NO
-
-# If this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespaces are hidden.
-
-EXTRACT_ANON_NSPACES   = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_MEMBERS     = NO
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES     = NO
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS  = NO
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
-
-HIDE_IN_BODY_DOCS      = NO
-
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
-
-INTERNAL_DOCS          = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-
-CASE_SENSE_NAMES       = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
-
-HIDE_SCOPE_NAMES       = NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
-
-SHOW_INCLUDE_FILES     = YES
-
-# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
-# will list include files with double quotes in the documentation
-# rather than with sharp brackets.
-
-FORCE_LOCAL_INCLUDES   = NO
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
-
-INLINE_INFO            = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
-
-SORT_MEMBER_DOCS       = NO
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
-
-SORT_BRIEF_DOCS        = NO
-
-# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
-# will sort the (brief and detailed) documentation of class members so that
-# constructors and destructors are listed first. If set to NO (the default)
-# the constructors will appear in the respective orders defined by
-# SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
-# This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
-# and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
-
-SORT_MEMBERS_CTORS_1ST = NO
-
-# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
-# hierarchy of group names into alphabetical order. If set to NO (the default)
-# the group names will appear in their defined order.
-
-SORT_GROUP_NAMES       = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
-
-SORT_BY_SCOPE_NAME     = NO
-
-# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to
-# do proper type resolution of all parameters of a function it will reject a
-# match between the prototype and the implementation of a member function even
-# if there is only one candidate or it is obvious which candidate to choose
-# by doing a simple string match. By disabling STRICT_PROTO_MATCHING doxygen
-# will still accept a match between prototype and implementation in such cases.
-
-STRICT_PROTO_MATCHING  = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
-
-GENERATE_TODOLIST      = YES
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
-
-GENERATE_TESTLIST      = YES
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
-
-GENERATE_BUGLIST       = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
-
-GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
-
-ENABLED_SECTIONS       =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or macro consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and macros in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
-
-MAX_INITIALIZER_LINES  = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
-# list will mention the files that were used to generate the documentation.
-
-SHOW_USED_FILES        = YES
-
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
-# This will remove the Files entry from the Quick Index and from the
-# Folder Tree View (if specified). The default is YES.
-
-SHOW_FILES             = YES
-
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
-# Namespaces page.
-# This will remove the Namespaces entry from the Quick Index
-# and from the Folder Tree View (if specified). The default is YES.
-
-SHOW_NAMESPACES        = YES
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from
-# the version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
-
-FILE_VERSION_FILTER    =
-
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
-# by doxygen. The layout file controls the global structure of the generated
-# output files in an output format independent way. The create the layout file
-# that represents doxygen's defaults, run doxygen with the -l option.
-# You can optionally specify a file name after the option, if omitted
-# DoxygenLayout.xml will be used as the name of the layout file.
-
-LAYOUT_FILE            =
-
-# The CITE_BIB_FILES tag can be used to specify one or more bib files
-# containing the references data. This must be a list of .bib files. The
-# .bib extension is automatically appended if omitted. Using this command
-# requires the bibtex tool to be installed. See also
-# http://en.wikipedia.org/wiki/BibTeX for more info. For LaTeX the style
-# of the bibliography can be controlled using LATEX_BIB_STYLE. To use this
-# feature you need bibtex and perl available in the search path.
-
-CITE_BIB_FILES         =
-
-#---------------------------------------------------------------------------
-# configuration options related to warning and progress messages
-#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
-
-QUIET                  = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
-
-WARNINGS               = YES
-
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
-
-WARN_IF_UNDOCUMENTED   = YES
-
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
-
-WARN_IF_DOC_ERROR      = YES
-
-# The WARN_NO_PARAMDOC option can be enabled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
-
-WARN_NO_PARAMDOC       = YES
-
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
-
-WARN_FORMAT            = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
-
-WARN_LOGFILE           =
-
-#---------------------------------------------------------------------------
-# configuration options related to the input files
-#---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
-
-INPUT                  = @top_srcdir@/src/freesasa.h @top_srcdir@/src/example.c
-INPUT                  += doxy_main.md 
-INPUT                  += README.md license.md
-INPUT                  += @top_srcdir@/bindings/python/freesasa.pyx
-USE_MDFILE_AS_MAINPAGE = doxy_main.md
-
-# This tag can be used to specify the character encoding of the source files
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
-# also the default input encoding. Doxygen uses libiconv (or the iconv built
-# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
-# the list of possible encodings.
-
-INPUT_ENCODING         = UTF-8
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.d *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh
-# *.hxx *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.dox *.py
-# *.f90 *.f *.for *.vhd *.vhdl
-
-FILE_PATTERNS          = 
-
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
-
-RECURSIVE              = NO
-
-# The EXCLUDE tag can be used to specify files and/or directories that should be
-# excluded from the INPUT source files. This way you can easily exclude a
-# subdirectory from a directory tree whose root is specified with the INPUT tag.
-# Note that relative paths are relative to the directory from which doxygen is
-# run.
-
-EXCLUDE                =
-
-# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
-# directories that are symbolic links (a Unix file system feature) are excluded
-# from the input.
-
-EXCLUDE_SYMLINKS       = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS       =
-
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-# (namespaces, classes, functions, etc.) that should be excluded from the
-# output. The symbol name can be a fully qualified name, a word, or if the
-# wildcard * is used, a substring. Examples: ANamespace, AClass,
-# AClass::ANamespace, ANamespace::*Test
-
-EXCLUDE_SYMBOLS        =
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
-
-EXAMPLE_PATH           =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
-
-EXAMPLE_PATTERNS       =
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
-
-EXAMPLE_RECURSIVE      = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
-
-IMAGE_PATH             =
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output.
-# If FILTER_PATTERNS is specified, this tag will be
-# ignored.
-
-INPUT_FILTER           =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis.
-# Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match.
-# The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty or if
-# non of the patterns match the file name, INPUT_FILTER is applied.
-
-FILTER_PATTERNS        =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
-
-FILTER_SOURCE_FILES    = NO
-
-# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file
-# pattern. A pattern will override the setting for FILTER_PATTERN (if any)
-# and it is also possible to disable source filtering for a specific pattern
-# using *.ext= (so without naming a filter). This option only has effect when
-# FILTER_SOURCE_FILES is enabled.
-
-FILTER_SOURCE_PATTERNS =
-
-#---------------------------------------------------------------------------
-# configuration options related to source browsing
-#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
-
-SOURCE_BROWSER         = YES
-
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
-
-INLINE_SOURCES         = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C and C++ comments will always remain visible.
-
-STRIP_CODE_COMMENTS    = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES
-# then for each documented function all documented
-# functions referencing it will be listed.
-
-REFERENCED_BY_RELATION = NO
-
-# If the REFERENCES_RELATION tag is set to YES
-# then for each documented function all documented entities
-# called/used by that function will be listed.
-
-REFERENCES_RELATION    = NO
-
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code.
-# Otherwise they will link to the documentation.
-
-REFERENCES_LINK_SOURCE = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
-
-USE_HTAGS              = NO
-
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
-
-VERBATIM_HEADERS       = YES
-
-#---------------------------------------------------------------------------
-# configuration options related to the alphabetical class index
-#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
-
-ALPHABETICAL_INDEX     = YES
-
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
-
-COLS_IN_ALPHA_INDEX    = 5
-
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
-
-IGNORE_PREFIX          =
-
-#---------------------------------------------------------------------------
-# configuration options related to the HTML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
-
-GENERATE_HTML          = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
-
-HTML_OUTPUT            = .
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
-
-HTML_FILE_EXTENSION    = .html
-
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header. Note that when using a custom header you are responsible
-#  for the proper inclusion of any scripts and style sheets that doxygen
-# needs, which is dependent on the configuration options used.
-# It is advised to generate a default header using "doxygen -w html
-# header.html footer.html stylesheet.css YourConfigFile" and then modify
-# that header. Note that the header is subject to change so you typically
-# have to redo this when upgrading to a newer version of doxygen or when
-# changing the value of configuration settings such as GENERATE_TREEVIEW!
-
-HTML_HEADER            = doxygen-header.html
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
-
-HTML_FOOTER            = doxygen-footer.html
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# style sheet in the HTML output directory as well, or it will be erased!
-
-HTML_STYLESHEET        =
-
-# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or
-# other source files which should be copied to the HTML output directory. Note
-# that these files will be copied to the base HTML output directory. Use the
-# $relpath$ marker in the HTML_HEADER and/or HTML_FOOTER files to load these
-# files. In the HTML_STYLESHEET file, use the file name only. Also note that
-# the files will be copied as-is; there are no commands or markers available.
-
-HTML_EXTRA_FILES       =
-
-# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
-# Doxygen will adjust the colors in the style sheet and background images
-# according to this color. Hue is specified as an angle on a colorwheel,
-# see http://en.wikipedia.org/wiki/Hue for more information.
-# For instance the value 0 represents red, 60 is yellow, 120 is green,
-# 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
-# The allowed range is 0 to 359.
-
-HTML_COLORSTYLE_HUE    = 220
-
-# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
-# the colors in the HTML output. For a value of 0 the output will use
-# grayscales only. A value of 255 will produce the most vivid colors.
-
-HTML_COLORSTYLE_SAT    = 100
-
-# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
-# the luminance component of the colors in the HTML output. Values below
-# 100 gradually make the output lighter, whereas values above 100 make
-# the output darker. The value divided by 100 is the actual gamma applied,
-# so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
-# and 100 does not change the gamma.
-
-HTML_COLORSTYLE_GAMMA  = 80
-
-# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
-# page will contain the date and time when the page was generated. Setting
-# this to NO can help when comparing the output of multiple runs.
-
-HTML_TIMESTAMP         = YES
-
-# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-# documentation will contain sections that can be hidden and shown after the
-# page has loaded. For this to work a browser that supports
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
-
-HTML_DYNAMIC_SECTIONS  = NO
-
-# If the GENERATE_DOCSET tag is set to YES, additional index files
-# will be generated that can be used as input for Apple's Xcode 3
-# integrated development environment, introduced with OSX 10.5 (Leopard).
-# To create a documentation set, doxygen will generate a Makefile in the
-# HTML output directory. Running make will produce the docset in that
-# directory and running "make install" will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
-# it at startup.
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
-# for more information.
-
-GENERATE_DOCSET        = NO
-
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
-# feed. A documentation feed provides an umbrella under which multiple
-# documentation sets from a single provider (such as a company or product suite)
-# can be grouped.
-
-DOCSET_FEEDNAME        = "Doxygen generated docs"
-
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
-# should uniquely identify the documentation set bundle. This should be a
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
-# will append .docset to the name.
-
-DOCSET_BUNDLE_ID       = org.doxygen.Project
-
-# When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
-# the documentation publisher. This should be a reverse domain-name style
-# string, e.g. com.mycompany.MyDocSet.documentation.
-
-DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
-
-# The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
-
-DOCSET_PUBLISHER_NAME  = Publisher
-
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
-# of the generated HTML documentation.
-
-GENERATE_HTMLHELP      = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
-# written to the html output directory.
-
-CHM_FILE               =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
-
-HHC_LOCATION           =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
-
-GENERATE_CHI           = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file
-# content.
-
-CHM_INDEX_ENCODING     =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
-
-BINARY_TOC             = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
-
-TOC_EXPAND             = NO
-
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
-# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
-# that can be used as input for Qt's qhelpgenerator to generate a
-# Qt Compressed Help (.qch) of the generated HTML documentation.
-
-GENERATE_QHP           = NO
-
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
-# be used to specify the file name of the resulting .qch file.
-# The path specified is relative to the HTML output folder.
-
-QCH_FILE               =
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#namespace
-
-QHP_NAMESPACE          = org.doxygen.Project
-
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#virtual-folders
-
-QHP_VIRTUAL_FOLDER     = doc
-
-# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
-# add. For more information please see
-# http://doc.trolltech.com/qthelpproject.html#custom-filters
-
-QHP_CUST_FILTER_NAME   =
-
-# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
-# custom filter to add. For more information please see
-# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
-# Qt Help Project / Custom Filters</a>.
-
-QHP_CUST_FILTER_ATTRS  =
-
-# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
-# project's
-# filter section matches.
-# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
-# Qt Help Project / Filter Attributes</a>.
-
-QHP_SECT_FILTER_ATTRS  =
-
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
-# be used to specify the location of Qt's qhelpgenerator.
-# If non-empty doxygen will try to run qhelpgenerator on the generated
-# .qhp file.
-
-QHG_LOCATION           =
-
-# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
-#  will be generated, which together with the HTML files, form an Eclipse help
-# plugin. To install this plugin and make it available under the help contents
-# menu in Eclipse, the contents of the directory containing the HTML and XML
-# files needs to be copied into the plugins directory of eclipse. The name of
-# the directory within the plugins directory should be the same as
-# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
-# the help appears.
-
-GENERATE_ECLIPSEHELP   = NO
-
-# A unique identifier for the eclipse help plugin. When installing the plugin
-# the directory name containing the HTML and XML files should also have
-# this name.
-
-ECLIPSE_DOC_ID         = org.doxygen.Project
-
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs)
-# at top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it. Since the tabs have the same information as the
-# navigation tree you can set this option to NO if you already set
-# GENERATE_TREEVIEW to YES.
-
-DISABLE_INDEX          = NO
-
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information.
-# If the tag value is set to YES, a side panel will be generated
-# containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
-# Windows users are probably better off using the HTML help feature.
-# Since the tree basically has the same information as the tab index you
-# could consider to set DISABLE_INDEX to NO when enabling this option.
-
-GENERATE_TREEVIEW      = NO
-
-# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values
-# (range [0,1..20]) that doxygen will group on one line in the generated HTML
-# documentation. Note that a value of 0 will completely suppress the enum
-# values from appearing in the overview section.
-
-ENUM_VALUES_PER_LINE   = 4
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
-
-TREEVIEW_WIDTH         = 250
-
-# When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
-# links to external symbols imported via tag files in a separate window.
-
-EXT_LINKS_IN_WINDOW    = NO
-
-# Use this tag to change the font size of Latex formulas included
-# as images in the HTML documentation. The default is 10. Note that
-# when you change the font size after a successful doxygen run you need
-# to manually remove any form_*.png images from the HTML output directory
-# to force them to be regenerated.
-
-FORMULA_FONTSIZE       = 10
-
-# Use the FORMULA_TRANPARENT tag to determine whether or not the images
-# generated for formulas are transparent PNGs. Transparent PNGs are
-# not supported properly for IE 6.0, but are supported on all modern browsers.
-# Note that when changing this option you need to delete any form_*.png files
-# in the HTML output before the changes have effect.
-
-FORMULA_TRANSPARENT    = YES
-
-# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax
-# (see http://www.mathjax.org) which uses client side Javascript for the
-# rendering instead of using prerendered bitmaps. Use this if you do not
-# have LaTeX installed or if you want to formulas look prettier in the HTML
-# output. When enabled you also need to install MathJax separately and
-# configure the path to it using the MATHJAX_RELPATH option.
-
-USE_MATHJAX            = YES
-
-# When MathJax is enabled you need to specify the location relative to the
-# HTML output directory using the MATHJAX_RELPATH option. The destination
-# directory should contain the MathJax.js script. For instance, if the mathjax
-# directory is located at the same level as the HTML output directory, then
-# MATHJAX_RELPATH should be ../mathjax. The default value points to the
-# mathjax.org site, so you can quickly see the result without installing
-# MathJax, but it is strongly recommended to install a local copy of MathJax
-# before deployment.
-
-MATHJAX_RELPATH        = https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML
-
-# The MATHJAX_EXTENSIONS tag can be used to specify one or MathJax extension
-# names that should be enabled during MathJax rendering.
-
-MATHJAX_EXTENSIONS     =
-
-# When the SEARCHENGINE tag is enabled doxygen will generate a search box
-# for the HTML output. The underlying search engine uses javascript
-# and DHTML and should work on any modern browser. Note that when using
-# HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
-# (GENERATE_DOCSET) there is already a search function so this one should
-# typically be disabled. For large projects the javascript based search engine
-# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
-
-SEARCHENGINE           = YES
-
-# When the SERVER_BASED_SEARCH tag is enabled the search engine will be
-# implemented using a PHP enabled web server instead of at the web client
-# using Javascript. Doxygen will generate the search PHP script and index
-# file to put on the web server. The advantage of the server
-# based approach is that it scales better to large projects and allows
-# full text search. The disadvantages are that it is more difficult to setup
-# and does not have live searching capabilities.
-
-SERVER_BASED_SEARCH    = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the LaTeX output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
-
-GENERATE_LATEX         = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
-
-LATEX_OUTPUT           = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-# Note that when enabling USE_PDFLATEX this option is only used for
-# generating bitmaps for formulas in the HTML output, but not in the
-# Makefile that is written to the output directory.
-
-LATEX_CMD_NAME         = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
-
-MAKEINDEX_CMD_NAME     = makeindex
-
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_LATEX          = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, letter, legal and
-# executive. If left blank a4wide will be used.
-
-PAPER_TYPE             = a4
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
-
-EXTRA_PACKAGES         =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
-
-LATEX_HEADER           =
-
-# The LATEX_FOOTER tag can be used to specify a personal LaTeX footer for
-# the generated latex document. The footer should contain everything after
-# the last chapter. If it is left blank doxygen will generate a
-# standard footer. Notice: only use this tag if you know what you are doing!
-
-LATEX_FOOTER           =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
-
-PDF_HYPERLINKS         = YES
-
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
-# higher quality PDF documentation.
-
-USE_PDFLATEX           = YES
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
-
-LATEX_BATCHMODE        = NO
-
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
-
-LATEX_HIDE_INDICES     = NO
-
-# If LATEX_SOURCE_CODE is set to YES then doxygen will include
-# source code with syntax highlighting in the LaTeX output.
-# Note that which sources are shown also depends on other settings
-# such as SOURCE_BROWSER.
-
-LATEX_SOURCE_CODE      = NO
-
-# The LATEX_BIB_STYLE tag can be used to specify the style to use for the
-# bibliography, e.g. plainnat, or ieeetr. The default style is "plain". See
-# http://en.wikipedia.org/wiki/BibTeX for more info.
-
-LATEX_BIB_STYLE        = plain
-
-#---------------------------------------------------------------------------
-# configuration options related to the RTF output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
-
-GENERATE_RTF           = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
-
-RTF_OUTPUT             = rtf
-
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
-
-COMPACT_RTF            = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
-
-RTF_HYPERLINKS         = NO
-
-# Load style sheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
-
-RTF_STYLESHEET_FILE    =
-
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
-
-RTF_EXTENSIONS_FILE    =
-
-#---------------------------------------------------------------------------
-# configuration options related to the man page output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
-
-GENERATE_MAN           = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
-
-MAN_OUTPUT             = man
-
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
-
-MAN_EXTENSION          = .3
-
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
-
-MAN_LINKS              = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the XML output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
-
-GENERATE_XML           = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
-
-XML_OUTPUT             = xml
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
-
-XML_PROGRAMLISTING     = YES
-
-#---------------------------------------------------------------------------
-# configuration options for the AutoGen Definitions output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
-
-GENERATE_AUTOGEN_DEF   = NO
-
-#---------------------------------------------------------------------------
-# configuration options related to the Perl module output
-#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
-
-GENERATE_PERLMOD       = NO
-
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
-
-PERLMOD_LATEX          = NO
-
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
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-	maintainer-clean maintainer-clean-generic mostlyclean \
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-	uninstall-am
-
-.PRECIOUS: Makefile
-
-
-@[email protected]: $(top_srcdir)/src/freesasa.h $(top_srcdir)/src/example.c \
-@HAVE_DOXYGEN_TRUE@	doxy_main.md $(top_srcdir)/README.md Doxyfile \
-@HAVE_DOXYGEN_TRUE@	doxygen-footer.html doxygen-header.html $(top_srcdir)/bindings/python/freesasa.pyx
-@HAVE_DOXYGEN_TRUE@	@if [ ! -d "html/" ]; then mkdir html; fi
-@HAVE_DOXYGEN_TRUE@	@if [ ! -d "html/fig/" ]; then mkdir html/fig; fi
-@HAVE_DOXYGEN_TRUE@	cp fig/* html/fig/
-@HAVE_DOXYGEN_TRUE@	$(DOXYGEN) Doxyfile
-@HAVE_DOXYGEN_TRUE@	echo Timestamp > doxyfile.stamp
-
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-
-@HAVE_DOXYGEN_FALSE@doxygen:
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-
-clean-local:
-	rm -f *.log *~ 
-	rm -rf html/doxygen
-	rm -rf html/fig
-
-# Tell versions [3.59,3.63) of GNU make to not export all variables.
-# Otherwise a system limit (for SysV at least) may be exceeded.
-.NOEXPORT:

aggrescan3d/aggrescan/data/freesasa-2.0.1/doc/README.md

@@ -1,136 +0,0 @@
-FreeSASA
-========
-
-[![DOI](https://zenodo.org/badge/18467/mittinatten/freesasa.svg)](https://zenodo.org/badge/latestdoi/18467/mittinatten/freesasa)
-[![Build Status](https://travis-ci.org/mittinatten/freesasa.svg?branch=master)](https://travis-ci.org/mittinatten/freesasa)
-[![Coverage Status](https://coveralls.io/repos/github/mittinatten/freesasa/badge.svg?branch=master)](https://coveralls.io/github/mittinatten/freesasa?branch=master)
-
-C-library for calculating Solvent Accessible Surface Areas.
-
-License: MIT (see file LICENSE). Copyright: Simon Mitternacht 2013-2016.
-
-FreeSASA is a C library and command line tool for calculating Solvent
-Accessible Surface Area (SASA) of biomolecules. It is designed to be
-simple to use with defaults, but allows customization of all
-parameters of the calculation and provides a few different tools to
-analyze the results. Python bindings are also included in the
-repository.
-
-By default Lee & Richards' algorithm is used, but Shrake & Rupley's is
-also available. Both can be parameterized to arbitrary precision, and
-for high resolution versions of the algorithms, the calculations give
-identical results.
-
-FreeSASA assigns a radius and a class to each atom. The atomic radii
-are by default the _ProtOr_ radii defined by Tsai et
-al. ([JMB 1999, 290: 253](http://www.ncbi.nlm.nih.gov/pubmed/10388571))
-for standard amino acids and nucleic acids, and the van der Waals
-radius of the element for other atoms. Each atom is also classified as
-either polar or apolar.
-
-Users can provide their own atomic radii and classifications via
-configuration files. The input format for configuration files is
-described in the
-[online documentation](http://freesasa.github.io/doxygen/Config-file.html),
-and the `share/` directory contains some sample configurations,
-including one for the NACCESS parameters
-([Hubbard & Thornton 1993](http://www.bioinf.manchester.ac.uk/naccess/)).
-
-Version 2.0 adds some new features and breaks a few parts of the
-interface from 1.x (mainly the API), see CHANGELOG.md for detailed
-information.
-
-Building and installing
-------------------------
-
-FreeSASA can be compiled and installed using the following
-
-    ./configure
-    make && make install
-
-NB: If the source is downloaded from the git repository the
-configure-script needs to be set up first using `autoreconf -i`. Users
-who don't have autotools installed, can download a tarball that
-includes the autogenerated scripts from http://freesasa.github.io/ or
-from the latest
-[GitHub-release](https://github.com/mittinatten/freesasa/releases).
-
-The above commands build and install the command line tool `freesasa`
-(built in `src/`), the command
-
-    freesasa -h
-
-gives an overview of options. To run a calculation from PDB-file input
-using the defaults, simply type
-
-    freesasa <pdb-file>
-
-In addition, `make install` installs the header `freesasa.h` and the
-library `libfreesasa`. If the configure script is called with the
-option `--enable-python-bindings`, the Python module is also built and
-installed.
-
-The configuration can be changed with these options:
-* `--enable-python-bindings` builds Python bindings, requires Cython
-    0.21 or higher. On some platforms the C library needs to be
-    compiled with `CFLAGS=-fPIC` to allow it to be linked to the
-    Python module.
-* `--with-python=<python>` specifies which python binary to use
-* `--disable-json` build without support for JSON output.
-* `--disable-xml` build without support for XML output.
-* `--disable-threads` build without multithreaded calculations
-* `--enable-doxygen` activates building of Doxygen documentation
-
-For developers:
-* `--enable-check` enables unit-testing using the Check framework
-* `--enable-gcov` adds compiler flags for measuring coverage of tests
-    using gcov
-* `--enable-parser-generator` rebuild parser/lexer source from
-    Flex/Bison sources (the autogenerated code is included in the
-    repository, so no need to do this if you are not going to change
-    the parser).
-
-Documentation
--------------
-
-Enabling Doxygen builds a [full reference
-manual](http://freesasa.github.io/doxygen/), documenting both CLI and
-API in the folder `doc/html/doxygen/`, also available on the web at
-http://freesasa.github.io/.
-
-After building the package, calling
- 
-    freesasa -h
-    
-explains how the commandline tool can be used.
-
-Compatibility and dependencies
-------------------------------
-
-The program has been tested successfully with several versions of GNU
-C Compiler and Clang/LLVM. The library can be built using only
-standard C and GNU libraries. The standard build depends on
-[json-c](https://github.com/json-c/json-c) and
-[libxml2](http://xmlsoft.org/). These can be disabled by configuring
-with `--disable-json` and `--disable-xml` respectively.
-
-Developers who want to do testing need to install the Check unit
-testing framework. Building the full reference manual requires Doxygen
-(version > 1.8.8). Building the Python bindings requires
-Cython. Changing the selection parser and lexer requires Flex and
-Bison. These build options, which add extra dependencies, are disabled
-by default to simplify installation for users only interested in the
-command line tool and and/or C Library.
-
-Citing FreeSASA
----------------
-
-FreeSASA can be cited using the following publication
-
-* Simon Mitternacht (2016) FreeSASA: An open source C library for
-  solvent accessible surface area calculations. _F1000Research_
-  5:189. (doi:
-  [10.12688/f1000research.7931.1](http://dx.doi.org/10.12688/f1000research.7931.1))
-
-The [DOI numbers from Zenodo](https://zenodo.org/badge/latestdoi/18467/mittinatten/freesasa)
-can be used to cite a specific version of FreeSASA.

aggrescan3d/aggrescan/data/freesasa-2.0.1/doc/doxy_main.md

@@ -1,1051 +0,0 @@
-FreeSASA
-========
-
-These pages document the 
-    
-  - @ref CLI
-  - @ref API "FreeSASA C API"
-  - @ref Python "FreeSASA Python interface"
-  - @ref Config-file
-  - @ref Selection
-  - @ref Geometry
-
-The library is released under the [MIT license](license.md).
-
-Installation instructions can be found in the [README](README.md) file.
-
-@page CLI Command-line Interface
-
-Building FreeSASA creates the binary `freesasa`, which is installed by
-`make install`. Calling
-
-    $ freesasa -h
-
-displays a help message listing all options. The following text
-explains how to use most of them.
-
-@section CLI-Default Run using defaults
-
-In the following we will use the RNA/protein complex PDB structure
-3WBM as an example. It has four protein chains A, B, C and D, and two
-RNA strands X and Y. To run a simple SASA calculation using default
-parameters, simply type:
-
-    $ freesasa 3wbm.pdb
-
-This generates the following output
-
-    ## FreeSASA 2.0 ##
-
-    PARAMETERS
-    algorithm    : Lee & Richards
-    probe-radius : 1.400
-    threads      : 2
-    slices       : 20
-
-    INPUT
-    source  : 3wbm.pdb
-    chains  : ABCDXY
-    atoms   : 3714
-
-    RESULTS (A^2)
-    Total   :   25190.77
-    Apolar  :   11552.38
-    Polar   :   13638.39
-    CHAIN A :    3785.49
-    CHAIN B :    4342.33
-    CHAIN C :    3961.12
-    CHAIN D :    4904.30
-    CHAIN X :    4156.46
-    CHAIN Y :    4041.08
-    
-The results are all in the unit Ångström-squared. 
-
-@section parameters Changing parameters
-
-If higher precision is needed, the command
-
-    $ freesasa -n 100 3wbm.pdb
-
-specifies that the calculation should use 100 slices per atom instead of
-the default 20. The command
-
-    $ freesasa --shrake-rupley -n 200 --probe-radius 1.2 --n-threads 4 3wbm.pdb
-
-instead calculates the SASA using Shrake & Rupley's algorithm with 200
-test points, a probe radius of 1.2 Å, using 4 parallel threads to
-speed things up.
-
-If the user wants to use their own atomic radii the command 
-
-    $ freesasa --config-file <file> 3wbm.pdb
-
-Reads a configuration from a file and uses it to assign atomic
-radii. The program will halt if it encounters atoms in the PDB input
-that are not present in the configuration. See @ref Config-file for
-instructions how to write a configuration.
-
-To use the atomic radii from NACCESS call 
-
-    $ freesasa --radii=naccess 3wbm.pdb
-
-Another way to specify a custom set of atomic radii is to store them as
-occupancies in the input PDB file
-
-    $ freesasa --radius-from-occupancy 3wbm.pdb
-
-This option allows the user to first use the option `--format=pdb` (see @ref CLI-PDB) to
-write generate a PDB file with the radii used in the calculation,
-modify the radii of individual atoms in that file, and then recalculate
-the SASA with these modified radii.
-
-
-@section Output Output formats
-
-In addition to the standard output format above FreeSASA can export
-the results as @ref CLI-JSON, @ref CLI-XML, @ref CLI-PDB, @ref
-CLI-RSA, @ref CLI-RES and @ref CLI-SEQ using the option
-`--format`. The level of detail of JSON and XML output can be
-controlled with the option `--output-depth=<depth>` which takes the
-values `atom`, `residue`, `chain` and `structure`. If `atom` is
-chosen, SASA values are shown for all levels of the structure,
-including individual atoms.  With `chain`, only structure and chain
-SASA values are printed (this is the default).
-
-The output can include relative SASA values for each residues. To
-calculate these a reference SASA value is needed, calculated using the
-same atomic radii. At the moment such values are only available for
-the ProtOr and NACCESS radii (selected using the option `--radii`), if
-other radii are used relative SASA will be excluded (in RSA output all
-REL columns will have the value 'N/A').
-
-The reference SASA values for residue X are calculated from Ala-X-Ala
-peptides in a stretched out configuration. The reference
-configurations are supplied for reference in the directory
-`rsa`. Since these are not always the most exposed possible
-configuration, and because bond lengths and bond angles vary, the
-relative SASA values will sometimes be larger than 100 %. At the
-moment there is no interface to supply user-defined reference values.
-
-
-@subsection CLI-JSON JSON
-
-The command
-
-    $ freesasa --format=xml --output-depth=residue 3wbm.pdb
-
-generates the following
-
-~~~~{.json}
-{
-  "source":"FreeSASA 2.0",
-  "length-unit":"Ångström",
-  "results":[
-    {
-      "input":"3wbm.pdb",
-      "classifier":"ProtOr",
-      "parameters":{
-        "algorithm":"Lee & Richards",
-        "probe-radius":1.3999999999999999,
-        "resolution":20
-      },
-      "structures":[
-        {
-          "chain-labels":"ABCDXY",
-          "area":{
-            "total":25190.768387067546,
-            "polar":13638.391677017404,
-            "apolar":11552.376710050148,
-            "main-chain":3337.1622502425053,
-            "side-chain":21853.606136825045
-          },
-          "chains":[
-            {
-              "label":"A",
-              "n-residues":86,
-              "area":{
-                "total":3785.4864049452635,
-                "polar":1733.8560208488598,
-                "apolar":2051.6303840964056,
-                "main-chain":723.34358684348558,
-                "side-chain":3062.1428181017791
-              }
-              "residues":[
-                {
-                  "name":"THR",
-                  "number":"5",
-                  "area":{
-                    "total":138.48216994006549,
-                    "polar":56.887951514571867,
-                    "apolar":81.594218425493622,
-                    "main-chain":38.898190013033592,
-                    "side-chain":99.583979927031905
-                  },
-                  "relative-area":{
-                    "total":104.05152148175331,
-                    "polar":113.98106895325961,
-                    "apolar":98.093554250413092,
-                    "main-chain":96.330336832673567,
-                    "side-chain":107.414496739329
-                  },
-                  "n-atoms":7
-               },
-
-            ...
-
-            },
-
-            ...
-
-          ]
-        }
-      ]
-    }
-  ]
-}
-~~~~
-
-Where ellipsis indicates the remaining residues and chains.
-
-@subsection CLI-XML XML
-
-The command
-
-    $ freesasa --format=xml 3wbm.pdb
-
-Generates the following
-
-~~~~{.xml}
-<?xml version="1.0" encoding="UTF-8"?>
-<results xmlns="http://freesasa.github.io/" source="FreeSASA 2.0" lengthUnit="&#xC5;ngstr&#xF6;m">
-  <result classifier="ProtOr" input="3wbm.pdb">
-    <parameters algorithm="Lee &amp; Richards" probeRadius="1.400000" resolution="20"/>
-    <structure chains="ABCDXY">
-      <area total="25190.768" polar="13638.392" apolar="11552.377" mainChain="3337.162" sideChain="21853.606"/>
-      <chain label="A" nResidues="86">
-        <area total="3785.486" polar="1733.856" apolar="2051.630" mainChain="723.344" sideChain="3062.143"/>
-      </chain>
-      <chain label="B" nResidues="84">
-        <area total="4342.334" polar="1957.114" apolar="2385.220" mainChain="853.707" sideChain="3488.627"/>
-      </chain>
-      <chain label="C" nResidues="86">
-        <area total="3961.119" polar="1838.724" apolar="2122.395" mainChain="782.652" sideChain="3178.468"/>
-      </chain>
-      <chain label="D" nResidues="89">
-        <area total="4904.298" polar="2332.306" apolar="2571.991" mainChain="977.459" sideChain="3926.838"/>
-      </chain>
-      <chain label="X" nResidues="25">
-        <area total="4156.455" polar="2919.576" apolar="1236.879" mainChain="0.000" sideChain="4156.455"/>
-      </chain>
-      <chain label="Y" nResidues="25">
-        <area total="4041.076" polar="2856.815" apolar="1184.261" mainChain="0.000" sideChain="4041.076"/>
-      </chain>
-    </structure>
-  </result>
-</results>
-
-~~~~
-
-@subsection CLI-PDB PDB
-
-The command-line interface can also be used as a PDB filter:
-
-    $ cat 3wbm.pdb | freesasa --format=pdb
-    REMARK 999 This PDB file was generated by FreeSASA 2.0.
-    REMARK 999 In the ATOM records temperature factors have been
-    REMARK 999 replaced by the SASA of the atom, and the occupancy
-    REMARK 999 by the radius used in the calculation.
-    MODEL        1
-    ATOM      1  N   THR A   5     -19.727  29.259  13.573  1.64  9.44
-    ATOM      2  CA  THR A   5     -19.209  28.356  14.602  1.88  5.01
-    ATOM      3  C   THR A   5     -18.747  26.968  14.116  1.61  0.40
-    ...
-
-The output is a PDB-file where the temperature factors have been
-replaced by SASA values (last column), and occupancy numbers by the
-radius of each atom (second to last column).
-
-Only the atoms and models used in the calculation will be present in
-the output (see @ref Input for how to modify this).
-
-@subsection CLI-RES SASA of each residue type
-
-Calculate the SASA of each residue type:
-
-    $ freesasa --format=res 3wbm.pdb
-    # Residue types in 3wbm.pdb
-    RES ALA :     251.57
-    RES ARG :    2868.98
-    RES ASN :    1218.87
-    ...
-    RES A :    1581.57
-    RES C :    2967.12
-    RES G :    1955.16
-    RES U :    1693.68
-
-@subsection CLI-SEQ SASA of each residue
-
-Calculate the SASA of each residue in the sequence:
-
-    $ freesasa --format=seq 3wbm.pdb
-    # Residues in 3wbm.pdb
-    SEQ A    5 THR :  138.48
-    SEQ A    6 PRO :   25.53
-    SEQ A    7 THR :   99.42
-    ...
-
-@subsection CLI-RSA RSA
-
-The CLI can also produce output similar to the RSA format from
-NACCESS. This format includes both absolute SASA values (ABS) and
-relative ones (REL) compared to a precalculated reference max
-value. The only significant difference between FreeSASA's RSA output
-format and that of NACCESS (except differences in areas due to
-different atomic radii), is that FreeSASA will print the value "N/A"
-where NACCESS prints "-99.9".
-
-    $ freesasa --format=rsa 3wbm.pdb
-    REM  FreeSASA 2.0
-    REM  Absolute and relative SASAs for 3wbm.pdb
-    REM  Atomic radii and reference values for relative SASA: ProtOr
-    REM  Chains: ABCDXY
-    REM  Algorithm: Lee & Richards
-    REM  Probe-radius: 1.40
-    REM  Slices: 20
-    REM RES _ NUM      All-atoms   Total-Side   Main-Chain    Non-polar    All polar
-    REM                ABS   REL    ABS   REL    ABS   REL    ABS   REL    ABS   REL
-    RES THR A   5   138.48 104.1  99.58 107.4  38.90  96.3  81.59  98.1  56.89 114.0
-    RES PRO A   6    25.53  19.3  11.31  11.0  14.23  47.7  21.67  18.7   3.86  23.9
-    ...
-    RES GLY A  15     0.64   0.9   0.00   N/A   0.64   0.9   0.00   0.0   0.64   2.0
-    ...
-    RES   U Y  23   165.16   N/A 165.16   N/A   0.00   N/A  52.01   N/A 113.15   N/A
-    RES   C Y  24   165.01   N/A 165.01   N/A   0.00   N/A  46.24   N/A 118.77   N/A
-    RES   C Y  25   262.46   N/A 262.46   N/A   0.00   N/A  85.93   N/A 176.52   N/A
-    END  Absolute sums over single chains surface
-    CHAIN  1 A     3785.5       3062.1        723.3       2051.6       1733.9
-    CHAIN  2 B     4342.3       3488.6        853.7       2385.2       1957.1
-    CHAIN  3 C     3961.1       3178.5        782.7       2122.4       1838.7
-    CHAIN  4 D     4904.3       3926.8        977.5       2572.0       2332.3
-    CHAIN  5 X     4156.5       4156.5          0.0       1236.9       2919.6
-    CHAIN  6 Y     4041.1       4041.1          0.0       1184.3       2856.8
-    END  Absolute sums over all chains
-    TOTAL         25190.8      21853.6       3337.2      11552.4      13638.4
-
-Note that each `RES` is a single residue, not a residue type as above
-(i.e. has the same meaning as `SEQ` above). This unfortunate confusion
-of labels is due to RSA support being added much later than the other
-options. Fixing it now would break the interface, and will thus
-earliest be dealt with in the next major release.
-
-@subsubsection RSA-naccess Using the NACCESS configuration
-
-The reference values for the NACCESS configuration in FreeSASA are not
-exactly the same as those that ship with NACCESS, but have been
-calculated from scratch using the tripeptides that ship with
-FreeSASA. Calling
-
-    $ freesasa 3wbm.pdb --format=rsa --radii=naccess
-
-will give an RSA file where the ABS columns should be identical to
-NACCESS (if the latter is run with the flag `-b`). REL values will
-differ slightly, due to the differences in reference values. NACCESS
-also gives different results for the nucleic acid main-chain and
-side-chain (possibly due to a bug in NACCESS?). FreeSASA defines the
-(deoxy)ribose and phosphate groups as main-chain and the base as
-side-chain.
-
-@section CLI-select Selecting groups of atoms
-
-The option `--select` can be used to define groups of atoms whose
-integrated SASA we are interested in. It uses a subset of the Pymol
-`select` command syntax, see @ref Selection for full
-documentation. The following example shows how to calculate the sum of
-exposed surface areas of all aromatic residues and of the four chains
-A, B, C and D (just the sum of the areas above).
-
-    $ freesasa --select "aromatic, resn phe+tyr+trp+his+pro" --select "abcd, chain A+B+C+D" 3wbm.pdb
-    ...
-    SELECTIONS
-    freesasa: warning: Found no matches to resn 'TRP', typo?
-    freesasa: warning: Found no matches to resn 'HIS', typo?
-    aromatic :    1196.45
-    abcd :   16993.24
-
-The lines shown above are appended to the regular output. This
-particular protein did not have any TRP or HIS residues, hence the
-warnings (written to stderr). The warnings can be supressed with the
-flag `-w`.
-
-@section Chain-groups Analyzing groups of chains
-
-Calculating the SASA of a given chain or group of chains separately
-from the rest of the structure, can be useful for measuring how buried
-a chain is in a given structure. The option `--chain-groups` can be
-used to do such a separate calculation, calling
-
-    $ freesasa --chain-groups=ABCD+XY 3wbm.pdb
-
-produces the regular output for the structure 3WBM, but in addition it
-runs a separate calculation for the chains A, B, C and D as though X
-and Y aren't in the structure, and vice versa:
-
-    PARAMETERS
-    algorithm    : Lee & Richards
-    probe-radius : 1.400
-    threads      : 2
-    slices       : 20
-
-
-    ####################
-
-    INPUT
-    source  : 3wbm.pdb
-    chains  : ABCDXY
-    atoms   : 3714
-
-    RESULTS (A^2)
-    Total   :   25190.77
-    Apolar  :   11552.38
-    Polar   :   13638.39
-    CHAIN A :    3785.49
-    CHAIN B :    4342.33
-    CHAIN C :    3961.12
-    CHAIN D :    4904.30
-    CHAIN X :    4156.46
-    CHAIN Y :    4041.08
-
-
-    ####################
-
-    INPUT
-    source  : 3wbm.pdb
-    chains  : ABCD
-    atoms   : 2664
-
-    RESULTS (A^2)
-    Total   :   18202.78
-    Apolar  :    9799.46
-    Polar   :    8403.32
-    CHAIN A :    4243.12
-    CHAIN B :    4595.18
-    CHAIN C :    4427.11
-    CHAIN D :    4937.38
-
-
-    ####################
-
-    INPUT
-    source  : 3wbm.pdb
-    chains  : XY
-    atoms   : 1050
-
-    RESULTS (A^2)
-    Total   :    9396.28
-    Apolar  :    2743.09
-    Polar   :    6653.19
-    CHAIN X :    4714.45
-    CHAIN Y :    4681.83
-
-@section Input PDB input
-
-@subsection Hetatom-hydrogen Including extra atoms
-
-The user can ask to include hydrogen atoms and HETATM entries in the
-calculation using the options `--hydrogen` and `--hetatm`. In both
-cases adding unknown atoms will emit a warning for each atom. This can
-either be amended by using the flag `-w` to suppress warnings, or by
-using a custom classifier so that they are recognized (see @ref
-Config-file).
-
-@subsection Halt-skip Skipping unknown atoms
-
-By default FreeSASA guesses the element of an unknown atom and uses
-that elements VdW radius. If this fails the radius is set to 0 (and
-hence the atom will not contribute to the calculated area). Users can
-request to either skip unknown atoms completely (i.e. no guessing) or
-to halt when unknown atoms are found and exit with an error. This is
-done with the option `--unknown` which takes one of the three
-arguments `skip`, `halt` or `guess` (default). Whenever an unknown
-atom is skipped or its radius is guessed a warning is printed to
-stderr.
-
-@subsection Chains-models Separating and joining chains and models
-
-If a PDB file has several chains and/or models, by default all chains
-of the first model are used, and the rest of the file is ignored. This
-behavior can be modified using the following options 
-
-  - `--join-models`: Joins all models in the input into one large
-    structure. Useful for biological assembly files were different
-    locations of the same chain in the oligomer are represented by
-    different MODEL entries.
-
-  - `--separate-models`: Calculate SASA separately for each model in
-    the input. Useful when the same file contains several
-    conformations of the same molecule.
-
-  - `--separate-chains`: Calculate SASA separately for each chain in
-    the input. Can be joined with `--separate-models` to calculate
-    SASA of each chain in each model.
-
-  - `--chain-groups`: see @ref Chain-groups
-
-@page API FreeSASA API
-
-@section Basic-API Basics
-
-The API is found in the header [freesasa.h](freesasa_8h.html). The
-other source-files and headers in the repository are for internal use,
-and are not presented here, but are documented in the source
-itself. The file [example.c](example_8c_source.html) contains a simple
-program that illustrates how to use the API to read a PDB file from
-`stdin` and calculate and print the SASA.
-
-To calculate the SASA of a structure, there are two main options:
-
-1. Initialize a structure from a PDB-file, using either the default
-   classifier or a custom one to determine the radius of each atom,
-   and then run the calculation.
-
-2. Provide an array of cartesian coordinates and an array containing
-   the radii of the corresponding atoms to freesasa\_calc\_coord().
-
-@subsection API-PDB Calculate SASA for a PDB file
-
-The following explains how to use FreeSASA to calculate the SASA of a
-fictive PDB file (1abc.pdb). At each step one or more error checks
-should have been done, but these are ignored here for brevity. See
-the documentation of each function to see what errors can occur.
-Default parameters are used at every step, the section @ref
-Customizing explains how to configure the calculations.
-
-@subsubsection API-Read-PDB Open PDB file
-
-The function freesasa\_structure\_from\_pdb() reads the atom
-coordinates from a PDB file and assigns a radius to each atom. The
-third argument can be used to pass options for how to read the PDB
-file.
-
-~~~{.c}
-    FILE *fp = fopen("1abc.pdb");
-    const freesasa_classifier *classifier = &freesasa_default_classifier;
-    freesasa_structure *structure = freesasa_structure_from_pdb(fp, classifier, 0);
-~~~
-
-@subsubsection API-Calc Perform calculation and get total SASA
-
-Next we use freesasa\_calc\_structure() to calculate SASA using the
-structure we just generated, and then print the total area. The argument
-`NULL` means use default freesasa_parameters.
-
-~~~{.c}
-    freesasa_result *result = freesasa_calc_structure(structure, NULL);
-    printf("Total area: %f A2\n",result->total);
-~~~
-
-@subsubsection API-Classes Get polar and apolar area
-
-We are commonly interested in the polar and apolar areas of a
-molecule, this can be calculated by freesasa\_result\_classes(). To
-get other classes of atoms we can either define our own classifier, or
-use freesasa\_select\_area() defined in the next section. The return
-type ::freesasa\_nodearea is a struct contains the total area and the
-area of all apolar and polar atoms, and main-chain and side-chain
-atoms.
-
-~~~{.c}
-    freesasa_nodearea area = freesasa_result_classes(structure, result);
-    printf("Total      : %f A2\n", area.total);
-    printf("Apolar     : %f A2\n", area.apolar);
-    printf("Polar      : %f A2\n", area.polar);
-    printf("Main-chain : %f A2\n", area.main_chain);
-    printf("Side-chain : %f A2\n", area.side_chain);
-~~~
-
-@see @ref Classification
-
-@subsubsection API-Select Get area of custom groups of atoms
-
-Groups of atoms can be defined using freesasa\_selection\_new(), which
-takes a selection definition uses a subset of the Pymol select syntax
-
-~~~{.c}
-    freesasa_selection *selection = 
-        freesasa_selection_new("aromatic, resn phe+tyr+trp+his+pro",
-                               structure, result);
-    printf("Area of selection '%s': %f A2\n",
-           freesasa_selection_name(selection), freesasa_selection_area(selection);
-~~~
-
-@see @ref Selection
-
-
-@subsubsection structure-node Navigating the results as a tree
-
-In addition to the flat array of results in ::freesasa\_result, and
-the global values returned by freesasa\_result\_classes(), FreeSASA
-has an interface for navigating the results as a tree. The leaf nodes
-are individual atoms, and there are parent nodes at the residue,
-chain, and structure levels. The function freesasa\_calc\_tree() does
-a SASA calculation and returns the root node of such a tree. (If one
-already has a ::freesasa\_result the function freesasa\_tree\_init()
-can be used instead). Each node stores a ::freesasa\_nodearea for the
-sum of all atoms belonging to the node. The tree can be traversed with
-freesasa\_node\_children(), freesasa\_node\_parent() and
-freesasa\_node\_next(), and the area, type and name using
-freesasa\_node\_area(), freesasa\_node\_type() and
-freesasa\_node\_name(). Additionally there are special properties for
-each level of the tree.
-
-@see node
-
-@subsubsection export-tree Exporting to RSA, JSON and XML
-
-The tree structure can also be exported to an RSA, JSON or XML file
-using freesasa\_tree\_export(). The RSA format is fixed, but the user
-can select which levels of the tree to include in JSON and XML. The
-following illustrates how one would generate a tree and export it to
-XML, including nodes for the whole structure, chains and residues (but
-excluding individual atoms).
-
-~~~~{.c}
-    freesasa_node *tree = freesasa_calc_tree(structure,
-                                             &freesasa_default_parameters,
-                                             &freesasa_default_classifier);
-    FILE *file = fopen("output.xml", "w");
-    freesasa_tree_export(file, tree, FREESASA_XML | FREESASA_OUTPUT_RESIDUE);
-    fclose(file);
-    freesasa_node_free(tree);
-~~~~
-
-    
-@subsection Coordinates
-
-If users wish to supply their own coordinates and radii, these are
-accepted as arrays of doubles passed to the function
-freesasa\_calc\_coord(). The coordinate-array should have size 3*n with
-coordinates in the order `x1,y1,z1,x2,y2,z2,...,xn,yn,zn`.
-
-~~~{.c}
-    double coord[] = {1.0, /* x */
-                      2.0, /* y */
-                      3.0  /* z */ };
-    double radius[] = {2.0};
-    int n_atoms = 1;
-    freesasa_result *result = freesasa_calc_coord(coord, radius, n_atoms, NULL);
-~~~
-
-    
-@subsection Error-handling
-
-The principle for error handling is that unpredictable errors should
-not cause a crash, but rather allow the user to exit gracefully or
-make another attempt. Therefore, errors due to user or system
-failures, such as faulty parameters, malformatted config-files, I/O
-errors or out of memory errors, are reported through return values,
-either ::FREESASA\_FAIL or ::FREESASA\_WARN, or by `NULL` pointers,
-depending on the context (see the documentation for the individual
-functions).
-
-Errors that are attributable to programmers using the library, such as
-passing null pointers where not allowed, are checked by asserts.
-
-@subsection Thread-safety 
-
-The only global state the library stores is the verbosity level (set
-by freesasa\_set\_verbosity()) and the pointer to the error-log
-(defaults to `stderr`, can be changed by freesasa\_set\_err\_out()). 
-
-It should be clear from the documentation when the other functions
-have side effects such as memory allocation and I/O, and thread-safety
-should generally not be an issue (to the extent that your C library
-has threadsafe I/O and dynamic memory allocation). The SASA
-calculation itself can be parallelized by using a
-::freesasa\_parameters struct with ::freesasa\_parameters.n\_threads
-\> 1 (default is 2) where appropriate. This only gives a significant
-effect on performance for large proteins or at high precision, and
-because not all steps are parallelized it is usually not worth it to
-go beyond 2 threads.
-
-@section Customizing Customizing behavior
-
-The types ::freesasa\_parameters and ::freesasa\_classifier can be
-used to change the parameters of the calculations. Users who wish to
-use the defaults can pass `NULL` wherever pointers to these are
-requested.
-
-@subsection Parameters Parameters
-
-Calculation parameters can be stored in a ::freesasa\_parameters
-object. It can be initialized to default by
-
-~~~{.c}
-freesasa_parameters param = freesasa_default_parameters;
-~~~
-
-The following code would run a high precision Shrake & Rupley
-calculation with 10000 test points on the provided structure.
-
-~~~{.c}
-freesasa_parameters param = freesasa_default_parameters;
-param.alg = FREESASA_SHRAKE_RUPLEY;
-param.shrake_rupley_n_points = 10000;
-freesasa_result *result = freesasa_calc_structure(structure, param);
-~~~
-
-@subsection Classification Specifying atomic radii and classes
-
-Classifiers are used to determine which atoms are polar or apolar, and
-to specify atomic radii. In addition the three standard classifiers
-(see below) have reference values for the maximum areas of the 20
-standard amino acids which can be used to calculate relative areas of
-residues, as in the RSA output.
-
-The default classifier is available through the const variable
-::freesasa\_default\_classifier. This uses the *ProtOr* radii, defined
-in the paper by Tsai et
-al. ([JMB 1999, 290: 253](http://www.ncbi.nlm.nih.gov/pubmed/10388571))
-for the standard amino acids (20 regular plus SEC, PYL, ASX and GLX),
-for some capping groups (ACE/NH2) and the standard nucleic acids. If
-the element can't be determined or is unknown, a zero radius is
-assigned. It classes all carbons as *apolar* and all other known atoms
-as *polar*.
-
-Early versions of FreeSASA used the atomic radii by Ooi et
-al. ([PNAS 1987, 84: 3086-3090](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC304812/)),
-this classifier is still available through ::freesasa_oons_classifier.
-
-Users can provide their own classifiers through @ref Config-file. At
-the moment these do not allow the user to specify reference values to
-calculate relative SASA values for RSA output.
-
-The default behavior of freesasa_structure_from_pdb(),
-freesasa_structure_array(), freesasa_structure_add_atom() and
-freesasa_structure_add_atom_wopt() is to first try the provided
-classifier and then guess the radius if necessary (emitting warnings
-if this is done, uses VdW radii defined by [Mantina et al. J Phys Chem
-2009, 113:5806](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3658832/)).
-
-See the documentation for these functions for what parameters to use
-to change the default behavior.
-
-@page Config-file Classifier configuration files
-
-The configuration files read by freesasa_classifier_from_file() or the
-command-line option `-c` should have two sections: `types:` and
-`atoms:`, and optionally the section `name:`.
-
-The types-section defines what types of atoms are available
-(aliphatic, aromatic, hydroxyl, ...), what the radius of that type is
-and what class a type belongs to ('polar' or 'apolar', case
-insensitive). The types are just shorthands to associate an atom with
-a given combination of class and radius. The user is free to define as
-many types and classes as necessary.
-
-The atoms-section consists of triplets of residue-name, atom-name (as
-in the corresponding PDB entries) and type. A prototype file would be
-
-~~~
-name: myclassifier  # tag and value must be on the same line (optional)
-
-types:
-C_ALIPHATIC 2.00 apolar
-C_AROMATIC  1.75 apolar
-N 1.55 polar
-
-atoms:
-ANY N  N
-ANY CA C_ALIPHATIC
-ANY CB C_ALIPHATIC
-
-ARG CG C_ALIPHATIC
-
-PRO CB C_AROMATIC  # overrides ANY CB
-~~~
-
-The residue type `ANY` can be used for atoms that are the same in all
-or most residues (such as backbone atoms). If there is an exception
-for a given amino acid this can be overridden as is shown for `PRO CB`
-in the example.
-
-A few example configurations are available in the directory
-[share/](https://github.com/mittinatten/freesasa/tree/master/share). The
-configuration-file
-[protor.config](https://github.com/mittinatten/freesasa/tree/master/share/protor.config)
-is a copy of the default classifier, and can be used to add extra
-atoms that need to be classified, while keeping the defaults for the
-standard residues (also see the file
-[scripts/chemcomp2config.pl](https://github.com/mittinatten/freesasa/tree/master/scripts/)
-for instructions on how to generate configurations for new chemical
-components semi-automatically). If something common is missing in the
-default classifier, [create an
-issue](https://github.com/mittinatten/freesasa/issues) on Github so
-that it can be added.
-
-FreeSASA also ships with some configuration-files that mimic other
-popular programs, such as
-[NACCESS](https://github.com/mittinatten/freesasa/tree/master/share/naccess.config)
-and
-[DSSP](https://github.com/mittinatten/freesasa/tree/master/share/dssp.config).
-
-The static classifiers in the API were generated using
-[scripts/config2c.pl](https://github.com/mittinatten/freesasa/tree/master/scripts/)
-to convert the correspoding configurations in `share` to C code.
-
-@page Selection Selection syntax
-
-FreeSASA uses a subset of the Pymol select commands to give users an
-easy way of summing up the SASA of groups of atoms. This is done by
-the function freesasa\_selection\_new() in the C API,
-freesasa.selectArea() in the Python interface and the option
-`--select` for the command line tool. All commands are case
-insensitive. A basic selection has a selection name, a property
-selector and a list of arguments
-
-    <selection-name>, <selector> <list>
-
-For example
-
-    aromatic, resn phe+tyr+trp+his+pro
-
-Several selectors can be joined using boolean logic and parentheses,
-
-    <selection-name>, (<s1> <l1>) and not (<s2> <l2> or <s3> <l3>)
-
-where s1, s2 and s3 are selectors and l1, l2 and l3 are lists. The
-operator `and` has precedence over `or`, so the second parentheses is
-necessary but not the first, in the example above. The selection name
-can include letters, numbers and underscores. The name can't be longer
-than ::FREESASA\_MAX\_SELECTION\_NAME characters.
-
-The following property selectors are supported
-
-- `resn` Residue names like "ala", "arg", "du", etc 
-- `resi` Residue index (positive or negative integers)
-- `chain` Chain labels (single characters)
-- `name` Atom names, such as "ca", "c", "oxt", etc
-- `symbol` Element symbols, such as "C", "O", "Se", "Fe", etc.
-
-A list of residues can be selected using
-
-    resn ala+val+leu+ile+met
-
-and similarly for the other four selectors. In addition `resi` and
-`chain` support ranges
-
-    resi 1-10             (residues 1 to 10)
-    resi -10              (residues indices < 10)
-    resi 10-              (residues indices > 10)
-    resi 1-10+20-30+35-   (residues 1 to 10, 20 to 30 and above 35)
-    resi \-20-\-15+\-10-5 (residues -20 to -15 and -10 to 5)
-    chain A+C-E           (chains A and C to E, no open intervals allowed here)
-
-Combining ranges with plus signs, as in the three last lines, is not
-allowed in Pymol but supported by FreeSASA.
-
-If a selection list contains elements not found in the molecule that
-is analyzed, a warning is printed and that part of the list does not
-contribute to the selection. Not finding a list element can be because
-it specifies a residue that does not exist in the particular molecule,
-or because of typos. The selector does not keep a list of valid
-elements, residue names, etc.
-
-@page Python Python interface
-
-If Python is enabled using 
-    
-    $ ./configure --enable-python-bindings
-
-Cython is used to build Python bindings for FreeSASA, and `make
-install` will install them. The option `--with-python=...` can be
-specified to specify which Python binary to use.
-
-Below follow some illustrations of how to use the package, see the
-@ref freesasa "package documentation" for details.
-
-@section Python-basics Basic calculations
-
-Using defaults everywhere a simple calculation can be carried out as
-follows (assuming the PDB structure 1UBQ is available)
-
-~~~{.py} 
-import freesasa
-
-structure = freesasa.Structure("1ubq.pdb")
-result = freesasa.calc(structure)
-area_classes = freesasa.classifyResults(result, structure)
-
-print "Total : %.2f A2" % result.totalArea()
-for key in area_classes:
-    print key, ": %.2f A2" % area_classes[key]
-~~~
-
-Which would give the following output
-
-    Total : 4804.06 A2
-    Polar : 2504.22 A2
-    Apolar : 2299.84 A2
-
-The following does a high precision L&R calculation
-
-~~~{.py}
-result = freesasa.calc(structure,
-                       freesasa.Parameters({'algorithm' : freesasa.LeeRichards,
-                                            'n-slices' : 100}))
-~~~
-
-Using the results from a calculation we can also integrate SASA over a selection of
-atoms, using a subset of the Pymol selection syntax (see @ref Selection):
-
-~~~{.py}
-selections = freesasa.selectArea(('alanine, resn ala', 'r1_10, resi 1-10'), 
-                                 structure, result)
-for key in selections:
-    print key, ": %.2f A2" % selections[key]
-~~~
-which gives the output
-
-    alanine : 120.08 A2
-    r1_10 : 634.31 A2
-
-@section Python-classification Customizing atom classification
-
-This uses the NACCESS parameters (the file 'naccess.config' is
-available in the share/ directory of the repository).
-
-~~~{.py}
-classifier = freesasa.Classifier("naccess.config")
-structure = freesasa.Structure("1ubq.pdb", classifier) 
-result = freesasa.calc(structure)
-area_classes = freesasa.classifyResults(result, structure, classifier)
-~~~
-
-Classification can be customized also by extending the Classifier
-interface. The code below is an illustration of a classifier that
-classes Nitrogens separately, and assigns radii based on element only
-(and crudely).
-
-~~~{.py}
-import freesasa
-import re
-
-class DerivedClassifier(Classifier):
-    def classify(self, residueName, atomName):
-        if re.match('\s*N', atomName):
-            return 'Nitrogen'
-        return 'Not-nitrogen'
-
-    def radius(self, residueName, atomName):
-        if re.match('\s*N',atomName): # Nitrogen 
-            return 1.6
-        if re.match('\s*C',atomName): # Carbon
-            return 1.7
-        if re.match('\s*O',atomName): # Oxygen
-            return 1.4
-        if re.match('\s*S',atomName): # Sulfur
-            return 1.8    
-    return 0;                     # everything else (Hydrogen, etc)
-
-classifier = DerivedClassifier()
-
-# use the DerivedClassifier to calculate atom radii
-structure = freesasa.Structure("1ubq.pdb", classifier)
-result = freesasa.calc(structure)
-
-# use the DerivedClassifier to classify atoms
-area_classes = freesasa.classifyResults(result,structure,classifier)
-~~~
-
-Of course, this example is somewhat contrived, if we only want the
-integrated area of Nitrogen atoms, the simpler choice would be
-~~~{.py}
-    selection = freesasa.selectArea('nitrogen, symbol n', structure, result)
-~~~
-
-However, extending freesasa.Classifier, as illustrated above, allows
-classification to arbitrary complexity and also lets us redefine the
-radii used in the calculation.
-
-@section BioPDB Bio.PDB
-
-FreeSASA can also calculate the SASA of a Bio.PDB structure
-
-~~~{.py}
-    from Bio.PDB import PDBParser
-    parser = PDBParser()
-    structure = parser.get_structure("Ubiquitin", "1ubq.pdb")
-    result, sasa_classes = freesasa.calcBioPDB(structure)
-~~~
-
-If one needs more control over the analysis the structure can be
-converted to a freesasa.Structure using freesasa.structureFromBioPDB()
-and the calculation can be performed the normal way using this
-structure.
-
-@page Geometry Geometry of Lee & Richards' algorithm
-
-This page explains the geometry of the calculations in L&R
-and can be used to understand the source code. As far as possible the
-code uses similar notation to the formulas here.
-
-We will use the following notation: An atom \f$i\f$ has a van der
-Waals radius \f$r_i\f$, the rolling sphere (or *probe*) has radius
-\f$r_\text{P}\f$ and when these are added we get an extended radius
-\f$R_i = r_i + r_\text{P}\f$. The sphere of radius \f$R_i\f$ centered
-at the position of atom \f$i\f$ represents the volume not accessible
-to the center of the probe. The SASA for a molecule is then obtained
-by calculating the non-buried surface area of the extended spheres.
-
-The L&R algorithm calculates the surface area by slicing the
-protein, calculating the length of the solvent exposed contours in
-each slice and then adding up the length multiplied by the slice
-thickness.
-
-![Slice in atom](../fig/lnr_slice.svg)
-
-Divide atom \f$i\f$ into \f$n\f$ slices, orthogonal to an arbitrary
-axis, of thickness \f$\delta = 2R_i/n\f$. The position of the middle
-of the slice along that axis is denoted \f$z\f$, and the center of
-atom \f$i\f$, along the same axis, is at \f$z_i\f$. In each slice, the
-atom is thus a circle of radius \f[R_i^\prime =
-\sqrt{R_i^2-(z-z_i)^2}\,.\f] These circles are either completely
-buried inside neighboring atoms, completely exposed, or partially
-exposed.
-
-![Overlap of circles](../fig/lnr_circles.svg)
-
-The exposed arc lengths for each atom can be calculated exactly. For
-each pair of atoms \f$i,j\f$, the distance between their centers
-projected on the slice is \f$d_{ij}\f$ (independent of \f$z\f$). If
-\f$d_{ij} > R_i^\prime + R_j^\prime\f$, there is no overlap. If
-\f$d_{ij} < R_j^\prime - R_i^\prime\f$ circle \f$i\f$ is completely
-inside \f$j\f$ (and the other way around). If \f$d_{ij}\f$ lies
-between these two cases the angle of circle \f$i\f$ that is buried due
-to circle \f$j\f$ is
-
-\f[ \alpha = 2\arccos \bigl[({R_i^\prime}^2_{\,}
-+ d_{ij}^2 - {R_{j}^\prime}^2_{\,})/(2R_i^\prime d_{ij})\bigr].  \f]
-
-If the middle point of this arc on the circle is at an angle
-\f$\beta\f$, the arc spans the interval
-\f$[\beta-\alpha/2,\beta+\alpha/2]\f$. By adding up these arcs and
-taking into account any overlap between them we get the total buried
-angle \f$\gamma\f$ in this slices. The exposed arc angle for this atom
-and slice is thus \f$2\pi-\gamma\f$ and the total SASA of that atom
-
-\f[ A_i =R_i \delta \!\! \sum_{s\in\text{slices}} \!\!
-\left[2\pi-\gamma_s\right]\,.  \f]
-
-The angle is multiplied by \f$R_i\f$ (not \f$R_i^\prime\f$) to give
-the area of a conical frustum circumscribing the sphere at the
-slice. Finally, the total area \f$A\f$ is the sum of all \f$A_i\f$.
-
-In FreeSASA, the L\&R SASA calculation begins by finding overlapping
-spheres and storing the contacts in an adjacency list. It then
-iterates through all the slices of each atom and checks for overlap
-with adjacent atoms in each slice, and adds up the exposed arcs to
-calculate the atom's contribution to the SASA of the slice. The
-calculations for each atom are completely independent and can thus be
-parallelized over an arbitrary number of threads, whereas the
-calculation of adjacency lists has not been parallelized.