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metal3d

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import gradio as gr

import urllib
import re
import sys
import warnings

import torch
import torch.nn as nn
import ipywidgets as widgets
from ipywidgets import interact, fixed

from utils.helpers import *
from utils.voxelization import processStructures
from utils.model import Model
import numpy as np

import os
import moleculekit

print(moleculekit.__version__)


def update(inp, file, mode):
    try:
        pdb_file = file.name
    except:
        print("using pdbfile")

    try:
        pdb_file = inp
        if (
            re.match(
                "[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}",
                pdb_file,
            ).group()
            == pdb_file
        ):
            urllib.request.urlretrieve(
                f"https://alphafold.ebi.ac.uk/files/AF-{pdb_file}-F1-model_v2.pdb",
                f"files/{pdb_file}.pdb",
            )
    except AttributeError:
        if len(inp) == 4:
            pdb_file = inp
            urllib.request.urlretrieve(
                f"http://files.rcsb.org/download/{pdb_file.lower()}.pdb1",
                f"files/{pdb_file}.pdb",
            )
        else:
            return "pdb code must be 4 letters or Uniprot code does not match", ""

    if mode == "All residues":
        ids = get_all_protein_resids(
            f"files/{pdb_file}.pdb",
        )
    else:
        ids = get_all_metalbinding_resids(f"files/{pdb_file}.pdb")

    voxels, prot_centers, prot_N, prots = processStructures(pdb_file, ids)
    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
    voxels.to(device)
    print(voxels.shape)
    model = Model()
    model.to(device)
    model.load_state_dict(torch.load("weights/metal_0.5A_v3_d0.2_16Abox.pth", map_location=torch.device('cpu')))
    model.eval()
    with warnings.catch_warnings():
        warnings.filterwarnings("ignore")
        output = model(voxels)
    print(output.shape)
    prot_v = np.vstack(prot_centers)
    output_v = output.flatten().cpu().detach().numpy()
    bb = get_bb(prot_v)
    gridres = 0.5
    grid, box_N = create_grid_fromBB(bb, voxelSize=gridres)
    probability_values = get_probability_mean(grid, prot_v, output_v)
    print(probability_values.shape)
    write_cubefile(
        bb,
        probability_values,
        box_N,
        outname=f"output/metal_{pdb_file}.cube",
        gridres=gridres,
    )
    message = find_unique_sites(
        probability_values,
        grid,
        writeprobes=True,
        probefile=f"output/probes_{pdb_file}.pdb",
        threshold=7,
        p=0.15,
    )

    return message, molecule(
        f"files/{pdb_file}.pdb",
        f"output/probes_{pdb_file}.pdb",
        f"output/metal_{pdb_file}.cube",
    )


def test():
    x = """<!DOCTYPE html>
        <html>
        <head>    
    <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
    </head>
    <body>  
    <script src="https://3Dmol.org/build/3Dmol-min.js" async></script> <div style="height: 400px; width: 400px; position: relative;" class="viewer_3Dmoljs" data-pdb="2POR" data-backgroundcolor="0xffffff" data-style="stick" ></div>
        </body></html>"""
    return f"""<iframe style="width: 100%; height: 480px" name="result" allow="midi; geolocation; microphone; camera; 
    display-capture; encrypted-media;" sandbox="allow-modals allow-forms 
    allow-scripts allow-same-origin allow-popups 
    allow-top-navigation-by-user-activation allow-downloads" allowfullscreen="" 
    allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""


def read_mol(molpath):
    with open(molpath, "r") as fp:
        lines = fp.readlines()
    mol = ""
    for l in lines:
        mol += l
    return mol


def molecule(pdb, probes, cube):
    mol = read_mol(pdb)
    probes = read_mol(probes)
    cubefile = read_mol(cube)
    x = (
        """<!DOCTYPE html>
        <html>
        <head>    
    <meta http-equiv="content-type" content="text/html; charset=UTF-8" />
    <style>
    body{
        font-family:sans-serif
    }
.mol-container {
  width: 100%;
  height: 400px;
  position: relative;
}
.slider{
    width:80%;
    margin:0 auto
}
.slidercontainer{
    display:flex;
}
.slidercontainer > * + * {
    margin-left: 0.5rem;
}
#isovalue{
 text-align:right}
</style>
<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/rangeslider.js/2.3.3/rangeslider.min.js" integrity="sha512-BUlWdwDeJo24GIubM+z40xcj/pjw7RuULBkxOTc+0L9BaGwZPwiwtbiSVzv31qR7TWx7bs6OPTE5IyfLOorboQ==" crossorigin="anonymous" referrerpolicy="no-referrer"></script>
    </head>
    <body>  
    <div class="slidercontainer">
    <span>Isovalue </span>
    <span id="isovalue">0.5</span>
    <input class="slider" type="range" id="rangeslider" min="0" max="1" step="0.025" value=0.5>
    </div>
    
    <div id="container" class="mol-container"></div>
            <script>
            let viewer = null;
            let voldata = null;
            $(document).ready(function () {
                let element = $("#container");
                let config = { backgroundColor: "white" };
                viewer = $3Dmol.createViewer( element, config );
                viewer.ui.initiateUI();
                let data = `"""
        + mol
        + """`
                viewer.addModel( data, "pdb" );
                
                let cubefile = `"""
        + cubefile
        + """`
                voldata = new $3Dmol.VolumeData(cubefile, "cube");
                viewer.addIsosurface(voldata, { isoval: 0.7 , color: "blue", alpha: 0.85, smoothness: 1 });
                viewer.getModel(0).setStyle({}, {cartoon: {color: "grayCarbon"}}); 
                let probes =`"""
        + probes
        + """`
                viewer.addModel(probes, "pdb");
                viewer.getModel(1).setStyle({ "resn": "ZN" }, { "sphere": { }});
                viewer.getModel(1).setHoverable({}, true,
                    function (atom, viewer, event, container) {
                        if (!atom.label) {
                            atom.label = viewer.addLabel("ZN p=" + atom.pdbline.substring(55, 60), { position: atom, backgroundColor: "mintcream", fontColor: "black" });
                        }
                    },
                    function (atom, viewer) {
                        if (atom.label) {
                            viewer.removeLabel(atom.label);
                            delete atom.label;
                        }
                    }
                );
                viewer.zoomTo();
                viewer.render();
                viewer.zoom(0.8, 2000);
        });
        </script>
         <script>
         $("#rangeslider").rangeslider().on("change", function (el) {
                isoval = parseFloat(el.target.value);
                $("#isovalue").text(el.target.value)
                viewer.addIsosurface(voldata, { isoval: parseFloat(el.target.value), color: "blue", alpha: 0.85, smoothness: 1 });
                viewer.render();
            });
            </script>
        </body></html>"""
    )

    return f"""<iframe style="width: 100%; height: 480px" name="result" allow="midi; geolocation; microphone; camera; 
    display-capture; encrypted-media;" sandbox="allow-modals allow-forms 
    allow-scripts allow-same-origin allow-popups 
    allow-top-navigation-by-user-activation allow-downloads" allowfullscreen="" 
    allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""


metal3d = gr.Blocks()

with metal3d:
    gr.Markdown("# Metal3D")
    gr.Markdown(
        """
        Details about implementation and code available here:
        >Duerr, Levy and Roethlisberger, Predicting zinc ion location using deep learning, BioRxiv, 2022 "
    """
    )
    with gr.Group():
        inp = gr.Textbox(
            placeholder="PDB Code or Uniprot identifier", label="Input molecule"
        )
        gr.Markdown("or upload a file")
        file = gr.File(file_count="single", type="file")
        mode = gr.Radio(
            ["All metalbinding residues (ASP, CYS, GLU, HIS)", "All residues"],
            label="Residues to use for prediction",
        )
        btn = gr.Button("Run")

    gr.Markdown("# Output")
    out = gr.Textbox(label="status")
    mol = gr.HTML()
    btn.click(fn=update, inputs=[inp, file, mode], outputs=[out, mol])

metal3d.launch()