vis

.gitattributes

@@ -33,3 +33,5 @@ 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
+GFN2all.exe filter=lfs diff=lfs merge=lfs -text
+GFN2all_crd.exe filter=lfs diff=lfs merge=lfs -text

1A30.pdb

@@ -0,0 +1,52 @@
+CRYST1   81.052   81.052   81.052 109.47 109.47 109.47               1
+ATOM      1  N   GLU   199      36.081  39.009  29.686  1.00  0.00           N  
+ATOM      2  H1  GLU   199      35.429  38.796  30.426  1.00  0.00           H  
+ATOM      3  H2  GLU   199      36.154  38.207  29.076  1.00  0.00           H  
+ATOM      4  H3  GLU   199      35.853  39.916  29.303  1.00  0.00           H  
+ATOM      5  CA  GLU   199      37.432  39.167  30.291  1.00  0.00           C  
+ATOM      6  HA  GLU   199      38.116  38.436  29.860  1.00  0.00           H  
+ATOM      7  CB  GLU   199      37.982  40.570  30.022  1.00  0.00           C  
+ATOM      8  HB2 GLU   199      38.901  40.671  30.598  1.00  0.00           H  
+ATOM      9  HB3 GLU   199      38.212  40.628  28.958  1.00  0.00           H  
+ATOM     10  CG  GLU   199      37.028  41.688  30.394  1.00  0.00           C  
+ATOM     11  HG2 GLU   199      36.079  41.510  29.887  1.00  0.00           H  
+ATOM     12  HG3 GLU   199      36.878  41.635  31.472  1.00  0.00           H  
+ATOM     13  CD  GLU   199      37.549  43.062  30.023  1.00  0.00           C  
+ATOM     14  OE1 GLU   199      38.098  43.217  28.907  1.00  0.00           O  
+ATOM     15  OE2 GLU   199      37.394  43.992  30.847  1.00  0.00           O  
+ATOM     16  C   GLU   199      37.378  38.880  31.790  1.00  0.00           C  
+ATOM     17  O   GLU   199      36.391  39.196  32.464  1.00  0.00           O  
+ATOM     18  N   ASP   200      38.421  38.232  32.294  1.00  0.00           N  
+ATOM     19  H   ASP   200      39.166  37.937  31.679  1.00  0.00           H  
+ATOM     20  CA  ASP   200      38.512  37.883  33.705  1.00  0.00           C  
+ATOM     21  HA  ASP   200      37.703  38.355  34.262  1.00  0.00           H  
+ATOM     22  CB  ASP   200      38.401  36.370  33.871  1.00  0.00           C  
+ATOM     23  HB2 ASP   200      39.160  35.871  33.269  1.00  0.00           H  
+ATOM     24  HB3 ASP   200      38.581  36.162  34.926  1.00  0.00           H  
+ATOM     25  CG  ASP   200      37.030  35.856  33.483  1.00  0.00           C  
+ATOM     26  OD1 ASP   200      36.116  35.958  34.323  1.00  0.00           O  
+ATOM     27  OD2 ASP   200      36.851  35.393  32.334  1.00  0.00           O  
+ATOM     28  C   ASP   200      39.827  38.407  34.256  1.00  0.00           C  
+ATOM     29  O   ASP   200      40.869  37.761  34.126  1.00  0.00           O  
+ATOM     30  N   LEU   201      39.771  39.607  34.828  1.00  0.00           N  
+ATOM     31  H   LEU   201      38.893  40.106  34.850  1.00  0.00           H  
+ATOM     32  CA  LEU   201      40.950  40.261  35.373  1.00  0.00           C  
+ATOM     33  HA  LEU   201      41.853  39.729  35.075  1.00  0.00           H  
+ATOM     34  CB  LEU   201      41.025  41.684  34.837  1.00  0.00           C  
+ATOM     35  HB2 LEU   201      40.080  42.153  35.112  1.00  0.00           H  
+ATOM     36  HB3 LEU   201      41.851  42.260  35.254  1.00  0.00           H  
+ATOM     37  CG  LEU   201      41.150  41.645  33.318  1.00  0.00           C  
+ATOM     38  HG  LEU   201      40.848  40.661  32.961  1.00  0.00           H  
+ATOM     39  CD1 LEU   201      40.276  42.692  32.696  1.00  0.00           C  
+ATOM     40 HD11 LEU   201      40.578  43.677  33.052  1.00  0.00           H  
+ATOM     41 HD12 LEU   201      40.375  42.652  31.612  1.00  0.00           H  
+ATOM     42 HD13 LEU   201      39.237  42.509  32.972  1.00  0.00           H  
+ATOM     43  CD2 LEU   201      42.612  41.790  32.919  1.00  0.00           C  
+ATOM     44 HD21 LEU   201      43.189  40.972  33.350  1.00  0.00           H  
+ATOM     45 HD22 LEU   201      42.697  41.762  31.833  1.00  0.00           H  
+ATOM     46 HD23 LEU   201      42.997  42.740  33.289  1.00  0.00           H  
+ATOM     47  C   LEU   201      40.979  40.272  36.891  1.00  0.00           C  
+ATOM     48  O   LEU   201      42.089  40.361  37.458  1.00  0.00           O  
+ATOM     49  OXT LEU   201      39.891  40.190  37.498  1.00  0.00           O  
+TER      50      LEU   201 
+END   

GFN2all.cpp

@@ -0,0 +1,210 @@
+#include <iostream>
+#include "ulysses/src/GFN.hpp"
+#include "ulysses/src/math/SolverPackage.hpp"
+#include "ulysses/src/Gas.hpp"
+
+int main(int argc, char** argv) {
+
+  //check the files gfn2-xtb_optg.cpp and pm6-corrected.cpp to extend the options here
+
+  //arguments
+  // 0 exe
+  // 1 geometry
+  // 2 charge
+  // 3 Telec = 300
+  // 4 solvation?
+  // 5 solvent name
+  // 6 optimise geometry?
+  // 7 name for new geometry file
+  // 8 thermo?
+  // 9 energy threshold for geometry optimization = 1.0e-6
+  // 10 gradient threshold for geometry optimization = 1.0e-3
+  // 11 calculate density?
+  // 12 name for density file
+  // 13 electronic reactivity indices?
+  // 14 orbital reactivity indices?
+  // 15 Koopman IP?
+  // 16 IP?
+  // 17 EA?
+  // 18 electronativity?
+  // 19 hardness?
+  
+  //parameters passed as argument
+  char *p;
+  int charge = strtol(argv[2],&p,10);
+  char *q;
+  double Telec = strtod(argv[3],&q);
+  char *r;
+  int solvation = strtol(argv[4],&r,10);
+  char *v;
+  int optgeom = strtol(argv[6],&v,10);
+  char *s;
+  int thermo = strtol(argv[8],&s,10);
+  char *t;
+  double energy_threshold = strtod(argv[9],&t);
+  char *u;
+  double gradient_threshold = strtod(argv[10],&u);
+  char *w;
+  int calcdensity = strtol(argv[11],&w,10);
+  char *z1;
+  int elecrx = strtol(argv[13],&z1,10);
+  char *z2;
+  int orbrx = strtol(argv[14],&z2,10);
+  char *z3;
+  int koopman = strtol(argv[15],&z3,10);
+  char *z4;
+  int ip = strtol(argv[16],&z4,10);
+  char *z5;
+  int ea = strtol(argv[17],&z5,10);
+  char *z6;
+  int electronegativity = strtol(argv[18],&z6,10);
+  char *z7;
+  int hardness = strtol(argv[19],&z7,10);
+  
+  //system declaration
+  std::cout << "running " << argv[1] << "\n";
+  std::cout << "charge          = " << charge << std::endl;
+  std::cout << "T electron = " << Telec << std::endl;
+
+  //allocate molecules
+  Molecule Mol1(argv[1],charge,1,"C1");
+  
+  //define method and basis set
+  BSet basis(Mol1,"gfn2");
+  GFN2 electron(basis,Mol1);
+  electron.setElectronTemp(Telec);
+  
+  //use ALPB solvation?
+  if (solvation > 0) {
+    electron.setSolvent(argv[5]);
+    // "water"
+    // "acetone"
+    // "acetonitrile"
+    // "aniline"
+    // "benzaldehyde"
+    // "benzene"
+    // "dichloromethane"
+    // "chloroform"
+    // "carbon disulfide"
+    // "dioxane"
+    // "dmf"
+    // "dmso"
+    // "ethanol"
+    // "diethyl ether"
+    // "ethyl acetate"
+    // "furane"
+    // "hexadecane"
+    // "hexane"
+    // "methanol"
+    // "nitromethane"
+    // "octanol"
+    // "phenol"
+    // "thf"
+    // "toluene"
+    // "water"
+    // "octanol wet"
+  }
+
+  electron.Calculate(0);
+  
+  //optimise geometry?
+  if (optgeom > 0) {
+    BFGSd solve(4,6);
+    SolverOpt(electron,solve,4,0,energy_threshold,gradient_threshold);
+    Molecule Mol2 = electron.Component();
+    Mol2.WriteXYZ(argv[7]);
+  }
+  
+  electron.Calculate(1);
+  
+  std::cout << std::setprecision(7) << "\n";
+  //perform thermodynamics?
+  if (thermo > 0) {
+    //get vibrations
+    std::vector<double> all_vibrations = electron.CalcVibrFrequencies();
+    int nvibrations = 6;
+    std::vector<double> vibrations(all_vibrations.size() - nvibrations);            //CalcVibrFrequencies returns also translation and rotation modes; these must be removed
+    for (size_t idvibr = 0; idvibr < vibrations.size(); ++idvibr) {
+      vibrations[idvibr] = all_vibrations[idvibr + nvibrations];
+    }
+    std::cout << ">all vibrational frequencies" << std::endl;
+    for (size_t idvibr = 0; idvibr < all_vibrations.size(); ++idvibr) {
+      std::cout << all_vibrations[idvibr] << std::endl;
+    }
+    std::cout << "<all vibrational frequencies" << std::endl;
+    //get electronic energies
+    std::vector<double> Eel;
+    Eel.push_back(electron.getEnergy(1));      //the one means that the D3H4X correction is applied to the total energy; use 0 if you want non-corrected energies
+    //get the degeneracy of ground state
+    std::vector<double> gel(1,1.0);
+    
+    //get the eigenvalues of inertia matrix
+    std::vector<double> inertia = electron.Component().InertiaEigenvalues();
+    
+    double T = 298.15;
+    bool grimmecorrection = true;
+    double numbermolecules = NA; //1 mol
+    double volume = 0.0224;
+    PBlRRlHOE IdealGas(T,argv[1],inertia,vibrations,Eel,gel,charge,1,"C1","0",grimmecorrection,numbermolecules,volume);
+    
+    //loop over temperatures and print out
+    double temperature = 100.0;  //K
+    std::cout << ">Thermodynamics" << std::endl;
+    for (size_t idx = 0; idx < 2201; ++idx) {
+      IdealGas.changeT(temperature);
+      std::cout << temperature << ";" << IdealGas.S() << ";" << IdealGas.H() << ";" << IdealGas.G() << ";" << IdealGas.U() << ";" << IdealGas.A() << ";" << IdealGas.CP() << ";" << IdealGas.CV() << std::endl;
+      temperature += 0.5;
+    }
+    std::cout << "<Thermodynamics" << std::endl;
+  }
+  
+  //get the density?
+  if (calcdensity > 0) {
+    electron.ElectronicDensity(argv[12]);
+  }
+
+  //get charges and polarisabilities
+  std::vector<size_t> atoms = Mol1.Atoms();
+  std::vector<double> AtmCharge = electron.getQAtoms();
+  std::vector<double> polarizabilities;
+  electron.AtomicPolarizabilities(polarizabilities,AtmCharge);
+  std::cout << ">atom;charge;pol\n";
+  for (size_t idx = 0; idx < atoms.size(); ++idx) {
+    std::cout << atoms[idx] << ";";
+    std::cout << AtmCharge[idx] << ";" << polarizabilities[idx] << "\n";
+  }
+  std::cout << "<atom;charge;pol\n";
+  double polbity = 0.0;
+  electron.TotalPolarizability(polbity,AtmCharge);
+  std::cout << " Total Polarizability          " << polbity << "\n";
+
+  //additional properties
+  matrixE RxData(1,1);
+  if (elecrx > 0) {
+    electron.ReactivityIndices(RxData,false);
+    std::cout << ">Electronic Reactivity indices" << std::endl;
+    RxData.Print(4);
+    std::cout << "<Electronic Reactivity indices" << std::endl;
+  }
+
+  if (orbrx > 0) {
+    electron.ReactivityIndices(RxData,true);
+    std::cout << ">Orbital Reactivity indices" << std::endl;
+    RxData.Print(4);
+    std::cout << "<Orbital Reactivity indices" << std::endl;
+  }
+
+  if (koopman > 0) {std::cout << "Ionization Potential (Koopman): " << electron.IonizationPotential(true)*au2eV << "   eV" << std::endl;}
+  if (ip > 0) {std::cout << "Ionization Potential (Definition): " << electron.IonizationPotential(false)*au2eV << "   eV" << std::endl;}
+  if (ea > 0) {std::cout << "Electron Affinity (Definition): " << electron.ElectronAffinity()*au2eV << "   eV" << std::endl;}
+  
+  if ((electronegativity > 0)||(hardness > 0)) {
+    double chi;
+    double eta;
+    electron.HSABdata(chi,eta);
+    std::cout << "Electronegativity: " << chi*au2eV << "   eV" << std::endl;
+    std::cout << "Hardness: " << eta*au2eV << "   eV" << std::endl;
+  }
+  
+  return 0;
+}

GFN2all.exe

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:342e15927cb35c6c4446d7f35491e4ce1a86fc00c8e1d21b270cabff6071d65a
+size 6962680

GFN2all_crd.cpp

@@ -0,0 +1,210 @@
+#include <iostream>
+#include "ulysses/src/GFN.hpp"
+#include "ulysses/src/math/SolverPackage.hpp"
+#include "ulysses/src/Gas.hpp"
+
+int main(int argc, char** argv) {
+
+  //check the files gfn2-xtb_optg.cpp and pm6-corrected.cpp to extend the options here
+
+  //arguments
+  // 0 exe
+  // 1 geometry
+  // 2 charge
+  // 3 Telec = 300
+  // 4 solvation?
+  // 5 solvent name
+  // 6 optimise geometry?
+  // 7 name for new geometry file
+  // 8 thermo?
+  // 9 energy threshold for geometry optimization = 1.0e-6
+  // 10 gradient threshold for geometry optimization = 1.0e-3
+  // 11 calculate density?
+  // 12 name for density file
+  // 13 electronic reactivity indices?
+  // 14 orbital reactivity indices?
+  // 15 Koopman IP?
+  // 16 IP?
+  // 17 EA?
+  // 18 electronativity?
+  // 19 hardness?
+  
+  //parameters passed as argument
+  char *p;
+  int charge = strtol(argv[2],&p,10);
+  char *q;
+  double Telec = strtod(argv[3],&q);
+  char *r;
+  int solvation = strtol(argv[4],&r,10);
+  char *v;
+  int optgeom = strtol(argv[6],&v,10);
+  char *s;
+  int thermo = strtol(argv[8],&s,10);
+  char *t;
+  double energy_threshold = strtod(argv[9],&t);
+  char *u;
+  double gradient_threshold = strtod(argv[10],&u);
+  char *w;
+  int calcdensity = strtol(argv[11],&w,10);
+  char *z1;
+  int elecrx = strtol(argv[13],&z1,10);
+  char *z2;
+  int orbrx = strtol(argv[14],&z2,10);
+  char *z3;
+  int koopman = strtol(argv[15],&z3,10);
+  char *z4;
+  int ip = strtol(argv[16],&z4,10);
+  char *z5;
+  int ea = strtol(argv[17],&z5,10);
+  char *z6;
+  int electronegativity = strtol(argv[18],&z6,10);
+  char *z7;
+  int hardness = strtol(argv[19],&z7,10);
+  
+  //system declaration
+  std::cout << "running " << argv[1] << "\n";
+  std::cout << "charge          = " << charge << std::endl;
+  std::cout << "T electron = " << Telec << std::endl;
+
+  //allocate molecules
+  Molecule Mol1(argv[1],charge,1,"C1");
+  
+  //define method and basis set
+  BSet basis(Mol1,"gfn2");
+  GFN2 electron(basis,Mol1);
+  electron.setElectronTemp(Telec);
+  
+  //use ALPB solvation?
+  if (solvation > 0) {
+    electron.setSolvent(argv[5]);
+    // "water"
+    // "acetone"
+    // "acetonitrile"
+    // "aniline"
+    // "benzaldehyde"
+    // "benzene"
+    // "dichloromethane"
+    // "chloroform"
+    // "carbon disulfide"
+    // "dioxane"
+    // "dmf"
+    // "dmso"
+    // "ethanol"
+    // "diethyl ether"
+    // "ethyl acetate"
+    // "furane"
+    // "hexadecane"
+    // "hexane"
+    // "methanol"
+    // "nitromethane"
+    // "octanol"
+    // "phenol"
+    // "thf"
+    // "toluene"
+    // "water"
+    // "octanol wet"
+  }
+
+  electron.Calculate(0);
+  
+  //optimise geometry?
+  if (optgeom > 0) {
+    BFGSd solve(4,6);
+    SolverOpt(electron,solve,4,0,energy_threshold,gradient_threshold);
+  }
+  Molecule Mol2 = electron.Component();
+  Mol2.WriteXYZ(argv[7]);
+  
+  electron.Calculate(1);
+  
+  std::cout << std::setprecision(7) << "\n";
+  //perform thermodynamics?
+  if (thermo > 0) {
+    //get vibrations
+    std::vector<double> all_vibrations = electron.CalcVibrFrequencies();
+    int nvibrations = 6;
+    std::vector<double> vibrations(all_vibrations.size() - nvibrations);            //CalcVibrFrequencies returns also translation and rotation modes; these must be removed
+    for (size_t idvibr = 0; idvibr < vibrations.size(); ++idvibr) {
+      vibrations[idvibr] = all_vibrations[idvibr + nvibrations];
+    }
+    std::cout << ">all vibrational frequencies" << std::endl;
+    for (size_t idvibr = 0; idvibr < all_vibrations.size(); ++idvibr) {
+      std::cout << all_vibrations[idvibr] << std::endl;
+    }
+    std::cout << "<all vibrational frequencies" << std::endl;
+    //get electronic energies
+    std::vector<double> Eel;
+    Eel.push_back(electron.getEnergy(1));      //the one means that the D3H4X correction is applied to the total energy; use 0 if you want non-corrected energies
+    //get the degeneracy of ground state
+    std::vector<double> gel(1,1.0);
+    
+    //get the eigenvalues of inertia matrix
+    std::vector<double> inertia = electron.Component().InertiaEigenvalues();
+    
+    double T = 298.15;
+    bool grimmecorrection = true;
+    double numbermolecules = NA; //1 mol
+    double volume = 0.0224;
+    PBlRRlHOE IdealGas(T,argv[1],inertia,vibrations,Eel,gel,charge,1,"C1","0",grimmecorrection,numbermolecules,volume);
+    
+    //loop over temperatures and print out
+    double temperature = 100.0;  //K
+    std::cout << ">Thermodynamics" << std::endl;
+    for (size_t idx = 0; idx < 2201; ++idx) {
+      IdealGas.changeT(temperature);
+      std::cout << temperature << ";" << IdealGas.S() << ";" << IdealGas.H() << ";" << IdealGas.G() << ";" << IdealGas.U() << ";" << IdealGas.A() << ";" << IdealGas.CP() << ";" << IdealGas.CV() << std::endl;
+      temperature += 0.5;
+    }
+    std::cout << "<Thermodynamics" << std::endl;
+  }
+  
+  //get the density?
+  if (calcdensity > 0) {
+    electron.ElectronicDensity(argv[12]);
+  }
+
+  //get charges and polarisabilities
+  std::vector<size_t> atoms = Mol1.Atoms();
+  std::vector<double> AtmCharge = electron.getQAtoms();
+  std::vector<double> polarizabilities;
+  electron.AtomicPolarizabilities(polarizabilities,AtmCharge);
+  std::cout << ">atom;charge;pol\n";
+  for (size_t idx = 0; idx < atoms.size(); ++idx) {
+    std::cout << atoms[idx] << ";";
+    std::cout << AtmCharge[idx] << ";" << polarizabilities[idx] << "\n";
+  }
+  std::cout << "<atom;charge;pol\n";
+  double polbity = 0.0;
+  electron.TotalPolarizability(polbity,AtmCharge);
+  std::cout << " Total Polarizability          " << polbity << "\n";
+
+  //additional properties
+  matrixE RxData(1,1);
+  if (elecrx > 0) {
+    electron.ReactivityIndices(RxData,false);
+    std::cout << ">Electronic Reactivity indices" << std::endl;
+    RxData.Print(4);
+    std::cout << "<Electronic Reactivity indices" << std::endl;
+  }
+
+  if (orbrx > 0) {
+    electron.ReactivityIndices(RxData,true);
+    std::cout << ">Orbital Reactivity indices" << std::endl;
+    RxData.Print(4);
+    std::cout << "<Orbital Reactivity indices" << std::endl;
+  }
+
+  if (koopman > 0) {std::cout << "Ionization Potential (Koopman): " << electron.IonizationPotential(true)*au2eV << "   eV" << std::endl;}
+  if (ip > 0) {std::cout << "Ionization Potential (Definition): " << electron.IonizationPotential(false)*au2eV << "   eV" << std::endl;}
+  if (ea > 0) {std::cout << "Electron Affinity (Definition): " << electron.ElectronAffinity()*au2eV << "   eV" << std::endl;}
+  
+  if ((electronegativity > 0)||(hardness > 0)) {
+    double chi;
+    double eta;
+    electron.HSABdata(chi,eta);
+    std::cout << "Electronegativity: " << chi*au2eV << "   eV" << std::endl;
+    std::cout << "Hardness: " << eta*au2eV << "   eV" << std::endl;
+  }
+  
+  return 0;
+}

GFN2all_crd.exe

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:51ae3dd4f618a652ac02f5544fdd98a0e539f1935e343ceb143773b5d18c02e0
+size 6962680

README.md

@@ -1,10 +1,10 @@
 ---
-title: Qm Property Calculation
-emoji: 👁
-colorFrom: purple
-colorTo: indigo
+title: QM Properties Of Molecules
+emoji: 📉
+colorFrom: red
+colorTo: gray
 sdk: gradio
-sdk_version: 3.49.0
+sdk_version: 3.48.0
 app_file: app.py
 pinned: false
 license: lgpl-2.1

app.py

@@ -0,0 +1,172 @@
+import gradio as gr
+import py3Dmol
+from Bio.PDB import *
+import numpy as np
+from Bio.PDB import PDBParser
+import pandas as pd
+import os, sys
+#sys.path.append(os.getcwd())
+print('importing...')
+from run_gfn import run_gfn2
+print('done')
+# JavaScript functions
+resid_hover = """function(atom,viewer) {{
+    if(!atom.label) {{
+        atom.label = viewer.addLabel('{0}:'+atom.atom+atom.serial,
+            {{position: atom, backgroundColor: 'mintcream', fontColor:'black'}});
+    }}
+}}"""
+hover_func = """
+function(atom,viewer) {
+    if(!atom.label) {
+        atom.label = viewer.addLabel(atom.interaction,
+            {position: atom, backgroundColor: 'black', fontColor:'white'});
+    }
+}"""
+unhover_func = """
+function(atom,viewer) {
+    if(atom.label) {
+        viewer.removeLabel(atom.label);
+        delete atom.label;
+    }
+}"""
+
+def get_qm_atom_features(gfn2_output, checked_features):
+    qm_atom_features = {}
+    qm_atom_features['atom type'] = gfn2_output["fetchatomicprops"]["atmlist"]
+    for checked_feature in checked_features:
+        if checked_feature == 'Charge':
+            qm_atom_features['Charge'] = gfn2_output["fetchatomicprops"]["charges"]
+        if checked_feature == 'Polarizability':
+            qm_atom_features['Polarizability'] = gfn2_output["fetchatomicprops"]["polarisabilities"]   
+    return qm_atom_features
+
+def get_qm_mol_features(gfn2_output, checked_features):
+    qm_mol_features = {}
+    qm_mol_features['Total Energy'] = gfn2_output["etotal"]
+    qm_mol_features['Total Polarizability'] = gfn2_output["totalpol"]
+  
+    return qm_mol_features
+
+def export_csv(d):
+    d.to_csv("qm_atom_features.csv")
+    return gr.File.update(value="qm_atom_features.csv", visible=True)
+
+def get_basic_visualization(input_f,input_format):
+    view = py3Dmol.view(width=600, height=400)
+    view.setBackgroundColor('white')
+    view.addModel(input_f, input_format)
+    view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': 'turquoise'}}})
+    #view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}},'cartoon': {'color': '#4c4e9e', 'alpha':"0.6"}})
+    view.zoomTo()
+    output = view._make_html().replace("'", '"')
+    print('output of html', output)
+    x = f"""<!DOCTYPE html><html> {output} </html>"""  # do not use ' in this input
+    visualization_html = f"""<iframe  style="width: 100%; height:420px" data-ui="true" 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>"""   
+    return visualization_html
+
+def add_spheres_feature_view(view, feature,xyz, viewnum, sizefactor, spec_color):
+    for i in range(len(feature)):
+        if feature[i]<0:
+            color="red"
+        else: 
+            color=spec_color
+        view.addSphere({'center':{
+        'x':xyz[i][0], 
+        'y':xyz[i][1],
+        'z':xyz[i][2]},
+        'radius':abs(feature[i])*sizefactor,'color':color,'alpha':1.00}, viewer=viewnum) 
+    return view
+
+def add_densities(view, dens, color, viewnum):
+    view.addVolumetricData(dens, "cube", {'isoval': 0.01, 'color': color, 'opacity': 1.0}, viewer=viewnum)
+    return view
+
+
+def get_feature_visualization(input_f,input_format, features, xyz):
+    view = py3Dmol.view(width=600, height=400, viewergrid=(2,2))
+    view.setBackgroundColor('white')
+    view.addModel(input_f, input_format, viewer=(0,0))
+    view.addModel(input_f, input_format, viewer=(0,1))
+    view.addModel(input_f, input_format, viewer=(1,0))
+    view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(0,0))
+    view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(0,1))
+    view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(1,0))
+    #view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}}}, viewer=(0,1))
+    add_spheres_feature_view(view, features["fetchatomicprops"]["charges"], xyz, (0,1), 20, 'blue')
+    add_spheres_feature_view(view, features["fetchatomicprops"]["polarisabilities"], xyz, (1,0), 0.2, 'orange')
+    add_densities(view, open('dummy_struct_dens.cub', "r").read(), 'green', (1,1))
+    #view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}},'cartoon': {'color': '#4c4e9e', 'alpha':"0.6"}})
+    view.zoomTo(viewer=(0,0))
+    output = view._make_html().replace("'", '"')
+    x = f"""<!DOCTYPE html><html> {output} </html>"""  # do not use ' in this input
+    visualization_html = f"""<iframe  style="width: 100%; height:420px" 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>"""   
+    return visualization_html
+
+
+
+def predict(checked_features, input_file, temperature):
+    input_f = open(input_file.name, "r").read()
+    input_format = input_file.name.split('.')[-1]
+    
+    with open('dummy_struct.'+input_format, "w") as oF:
+        oF.write(input_f)
+    
+    input_f2 = open('dummy_struct.'+input_format, "r").read()
+    gfn2_input = ["filename","geom=dummy_struct."+input_format, 'calcdens=1']
+    gfn2_output = run_gfn2(gfn2_input)
+
+    qm_atom_features = get_qm_atom_features(gfn2_output, checked_features)
+    qm_mol_features = get_qm_mol_features(gfn2_output, checked_features)
+    #basic_visualization_html = get_basic_visualization(input_f,input_format)
+    feature_visualization_html = get_feature_visualization(input_f,input_format, gfn2_output, gfn2_output['xyz'])
+
+
+    return feature_visualization_html, pd.DataFrame(qm_atom_features)#, pd.DataFrame(qm_mol_features, index=[0])
+
+with gr.Blocks() as demo:
+    gr.Markdown("# QM property calculation")
+    
+    #text_input = gr.Textbox()
+    #text_output = gr.Textbox()
+    #text_button = gr.Button("Flip")
+    
+    
+
+    with gr.Row():
+        input_file = gr.File(label="Structure file for input")
+        charge = gr.Textbox(placeholder="Total charge", label="Give the total charge of the input molecule. (Default=0)")
+    checked_features = gr.CheckboxGroup(["Charge", "Polarizability", "Koopman IP", "Electronic Density"], label="QM features", info="Which features shall be calculated?")
+    temperature = gr.Slider(value=300,minimum=0, maximum=1000, label="Temperature for Thermodynamics evaluation in K", step=5)
+    #with gr.Row():
+    #    helix = gr.ColorPicker(label="helix")
+    #    sheet = gr.ColorPicker(label="sheet")
+    #    loop = gr.ColorPicker(label="loop")
+    single_btn = gr.Button(label="Run")
+    with gr.Row():
+        basic_html = gr.HTML()
+        gr.HighlightedText(value=[("Positive Charge","blue"),("Negative charge","red"),("Polarizability","orange"), ("Electronic Densities", "Green")], color_map={"red":"red", "blue":"blue", "orange":"orange", "Green":"green"})
+    #with gr.Row():    
+    #    basic_html = gr.HTML()
+    with gr.Row():
+        Dbutton = gr.Button("Download  calculated atom features")
+        csv = gr.File(interactive=False, visible=False)
+    with gr.Row():
+        df_atom_features = gr.Dataframe()
+        #df_mol_features = gr.Dataframe()
+
+    single_btn.click(fn=predict, inputs=[checked_features, input_file, temperature], outputs=[basic_html, df_atom_features])
+    Dbutton.click(export_csv, df_atom_features, csv)
+
+        
+
+
+    demo.launch(server_name="0.0.0.0", server_port=7860)

cyclohexane.xyz

@@ -0,0 +1,20 @@
+18
+
+C         1.1681569 -0.2550550  0.8756595 
+C         1.3484628  0.1965789 -0.5826021 
+C        -0.1630149  0.2550556  1.4507918 
+C        -1.3484630 -0.1965791  0.5826038 
+C        -1.1681567  0.2550548 -0.8756576 
+C         0.1630149 -0.2550556 -1.4507899 
+H        -1.4440620 -1.2992544  0.6239080 
+H        -2.2954881  0.2017985  0.9917659 
+H        -0.2922653 -0.1016823  2.4895446 
+H        -0.1446071  1.3607175  1.5133326 
+H         1.4440620  1.2992544 -0.6239060 
+H         2.2954880 -0.2017985 -0.9917640 
+H         2.0131366  0.1016836  1.4934968 
+H         1.2010813 -1.3607168  0.9319297 
+H         0.2922653  0.1016827 -2.4895433 
+H         0.1446071 -1.3607176 -1.5133316 
+H        -2.0131365 -0.1016835 -1.4934950 
+H        -1.2010813  1.3607168 -0.9319277 

dummy_struct.xyz

@@ -0,0 +1,20 @@
+18
+
+C         1.1681569 -0.2550550  0.8756595 
+C         1.3484628  0.1965789 -0.5826021 
+C        -0.1630149  0.2550556  1.4507918 
+C        -1.3484630 -0.1965791  0.5826038 
+C        -1.1681567  0.2550548 -0.8756576 
+C         0.1630149 -0.2550556 -1.4507899 
+H        -1.4440620 -1.2992544  0.6239080 
+H        -2.2954881  0.2017985  0.9917659 
+H        -0.2922653 -0.1016823  2.4895446 
+H        -0.1446071  1.3607175  1.5133326 
+H         1.4440620  1.2992544 -0.6239060 
+H         2.2954880 -0.2017985 -0.9917640 
+H         2.0131366  0.1016836  1.4934968 
+H         1.2010813 -1.3607168  0.9319297 
+H         0.2922653  0.1016827 -2.4895433 
+H         0.1446071 -1.3607176 -1.5133316 
+H        -2.0131365 -0.1016835 -1.4934950 
+H        -1.2010813  1.3607168 -0.9319277 

geom_cyclohexane.xyz

@@ -0,0 +1,20 @@
+18
+
+C         1.1681569 -0.2550550  0.8756595 
+C         1.3484628  0.1965789 -0.5826021 
+C        -0.1630149  0.2550556  1.4507918 
+C        -1.3484630 -0.1965791  0.5826038 
+C        -1.1681567  0.2550548 -0.8756576 
+C         0.1630149 -0.2550556 -1.4507899 
+H        -1.4440620 -1.2992544  0.6239080 
+H        -2.2954881  0.2017985  0.9917659 
+H        -0.2922653 -0.1016823  2.4895446 
+H        -0.1446071  1.3607175  1.5133326 
+H         1.4440620  1.2992544 -0.6239060 
+H         2.2954880 -0.2017985 -0.9917640 
+H         2.0131366  0.1016836  1.4934968 
+H         1.2010813 -1.3607168  0.9319297 
+H         0.2922653  0.1016827 -2.4895433 
+H         0.1446071 -1.3607176 -1.5133316 
+H        -2.0131365 -0.1016835 -1.4934950 
+H        -1.2010813  1.3607168 -0.9319277 

geometry.xyz

@@ -0,0 +1,20 @@
+18
+
+C         1.1681569 -0.2550550  0.8756595 
+C         1.3484628  0.1965789 -0.5826021 
+C        -0.1630149  0.2550556  1.4507918 
+C        -1.3484630 -0.1965791  0.5826038 
+C        -1.1681567  0.2550548 -0.8756576 
+C         0.1630149 -0.2550556 -1.4507899 
+H        -1.4440620 -1.2992544  0.6239080 
+H        -2.2954881  0.2017985  0.9917659 
+H        -0.2922653 -0.1016823  2.4895446 
+H        -0.1446071  1.3607175  1.5133326 
+H         1.4440620  1.2992544 -0.6239060 
+H         2.2954880 -0.2017985 -0.9917640 
+H         2.0131366  0.1016836  1.4934968 
+H         1.2010813 -1.3607168  0.9319297 
+H         0.2922653  0.1016827 -2.4895433 
+H         0.1446071 -1.3607176 -1.5133316 
+H        -2.0131365 -0.1016835 -1.4934950 
+H        -1.2010813  1.3607168 -0.9319277 

main.py

@@ -0,0 +1,98 @@
+import gradio as gr
+import py3Dmol
+from Bio.PDB import *
+import numpy as np
+from Bio.PDB import PDBParser
+import pandas as pd
+import os, sys
+#sys.path.append(os.getcwd())
+print('importing...')
+from run_gfn import run_gfn2
+print('done')
+# JavaScript functions
+resid_hover = """function(atom,viewer) {{
+    if(!atom.label) {{
+        atom.label = viewer.addLabel('{0}:'+atom.atom+atom.serial,
+            {{position: atom, backgroundColor: 'mintcream', fontColor:'black'}});
+    }}
+}}"""
+hover_func = """
+function(atom,viewer) {
+    if(!atom.label) {
+        atom.label = viewer.addLabel(atom.interaction,
+            {position: atom, backgroundColor: 'black', fontColor:'white'});
+    }
+}"""
+unhover_func = """
+function(atom,viewer) {
+    if(atom.label) {
+        viewer.removeLabel(atom.label);
+        delete atom.label;
+    }
+}"""
+
+
+def predict(input_id, input_file):
+
+
+    input_f = open(input_file.name, "r").read()
+    input_format = input_file.name.split('.')[-1]
+    
+    #with open('geometry.'+input_format, "w") as oF:
+    #    oF.write(input_f)
+    #
+    #input_f2 = open('geometry.'+input_format, "r").read()
+    #print(len(input_f),len(input_f))
+    #for c in range(len(input_f)):
+    #    if input_f[c] != input_f2[c]:
+    #        print(input_f[c], input_f2[c])
+
+    gfn2_output = run_gfn2(["filename","geom=cyclohexane."+input_format])
+    print(gfn2_output)
+    charges = gfn2_output["fetchatomicprops"]["charges"]
+    
+
+
+    view = py3Dmol.view(width=600, height=400)
+    view.setBackgroundColor('white')
+    view.addModel(input_f, input_format)
+    view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': 'turquoise'}}})
+    #view.setStyle({'stick': {'colorscheme': {'prop': 'resi', 'C': '#cccccc'}},'cartoon': {'color': '#4c4e9e', 'alpha':"0.6"}})
+    view.zoomTo()
+
+    output = view._make_html().replace("'", '"')
+    print("got a view")
+    x = f"""<!DOCTYPE html><html> {output} </html>"""  # do not use ' in this input
+    return f"""<iframe  style="width: 100%; height:420px" 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>"""   
+
+print('run 1')
+callback = gr.CSVLogger()
+with gr.Blocks() as demo:
+    gr.Markdown("# Protein Adaptability Prediction")
+    
+    #text_input = gr.Textbox()
+    #text_output = gr.Textbox()
+    #text_button = gr.Button("Flip")
+    inp = gr.Textbox(placeholder="PDB Code or upload file below", label="Input structure")
+    pdb_file = gr.File(label="PDB File Upload")
+    #with gr.Row():
+    #    helix = gr.ColorPicker(label="helix")
+    #    sheet = gr.ColorPicker(label="sheet")
+    #    loop = gr.ColorPicker(label="loop")
+    single_btn = gr.Button(label="Run")
+    with gr.Row():
+        html = gr.HTML()
+    with gr.Row():
+        dataframe = gr.Dataframe()
+            
+    single_btn.click(fn=predict, inputs=[inp, pdb_file], outputs=[html])
+
+#out_d = run_gfn2("geom=cyclohexane.xyz")
+
+
+#demo.launch(debug=True)
+demo.launch(server_name="0.0.0.0", server_port=7860)

qm_atom_features.csv

@@ -0,0 +1,19 @@
+,atom type
+0,6
+1,6
+2,6
+3,6
+4,6
+5,6
+6,1
+7,1
+8,1
+9,1
+10,1
+11,1
+12,1
+13,1
+14,1
+15,1
+16,1
+17,1

requirements.txt

@@ -0,0 +1,2 @@
+gradio
+numpy

requirements_full.txt

@@ -0,0 +1,6 @@
+gradio
+requests
+py3Dmol
+biopython
+pandas
+numpy

runGFN2.py

@@ -0,0 +1,318 @@
+import os
+import sys
+import subprocess
+
+
+def run_gfn2(argv):
+    #arguments and give them default values
+    exe = "./GFN2all.exe"
+    geometryfile = ""
+    charge = "0"
+    Telec = "300"
+    solvation = "0"
+    solventname = "gas"
+    optimisegeometry = "0"
+    newgeometryfile = ""
+    thermo = "0"
+    energythresh = "1.0e-6"
+    gradientthresh = "1.0e-3"
+    calcdensity = "0"
+    densityfile = ""
+    electronicreactivity = "0"
+    orbitalreactivity = "0"
+    KoopmanIP = "0"
+    IP = "0"
+    EA = "0"
+    electronegativity = "0"
+    hardness = "0"
+
+    #parse whatever we get
+    for iarg in range(1,len(argv)):
+        argument = argv[iarg].lower().replace("=","")
+        if argument.startswith("geometry") or argument.startswith("geom"):
+            geometryfile = argument.replace("geometry","").replace("geom","")
+        elif argument.startswith("charge") or argument.startswith("chrg"):
+            charge = argument.replace("charge","").replace("chrg","")
+        elif argument.startswith("telec") or argument.startswith("telectronic"):
+            Telec = argument.replace("telectronic","").replace("telec","")
+        elif argument.startswith("usesolv") or argument.startswith("usesolvent"):
+            solvation = argument.replace("usesolvent","").replace("usesolv","")
+        elif argument.startswith("solvent") or argument.startswith("solventname"):
+            solventname = argument.replace("solventname","").replace("solvent","")
+        elif argument.startswith("optg") or argument.startswith("optimisegeom") or argument.startswith("optimizegeom") or argument.startswith("optimisegeometry") or argument.startswith("optimizegeometry"):
+            optimisegeometry = argument.replace("optg","").replace("optimise","").replace("optimize","").replace("geometry","").replace("geom","")
+        elif argument.startswith("newgeom") or argument.startswith("newgeomfile") or argument.startswith("newgeometryfile"):
+            newgeometryfile = argument.replace("newgeometryfile","").replace("newgeomfile","").replace("newgeom","")
+        elif argument.startswith("dothermo") or argument.startswith("thermo") or argument.startswith("thermodynamics"):
+            thermo = argument.replace("dothermo","").replace("thermodynamics","").replace("thermo","")
+        elif argument.startswith("ethresh") or argument.startswith("energythresh") or argument.startswith("energythreshold"):
+            energythresh = argument.replace("ethresh","").replace("energythreshold","").replace("energythresh","")
+        elif argument.startswith("gthresh") or argument.startswith("gradthresh") or argument.startswith("gradientthreshold"):
+            gradientthresh = argument.replace("gthresh","").replace("gradientthreshold","").replace("gradthresh","")
+        elif argument.startswith("calcdens") or argument.startswith("calcdensity") or argument.startswith("calculatedensity"):
+            calcdensity = argument.replace("calcdensity","").replace("calcdens","").replace("calculatedensity","")
+        elif argument.startswith("densityfile") or argument.startswith("densfile"):
+            calcdensity = argument.replace("densityfile","").replace("densfile","")
+        elif argument.startswith("ereact") or argument.startswith("electronicreactivity"):
+            electronicreactivity = argument.replace("ereact","").replace("electronicreactivity","")
+        elif argument.startswith("oreact") or argument.startswith("orbreact") or argument.startswith("orbitalreactivity"):
+            orbitalreactivity = argument.replace("oreact","").replace("orbreact","").replace("orbitalreactivity","")
+        elif argument.startswith("koopman") or argument.startswith("ipkoopman") or argument.startswith("koopmanip"):
+            KoopmanIP = argument.replace("ip","").replace("koopman","")
+        elif argument.startswith("ip") or argument.startswith("ionizationpotential") or argument.startswith("ionisationpotential") or argument.startswith("ipot"):
+            IP = argument.replace("ip","").replace("ionizationpotential","").replace("ionisationpotential","").replace("ipot","")
+        elif argument.startswith("ea") or argument.startswith("electronaffinity") or argument.startswith("eaffin"):
+            EA = argument.replace("ea","").replace("electronaffinity","").replace("eaffin","")
+        elif argument.startswith("electronegativity"):
+            electronegativity = argument.replace("electronegativity","")
+        elif argument.startswith("hardness"):
+            hardness = argument.replace("hardness","")
+
+    #ensure consistency
+    if geometryfile + "blahblah" == "blahblah":
+        print("ERROR: geometry file is needed")
+        sys.exit()
+
+    newgeometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","")
+    if (newgeometryfile + "blahblah" == "blahblah") and (optimisegeometry == "1"): 
+        newgeometryfile = geometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","") + "_opt"
+
+    if (solvation == "1"):
+        if (solventname == "water") or (solventname == "h2o") or (solventname == "o"): solventname = "water"
+        elif (solventname == "acetone") or (solventname == "cc(o)c"): solventname = "acetone"
+        elif (solventname == "acetonitrile") or (solventname == "ch3cn") or (solventname == "ccn"): solventname = "acetonitrile"
+        elif (solventname == "aniline") or (solventname == "phnh2") or (solventname == "nc1ccccc1") or (solventname == "c1ccc(cc1)n"): solventname = "aniline"
+        elif (solventname == "benzaldehyde") or (solventname == "phcho") or (solventname == "occ1ccccc1") or (solventname == "c1ccc(cc1)co"): solventname = "benzaldehyde"
+        elif (solventname == "benzene") or (solventname == "c6h6") or (solventname == "phh") or (solventname == "c1ccccc1"): solventname = "benzene"
+        elif (solventname == "dichloromethane") or (solventname == "ch2cl2") or (solventname == "c(cl)cl") or (solventname == "c(cl)(cl)"): solventname = "dichloromethane"
+        elif (solventname == "chloroform") or (solventname == "chcl3") or (solventname == "c(cl)(cl)cl") or (solventname == "c(cl)(cl)(cl)"): solventname = "chloroform"
+        elif (solventname == "carbon disulfide") or (solventname == "carbondisulfide") or (solventname == "cs2") or (solventname == "scs"): solventname = "carbon disulfide"
+        elif (solventname == "dioxane") or (solventname == "o1ccocc1"): solventname = "dioxane"
+        elif (solventname == "dmf") or (solventname == "dimethylformamide") or (solventname == "cn(c)co"): solventname = "dmf"
+        elif (solventname == "dmso") or (solventname == "dimethylsulfoxide") or (solventname == "cs(o)c") or (solventname == "cs(c)o"): solventname = "dmso"
+        elif (solventname == "ethanol") or (solventname == "etoh") or (solventname == "ch3ch2oh") or (solventname == "cco"): solventname = "ethanol"
+        elif (solventname == "diethyl ether") or (solventname == "etoet") or (solventname == "ccocc") or (solventname == "ch3ch2och2ch3"): solventname = "diethyl ether"
+        elif (solventname == "ethyl acetate") or (solventname == "acoet") or (solventname == "etoac") or (solventname == "ccoc(o)c"): solventname = "ethyl acetate"
+        elif (solventname == "furan") or (solventname == "furane"): solventname = "furane"
+        elif (solventname == "hexadecane") or (solventname == "c16"): solventname = "hexadecane"
+        elif (solventname == "hexane") or (solventname == "cccccc") or (solventname == "c6"): solventname = "hexane"
+        elif (solventname == "methanol") or (solventname == "meoh") or (solventname == "co") or (solventname == "ch3oh"): solventname = "methanol"
+        elif (solventname == "nitromethane") or (solventname == "meno2") or (solventname == "ch3no2") or (solventname == "cn(o)o"): solventname = "nitromethane"
+        elif (solventname == "octanol") or (solventname == "cccccccc") or (solventname == "c8"): solventname = "octanol"
+        elif (solventname == "phenol") or (solventname == "phoh") or (solventname == "oc1ccccc1") or (solventname == "c1ccc(cc1)o"): solventname = "phenol"
+        elif (solventname == "thf") or (solventname == "tetrahydrofuran"): solventname = "thf"
+        elif (solventname == "toluene") or (solventname == "phme") or (solventname == "cc1ccccc1"): solventname = "toluene"
+        elif (solventname == "octanol wet") or (solventname == "octanolwet") or (solventname == "wet octanol") or (solventname == "wetoctanol"): solventname = "octanol wet"
+
+    if (densityfile + "blahblah" == "blahblah") and (calcdensity == "1"): 
+        densityfile = geometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","") + "_dens"
+
+    def RunQMOptg():
+        proc = subprocess.Popen([exe,geometryfile,charge,Telec,solvation,solventname,optimisegeometry,newgeometryfile,thermo,energythresh,gradientthresh,calcdensity,densityfile,electronicreactivity,orbitalreactivity,KoopmanIP,IP,EA,electronegativity,hardness], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        out,err = proc.communicate()
+        return out,err
+    out,err = RunQMOptg()
+
+    if err.decode("utf-8") + "blahblah" != "blahblah": print("error:",err)
+    else:
+        #process data from output file
+        outputfile = out.decode("utf-8").split("\n")
+        print(out.decode("utf-8"))
+        etotal = 0.0
+        gsolvation = 0.0
+        fetchvibr = False
+        vibrations = []
+        fetchthermo = False
+        temperature = []
+        entropy = []
+        enthalpy = []
+        gibbs = []
+        internalenergy = []
+        helmholtz = []
+        cp = []
+        cv = []
+        fetchatomicprops = False
+        atmlist = []
+        charges = []
+        polarisabilities = []
+        totalpol = 0.0
+        fetchelecreact = False
+        fetchorbreact = False
+        eFukuiElctrophilie = []
+        eFukuiNucleophilie = []
+        eFukuiRadical = []
+        eSoftnessElctrophilie = []
+        eSoftnessNucleophilie = []
+        eSoftnessRadical = []
+        oFukuiElctrophilie = []
+        oFukuiNucleophilie = []
+        oFukuiRadical = []
+        oSoftnessElctrophilie = []
+        oSoftnessNucleophilie = []
+        oSoftnessRadical = []
+        ipkoopman = 0.0
+        ip = 0.0
+        ea = 0.0
+        eneg = 0.0
+        hard = 0.0
+        out_dict = {}
+        for iline in range(len(outputfile)):
+            line = outputfile[iline]
+            #check whether array data is available
+            if line.startswith(">all vibrational frequencies"): 
+                fetchvibr = True
+                continue
+            elif line.startswith("<all vibrational frequencies"): 
+                fetchvibr = False
+                continue
+            elif line.startswith(">Thermodynamics"): 
+                fetchthermo = True
+                continue
+            elif line.startswith("<Thermodynamics"): 
+                fetchthermo = False
+                continue
+            elif line.startswith(">atom;charge;pol"): 
+                fetchatomicprops = True
+                continue
+            elif line.startswith("<atom;charge;pol"): 
+                fetchatomicprops = False
+                continue
+            elif line.startswith(">Electronic Reactivity indices"): 
+                fetchelecreact = True
+                continue
+            elif line.startswith("<Electronic Reactivity indices"): 
+                fetchelecreact = False
+                continue
+            elif line.startswith(">Orbital Reactivity indices"): 
+                fetchorbreact = True
+                continue
+            elif line.startswith("<Orbital Reactivity indices"): 
+                fetchorbreact = False
+                continue
+            #fetch data
+            if line.startswith("Total Energy = "): 
+                etotal = float(line.replace("Total Energy = ",""))
+                out_dict['etotal']=etotal
+            elif line.startswith("Gsolv = "): 
+                gsolvation = float(line.replace("Gsolv = ",""))
+                out_dict['gsolvation']=gsolvation
+            elif "Total Polarizability" in line: 
+                totalpol = float(line.replace("Total Polarizability","").replace(" ",""))
+                out_dict['totalpol']=totalpol                
+            elif line.startswith("Ionization Potential (Koopman):"): 
+                ipkoopman = float(line.replace("Ionization Potential (Koopman):","").replace("   eV",""))
+                out_dict['ipkoopman']=ipkoopman
+            elif line.startswith("Ionization Potential (Definition): "): 
+                ip = float(line.replace("Ionization Potential (Definition): ","").replace("   eV",""))
+                out_dict['ip']=ip
+            elif line.startswith("Electron Affinity (Definition): "): 
+                ea = float(line.replace("Electron Affinity (Definition): ","").replace("   eV",""))
+                out_dict['ea']=ea
+            elif line.startswith("Electronegativity: "): 
+                eneg = float(line.replace("Electronegativity: ","").replace("   eV",""))
+                out_dict['eneg']=eneg
+            elif line.startswith("Hardness: "): 
+                hard = float(line.replace("Hardness: ","").replace("   eV",""))
+                out_dict['hard']=hard
+            elif fetchvibr: 
+                vibrations.append(float(line))
+                out_dict['vibrations']=vibrations
+            elif fetchthermo: 
+                data = line.split(";")
+                temperature.append(float(data[0]))
+                entropy.append(float(data[1]))
+                enthalpy.append(float(data[2]))
+                gibbs.append(float(data[3]))
+                internalenergy.append(float(data[4]))
+                helmholtz.append(float(data[5]))
+                cp.append(float(data[6]))
+                cv.append(float(data[7]))
+                out_dict['fetchthermo']={"temperature":temperature,
+                "entropy":entropy,
+                "enthalpy":enthalpy,
+                "gibbs":gibbs,
+                "internalenergy":internalenergy,
+                "helmholtz":helmholtz,
+                "cp":cp,
+                "cv":cv
+                }
+            elif fetchatomicprops:
+                data = line.split(";")
+                atmlist.append(int(data[0]))
+                charges.append(float(data[1]))
+                polarisabilities.append(float(data[2]))
+                out_dict['fetchatomicprops']={"atmlist":atmlist,
+                "charges":charges,
+                "polarisabilities":polarisabilities
+                }
+            elif fetchelecreact:
+                data = line.strip().rstrip().replace("  "," ").split(" ")
+                eFukuiElctrophilie.append(float(data[0]))
+                eFukuiNucleophilie.append(float(data[1]))
+                eFukuiRadical.append(float(data[2]))
+                eSoftnessElctrophilie.append(float(data[3]))
+                eSoftnessNucleophilie.append(float(data[4]))
+                eSoftnessRadical.append(float(data[5]))
+                out_dict['fetchelecreact']=fetchelecreact
+            elif fetchorbreact:
+                data = line.strip().rstrip().replace("  "," ").split(" ")
+                oFukuiElctrophilie.append(float(data[0]))
+                oFukuiNucleophilie.append(float(data[1]))
+                oFukuiRadical.append(float(data[2]))
+                oSoftnessElctrophilie.append(float(data[3]))
+                oSoftnessNucleophilie.append(float(data[4]))
+                oSoftnessRadical.append(float(data[5]))
+                out_dict['fetchorbreact']=fetchorbreact
+        print(argv)
+        return out_dict
+        #data collected; if there is a whether, then variable is boolean
+        #geometryfile               the geometry of the molecule
+        #charge                     the total charge
+        #solventname                the name of the solvent
+        #optimisegeometry           whether geometry was optimised
+        #newgeometryfile            the name of the file containing optimised geometry
+        #thermo                     whether thermodynamics was done
+        #calcdensity                whether the electronic density was calculated
+        #densityfile                the name of the file containing electronic density
+        #electronicreactivity       whether electronic reactivity data was calculated
+        #orbitalreactivity          whether orbital reacticity data was calculated
+        #KoopmanIP                  whether the Koopman ionisation potential was calculated
+        #IP                         whether the ionisation potential was calculated
+        #EA                         whether electron affinity was calculated
+        #electronegativity          whether electronegativity was calculated
+        #hardness                   whether hardness was calculated
+        #etotal                     the molecule's total energy in Hartree
+        #gsolvation                 solvation Gibbs free energy in Hartree
+        #vibrations                 array containing vibrational frequencies in cm-1
+        #temperature                array containing temperatures
+        #entropy                    array containing entropies
+        #enthalpy                   array containing enthalpies
+        #gibbs                      array containing Gibbs free energies
+        #internalenergy             array containing internal energies
+        #helmholtz                  array containing Helmholts energies
+        #cp                         array containing heat capacities at constant pressure
+        #cv                         array containing heat capacities at constant volume
+        #atmlist                    list of atoms
+        #charges                    partial charges in electrons
+        #polarisabilities           atomic polarisabilities in bohr
+        #totalpol                   total polarisability in cubic bohr
+        #eFukuiElctrophilie         Fukui index for electrophilicity (calculated from charges)
+        #eFukuiNucleophilie         Fukui index for nucleophilicity (calculated from charges)
+        #eFukuiRadical              Fukui index for radical reactivity (calculated from charges)
+        #eSoftnessElctrophilie      softness index for electrophilicity (calculated from charges)
+        #eSoftnessNucleophilie      softness index for nucleophilicity (calculated from charges)
+        #eSoftnessRadical           softness index for radical reactivity (calculated from charges)
+        #oFukuiElctrophilie         Fukui index for electrophilicity (calculated from frontier orbitals)
+        #oFukuiNucleophilie         Fukui index for nucleophilicity (calculated from frontier orbitals)
+        #oFukuiRadical              Fukui index for radical reactivity (calculated from frontier orbitals)
+        #oSoftnessElctrophilie      softness index for electrophilicity (calculated from frontier orbitals)
+        #oSoftnessNucleophilie      softness index for nucleophilicity (calculated from frontier orbitals)
+        #oSoftnessRadical           softness index for radical reactivity (calculated from frontier orbitals)
+        #ipkoopman                  Koopman ionisation potential in eV
+        #ip                         ionisation potential in eV
+        #ea                         electron affinity in eV
+        #eneg                       electronegativity in eV
+        #hard                       hardness in eV
+out_dict = run_gfn2(sys.argv)
+
+print(out_dict)

runGFN2_crd.txt

@@ -0,0 +1,299 @@
+import os
+import sys
+import subprocess
+
+#arguments and give them default values
+exe = "./GFN2all.exe"
+geometryfile = ""
+charge = "0"
+Telec = "300"
+solvation = "0"
+solventname = "gas"
+optimisegeometry = "0"
+newgeometryfile = ""
+thermo = "0"
+energythresh = "1.0e-6"
+gradientthresh = "1.0e-3"
+calcdensity = "0"
+densityfile = ""
+electronicreactivity = "0"
+orbitalreactivity = "0"
+KoopmanIP = "0"
+IP = "0"
+EA = "0"
+electronegativity = "0"
+hardness = "0"
+
+#parse whatever we get
+for iarg in range(1,len(sys.argv)):
+    argument = sys.argv[iarg].lower().replace("=","")
+    if argument.startswith("geometry") or argument.startswith("geom"):
+        geometryfile = argument.replace("geometry","").replace("geom","")
+    elif argument.startswith("charge") or argument.startswith("chrg"):
+        charge = argument.replace("charge","").replace("chrg","")
+    elif argument.startswith("telec") or argument.startswith("telectronic"):
+        Telec = argument.replace("telectronic","").replace("telec","")
+    elif argument.startswith("usesolv") or argument.startswith("usesolvent"):
+        solvation = argument.replace("usesolvent","").replace("usesolv","")
+    elif argument.startswith("solvent") or argument.startswith("solventname"):
+        solventname = argument.replace("solventname","").replace("solvent","")
+    elif argument.startswith("optg") or argument.startswith("optimisegeom") or argument.startswith("optimizegeom") or argument.startswith("optimisegeometry") or argument.startswith("optimizegeometry"):
+        optimisegeometry = argument.replace("optg","").replace("optimise","").replace("optimize","").replace("geometry","").replace("geom","")
+    elif argument.startswith("newgeom") or argument.startswith("newgeomfile") or argument.startswith("newgeometryfile"):
+        newgeometryfile = argument.replace("newgeometryfile","").replace("newgeomfile","").replace("newgeom","")
+    elif argument.startswith("dothermo") or argument.startswith("thermo") or argument.startswith("thermodynamics"):
+        thermo = argument.replace("dothermo","").replace("thermodynamics","").replace("thermo","")
+    elif argument.startswith("ethresh") or argument.startswith("energythresh") or argument.startswith("energythreshold"):
+        energythresh = argument.replace("ethresh","").replace("energythreshold","").replace("energythresh","")
+    elif argument.startswith("gthresh") or argument.startswith("gradthresh") or argument.startswith("gradientthreshold"):
+        gradientthresh = argument.replace("gthresh","").replace("gradientthreshold","").replace("gradthresh","")
+    elif argument.startswith("calcdens") or argument.startswith("calcdensity") or argument.startswith("calculatedensity"):
+        calcdensity = argument.replace("calcdensity","").replace("calcdens","").replace("calculatedensity","")
+    elif argument.startswith("densityfile") or argument.startswith("densfile"):
+        calcdensity = argument.replace("densityfile","").replace("densfile","")
+    elif argument.startswith("ereact") or argument.startswith("electronicreactivity"):
+        electronicreactivity = argument.replace("ereact","").replace("electronicreactivity","")
+    elif argument.startswith("oreact") or argument.startswith("orbreact") or argument.startswith("orbitalreactivity"):
+        orbitalreactivity = argument.replace("oreact","").replace("orbreact","").replace("orbitalreactivity","")
+    elif argument.startswith("koopman") or argument.startswith("ipkoopman") or argument.startswith("koopmanip"):
+        KoopmanIP = argument.replace("ip","").replace("koopman","")
+    elif argument.startswith("ip") or argument.startswith("ionizationpotential") or argument.startswith("ionisationpotential") or argument.startswith("ipot"):
+        IP = argument.replace("ip","").replace("ionizationpotential","").replace("ionisationpotential","").replace("ipot","")
+    elif argument.startswith("ea") or argument.startswith("electronaffinity") or argument.startswith("eaffin"):
+        EA = argument.replace("ea","").replace("electronaffinity","").replace("eaffin","")
+    elif argument.startswith("electronegativity"):
+        electronegativity = argument.replace("electronegativity","")
+    elif argument.startswith("hardness"):
+        hardness = argument.replace("hardness","")
+
+#ensure consistency
+if geometryfile + "blahblah" == "blahblah":
+    print("ERROR: geometry file is needed")
+    sys.exit()
+
+newgeometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","")
+if (newgeometryfile + "blahblah" == "blahblah") and (optimisegeometry == "1"): newgeometryfile = geometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","") + "_opt"
+
+if (solvation == "1"):
+    if (solventname == "water") or (solventname == "h2o") or (solventname == "o"): solventname = "water"
+    elif (solventname == "acetone") or (solventname == "cc(o)c"): solventname = "acetone"
+    elif (solventname == "acetonitrile") or (solventname == "ch3cn") or (solventname == "ccn"): solventname = "acetonitrile"
+    elif (solventname == "aniline") or (solventname == "phnh2") or (solventname == "nc1ccccc1") or (solventname == "c1ccc(cc1)n"): solventname = "aniline"
+    elif (solventname == "benzaldehyde") or (solventname == "phcho") or (solventname == "occ1ccccc1") or (solventname == "c1ccc(cc1)co"): solventname = "benzaldehyde"
+    elif (solventname == "benzene") or (solventname == "c6h6") or (solventname == "phh") or (solventname == "c1ccccc1"): solventname = "benzene"
+    elif (solventname == "dichloromethane") or (solventname == "ch2cl2") or (solventname == "c(cl)cl") or (solventname == "c(cl)(cl)"): solventname = "dichloromethane"
+    elif (solventname == "chloroform") or (solventname == "chcl3") or (solventname == "c(cl)(cl)cl") or (solventname == "c(cl)(cl)(cl)"): solventname = "chloroform"
+    elif (solventname == "carbon disulfide") or (solventname == "carbondisulfide") or (solventname == "cs2") or (solventname == "scs"): solventname = "carbon disulfide"
+    elif (solventname == "dioxane") or (solventname == "o1ccocc1"): solventname = "dioxane"
+    elif (solventname == "dmf") or (solventname == "dimethylformamide") or (solventname == "cn(c)co"): solventname = "dmf"
+    elif (solventname == "dmso") or (solventname == "dimethylsulfoxide") or (solventname == "cs(o)c") or (solventname == "cs(c)o"): solventname = "dmso"
+    elif (solventname == "ethanol") or (solventname == "etoh") or (solventname == "ch3ch2oh") or (solventname == "cco"): solventname = "ethanol"
+    elif (solventname == "diethyl ether") or (solventname == "etoet") or (solventname == "ccocc") or (solventname == "ch3ch2och2ch3"): solventname = "diethyl ether"
+    elif (solventname == "ethyl acetate") or (solventname == "acoet") or (solventname == "etoac") or (solventname == "ccoc(o)c"): solventname = "ethyl acetate"
+    elif (solventname == "furan") or (solventname == "furane"): solventname = "furane"
+    elif (solventname == "hexadecane") or (solventname == "c16"): solventname = "hexadecane"
+    elif (solventname == "hexane") or (solventname == "cccccc") or (solventname == "c6"): solventname = "hexane"
+    elif (solventname == "methanol") or (solventname == "meoh") or (solventname == "co") or (solventname == "ch3oh"): solventname = "methanol"
+    elif (solventname == "nitromethane") or (solventname == "meno2") or (solventname == "ch3no2") or (solventname == "cn(o)o"): solventname = "nitromethane"
+    elif (solventname == "octanol") or (solventname == "cccccccc") or (solventname == "c8"): solventname = "octanol"
+    elif (solventname == "phenol") or (solventname == "phoh") or (solventname == "oc1ccccc1") or (solventname == "c1ccc(cc1)o"): solventname = "phenol"
+    elif (solventname == "thf") or (solventname == "tetrahydrofuran"): solventname = "thf"
+    elif (solventname == "toluene") or (solventname == "phme") or (solventname == "cc1ccccc1"): solventname = "toluene"
+    elif (solventname == "octanol wet") or (solventname == "octanolwet") or (solventname == "wet octanol") or (solventname == "wetoctanol"): solventname = "octanol wet"
+
+if (densityfile + "blahblah" == "blahblah") and (calcdensity == "1"): densityfile = geometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","") + "_dens"
+
+def RunQMOptg():
+    proc = subprocess.Popen([exe,geometryfile,charge,Telec,solvation,solventname,optimisegeometry,newgeometryfile,thermo,energythresh,gradientthresh,calcdensity,densityfile,electronicreactivity,orbitalreactivity,KoopmanIP,IP,EA,electronegativity,hardness], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    out,err = proc.communicate()
+    return out,err
+out,err = RunQMOptg()
+
+def ReadXYZ(filename):
+    #function reading xyz format
+    rfile = open(filename,"r")
+    rfilelines = rfile.readlines()
+    natoms = int(rfilelines[0])
+    geometry = []
+    for iatm in range(natoms):
+        line = rfilelines[iatm + 2]
+        cleanline = line
+        for idx in range(250):
+            line = cleanline.replace("  "," ")
+            cleanline = line
+            if not ("  " in cleanline): break
+        data = cleanline.split(" ")
+        aux = [float(data[1]),float(data[2]),float(data[3])]
+        geometry.append(aux)
+    return geometry
+
+if err.decode("utf-8") + "blahblah" != "blahblah": print("error:",err)
+else:
+    #process data from output file
+    outputfile = out.decode("utf-8").split("\n")
+    print(out.decode("utf-8"))
+    etotal = 0.0
+    gsolvation = 0.0
+    fetchvibr = False
+    vibrations = []
+    fetchthermo = False
+    temperature = []
+    entropy = []
+    enthalpy = []
+    gibbs = []
+    internalenergy = []
+    helmholtz = []
+    cp = []
+    cv = []
+    fetchatomicprops = False
+    atmlist = []
+    charges = []
+    polarisabilities = []
+    totalpol = 0.0
+    fetchelecreact = False
+    fetchorbreact = False
+    eFukuiElctrophilie = []
+    eFukuiNucleophilie = []
+    eFukuiRadical = []
+    eSoftnessElctrophilie = []
+    eSoftnessNucleophilie = []
+    eSoftnessRadical = []
+    oFukuiElctrophilie = []
+    oFukuiNucleophilie = []
+    oFukuiRadical = []
+    oSoftnessElctrophilie = []
+    oSoftnessNucleophilie = []
+    oSoftnessRadical = []
+    ipkoopman = 0.0
+    geometry = []
+    ip = 0.0
+    ea = 0.0
+    eneg = 0.0
+    hard = 0.0
+    for iline in range(len(outputfile)):
+        line = outputfile[iline]
+        #check whether array data is available
+        if line.startswith(">all vibrational frequencies"): 
+            fetchvibr = True
+            continue
+        elif line.startswith("<all vibrational frequencies"): 
+            fetchvibr = False
+            continue
+        elif line.startswith(">Thermodynamics"): 
+            fetchthermo = True
+            continue
+        elif line.startswith("<Thermodynamics"): 
+            fetchthermo = False
+            continue
+        elif line.startswith(">atom;charge;pol"): 
+            fetchatomicprops = True
+            continue
+        elif line.startswith("<atom;charge;pol"): 
+            fetchatomicprops = False
+            continue
+        elif line.startswith(">Electronic Reactivity indices"): 
+            fetchelecreact = True
+            continue
+        elif line.startswith("<Electronic Reactivity indices"): 
+            fetchelecreact = False
+            continue
+        elif line.startswith(">Orbital Reactivity indices"): 
+            fetchorbreact = True
+            continue
+        elif line.startswith("<Orbital Reactivity indices"): 
+            fetchorbreact = False
+            continue
+        #fetch data
+        if line.startswith("Total Energy = "): etotal = float(line.replace("Total Energy = ",""))
+        elif line.startswith("Gsolv = "): gsolvation = float(line.replace("Gsolv = ",""))
+        elif "Total Polarizability" in line: totalpol = float(line.replace("Total Polarizability","").replace(" ",""))
+        elif line.startswith("Ionization Potential (Koopman):"): ipkoopman = float(line.replace("Ionization Potential (Koopman):","").replace("   eV",""))
+        elif line.startswith("Ionization Potential (Definition): "): ip = float(line.replace("Ionization Potential (Definition): ","").replace("   eV",""))
+        elif line.startswith("Electron Affinity (Definition): "): ea = float(line.replace("Electron Affinity (Definition): ","").replace("   eV",""))
+        elif line.startswith("Electronegativity: "): eneg = float(line.replace("Electronegativity: ","").replace("   eV",""))
+        elif line.startswith("Hardness: "): hard = float(line.replace("Hardness: ","").replace("   eV",""))
+        elif fetchvibr: vibrations.append(float(line))
+        elif fetchthermo: 
+            data = line.split(";")
+            temperature.append(float(data[0]))
+            entropy.append(float(data[1]))
+            enthalpy.append(float(data[2]))
+            gibbs.append(float(data[3]))
+            internalenergy.append(float(data[4]))
+            helmholtz.append(float(data[5]))
+            cp.append(float(data[6]))
+            cv.append(float(data[7]))
+        elif fetchatomicprops:
+            data = line.split(";")
+            atmlist.append(int(data[0]))
+            charges.append(float(data[1]))
+            polarisabilities.append(float(data[2]))
+        elif fetchelecreact:
+            data = line.strip().rstrip().replace("  "," ").split(" ")
+            eFukuiElctrophilie.append(float(data[0]))
+            eFukuiNucleophilie.append(float(data[1]))
+            eFukuiRadical.append(float(data[2]))
+            eSoftnessElctrophilie.append(float(data[3]))
+            eSoftnessNucleophilie.append(float(data[4]))
+            eSoftnessRadical.append(float(data[5]))
+        elif fetchorbreact:
+            data = line.strip().rstrip().replace("  "," ").split(" ")
+            oFukuiElctrophilie.append(float(data[0]))
+            oFukuiNucleophilie.append(float(data[1]))
+            oFukuiRadical.append(float(data[2]))
+            oSoftnessElctrophilie.append(float(data[3]))
+            oSoftnessNucleophilie.append(float(data[4]))
+            oSoftnessRadical.append(float(data[5]))
+    if (optimisegeometry == "0"): newgeometryfile = geometryfile
+    if not newgeometryfile.endswith(".xyz"): newgeometryfile += ".xyz"
+    geometry = ReadXYZ(newgeometryfile)
+    print(geometry)
+    #data collected; if there is a whether, then variable is boolean
+    #geometryfile               the geometry of the molecule
+    #charge                     the total charge
+    #solventname                the name of the solvent
+    #optimisegeometry           whether geometry was optimised
+    #newgeometryfile            the name of the file containing optimised geometry
+    #geometry                   contains the best geometry (either the input one if not optg takes place, or the optimized geometry if optg took place)
+    #thermo                     whether thermodynamics was done
+    #calcdensity                whether the electronic density was calculated
+    #densityfile                the name of the file containing electronic density
+    #electronicreactivity       whether electronic reactivity data was calculated
+    #orbitalreactivity          whether orbital reacticity data was calculated
+    #KoopmanIP                  whether the Koopman ionisation potential was calculated
+    #IP                         whether the ionisation potential was calculated
+    #EA                         whether electron affinity was calculated
+    #electronegativity          whether electronegativity was calculated
+    #hardness                   whether hardness was calculated
+    #etotal                     the molecule's total energy in Hartree
+    #gsolvation                 solvation Gibbs free energy in Hartree
+    #vibrations                 array containing vibrational frequencies in cm-1
+    #temperature                array containing temperatures
+    #entropy                    array containing entropies
+    #enthalpy                   array containing enthalpies
+    #gibbs                      array containing Gibbs free energies
+    #internalenergy             array containing internal energies
+    #helmholtz                  array containing Helmholts energies
+    #cp                         array containing heat capacities at constant pressure
+    #cv                         array containing heat capacities at constant volume
+    #atmlist                    list of atoms
+    #charges                    partial charges in electrons
+    #polarisabilities           atomic polarisabilities in bohr
+    #totalpol                   total polarisability in cubic bohr
+    #eFukuiElctrophilie         Fukui index for electrophilicity (calculated from charges)
+    #eFukuiNucleophilie         Fukui index for nucleophilicity (calculated from charges)
+    #eFukuiRadical              Fukui index for radical reactivity (calculated from charges)
+    #eSoftnessElctrophilie      softness index for electrophilicity (calculated from charges)
+    #eSoftnessNucleophilie      softness index for nucleophilicity (calculated from charges)
+    #eSoftnessRadical           softness index for radical reactivity (calculated from charges)
+    #oFukuiElctrophilie         Fukui index for electrophilicity (calculated from frontier orbitals)
+    #oFukuiNucleophilie         Fukui index for nucleophilicity (calculated from frontier orbitals)
+    #oFukuiRadical              Fukui index for radical reactivity (calculated from frontier orbitals)
+    #oSoftnessElctrophilie      softness index for electrophilicity (calculated from frontier orbitals)
+    #oSoftnessNucleophilie      softness index for nucleophilicity (calculated from frontier orbitals)
+    #oSoftnessRadical           softness index for radical reactivity (calculated from frontier orbitals)
+    #ipkoopman                  Koopman ionisation potential in eV
+    #ip                         ionisation potential in eV
+    #ea                         electron affinity in eV
+    #eneg                       electronegativity in eV
+    #hard                       hardness in eV

run_gfn.py

@@ -0,0 +1,342 @@
+import os
+import sys
+import subprocess
+
+
+def ReadXYZ(filename):
+    #function reading xyz format
+    rfile = open(filename,"r")
+    rfilelines = rfile.readlines()
+    natoms = int(rfilelines[0])
+    geometry = []
+    for iatm in range(natoms):
+        line = rfilelines[iatm + 2]
+        cleanline = line
+        for idx in range(250):
+            line = cleanline.replace("  "," ")
+            cleanline = line
+            if not ("  " in cleanline): break
+        data = cleanline.split(" ")
+        aux = [float(data[1]),float(data[2]),float(data[3])]
+        geometry.append(aux)
+    return geometry
+
+def run_gfn2(argv):
+    #arguments and give them default values
+    exe = "./GFN2all_crd.exe"
+    geometryfile = ""
+    charge = "0"
+    Telec = "300"
+    solvation = "0"
+    solventname = "gas"
+    optimisegeometry = "0"
+    newgeometryfile = ""
+    thermo = "0"
+    energythresh = "1.0e-6"
+    gradientthresh = "1.0e-3"
+    calcdensity = "0"
+    densityfile = ""
+    electronicreactivity = "0"
+    orbitalreactivity = "0"
+    KoopmanIP = "0"
+    IP = "0"
+    EA = "0"
+    electronegativity = "0"
+    hardness = "0"
+
+    #parse whatever we get
+    for iarg in range(1,len(argv)):
+        argument = argv[iarg].lower().replace("=","")
+        if argument.startswith("geometry") or argument.startswith("geom"):
+            geometryfile = argument.replace("geometry","").replace("geom","")
+        elif argument.startswith("charge") or argument.startswith("chrg"):
+            charge = argument.replace("charge","").replace("chrg","")
+        elif argument.startswith("telec") or argument.startswith("telectronic"):
+            Telec = argument.replace("telectronic","").replace("telec","")
+        elif argument.startswith("usesolv") or argument.startswith("usesolvent"):
+            solvation = argument.replace("usesolvent","").replace("usesolv","")
+        elif argument.startswith("solvent") or argument.startswith("solventname"):
+            solventname = argument.replace("solventname","").replace("solvent","")
+        elif argument.startswith("optg") or argument.startswith("optimisegeom") or argument.startswith("optimizegeom") or argument.startswith("optimisegeometry") or argument.startswith("optimizegeometry"):
+            optimisegeometry = argument.replace("optg","").replace("optimise","").replace("optimize","").replace("geometry","").replace("geom","")
+        elif argument.startswith("newgeom") or argument.startswith("newgeomfile") or argument.startswith("newgeometryfile"):
+            newgeometryfile = argument.replace("newgeometryfile","").replace("newgeomfile","").replace("newgeom","")
+        elif argument.startswith("dothermo") or argument.startswith("thermo") or argument.startswith("thermodynamics"):
+            thermo = argument.replace("dothermo","").replace("thermodynamics","").replace("thermo","")
+        elif argument.startswith("ethresh") or argument.startswith("energythresh") or argument.startswith("energythreshold"):
+            energythresh = argument.replace("ethresh","").replace("energythreshold","").replace("energythresh","")
+        elif argument.startswith("gthresh") or argument.startswith("gradthresh") or argument.startswith("gradientthreshold"):
+            gradientthresh = argument.replace("gthresh","").replace("gradientthreshold","").replace("gradthresh","")
+        elif argument.startswith("calcdens") or argument.startswith("calcdensity") or argument.startswith("calculatedensity"):
+            calcdensity = argument.replace("calcdensity","").replace("calcdens","").replace("calculatedensity","")
+        elif argument.startswith("densityfile") or argument.startswith("densfile"):
+            calcdensity = argument.replace("densityfile","").replace("densfile","")
+        elif argument.startswith("ereact") or argument.startswith("electronicreactivity"):
+            electronicreactivity = argument.replace("ereact","").replace("electronicreactivity","")
+        elif argument.startswith("oreact") or argument.startswith("orbreact") or argument.startswith("orbitalreactivity"):
+            orbitalreactivity = argument.replace("oreact","").replace("orbreact","").replace("orbitalreactivity","")
+        elif argument.startswith("koopman") or argument.startswith("ipkoopman") or argument.startswith("koopmanip"):
+            KoopmanIP = argument.replace("ip","").replace("koopman","")
+        elif argument.startswith("ip") or argument.startswith("ionizationpotential") or argument.startswith("ionisationpotential") or argument.startswith("ipot"):
+            IP = argument.replace("ip","").replace("ionizationpotential","").replace("ionisationpotential","").replace("ipot","")
+        elif argument.startswith("ea") or argument.startswith("electronaffinity") or argument.startswith("eaffin"):
+            EA = argument.replace("ea","").replace("electronaffinity","").replace("eaffin","")
+        elif argument.startswith("electronegativity"):
+            electronegativity = argument.replace("electronegativity","")
+        elif argument.startswith("hardness"):
+            hardness = argument.replace("hardness","")
+
+    #ensure consistency
+    if geometryfile + "blahblah" == "blahblah":
+        print("ERROR: geometry file is needed")
+        sys.exit()
+
+    newgeometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","")
+    if (newgeometryfile + "blahblah" == "blahblah") and (optimisegeometry == "1"): 
+        newgeometryfile = geometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","") + "_opt"
+
+    if (solvation == "1"):
+        if (solventname == "water") or (solventname == "h2o") or (solventname == "o"): solventname = "water"
+        elif (solventname == "acetone") or (solventname == "cc(o)c"): solventname = "acetone"
+        elif (solventname == "acetonitrile") or (solventname == "ch3cn") or (solventname == "ccn"): solventname = "acetonitrile"
+        elif (solventname == "aniline") or (solventname == "phnh2") or (solventname == "nc1ccccc1") or (solventname == "c1ccc(cc1)n"): solventname = "aniline"
+        elif (solventname == "benzaldehyde") or (solventname == "phcho") or (solventname == "occ1ccccc1") or (solventname == "c1ccc(cc1)co"): solventname = "benzaldehyde"
+        elif (solventname == "benzene") or (solventname == "c6h6") or (solventname == "phh") or (solventname == "c1ccccc1"): solventname = "benzene"
+        elif (solventname == "dichloromethane") or (solventname == "ch2cl2") or (solventname == "c(cl)cl") or (solventname == "c(cl)(cl)"): solventname = "dichloromethane"
+        elif (solventname == "chloroform") or (solventname == "chcl3") or (solventname == "c(cl)(cl)cl") or (solventname == "c(cl)(cl)(cl)"): solventname = "chloroform"
+        elif (solventname == "carbon disulfide") or (solventname == "carbondisulfide") or (solventname == "cs2") or (solventname == "scs"): solventname = "carbon disulfide"
+        elif (solventname == "dioxane") or (solventname == "o1ccocc1"): solventname = "dioxane"
+        elif (solventname == "dmf") or (solventname == "dimethylformamide") or (solventname == "cn(c)co"): solventname = "dmf"
+        elif (solventname == "dmso") or (solventname == "dimethylsulfoxide") or (solventname == "cs(o)c") or (solventname == "cs(c)o"): solventname = "dmso"
+        elif (solventname == "ethanol") or (solventname == "etoh") or (solventname == "ch3ch2oh") or (solventname == "cco"): solventname = "ethanol"
+        elif (solventname == "diethyl ether") or (solventname == "etoet") or (solventname == "ccocc") or (solventname == "ch3ch2och2ch3"): solventname = "diethyl ether"
+        elif (solventname == "ethyl acetate") or (solventname == "acoet") or (solventname == "etoac") or (solventname == "ccoc(o)c"): solventname = "ethyl acetate"
+        elif (solventname == "furan") or (solventname == "furane"): solventname = "furane"
+        elif (solventname == "hexadecane") or (solventname == "c16"): solventname = "hexadecane"
+        elif (solventname == "hexane") or (solventname == "cccccc") or (solventname == "c6"): solventname = "hexane"
+        elif (solventname == "methanol") or (solventname == "meoh") or (solventname == "co") or (solventname == "ch3oh"): solventname = "methanol"
+        elif (solventname == "nitromethane") or (solventname == "meno2") or (solventname == "ch3no2") or (solventname == "cn(o)o"): solventname = "nitromethane"
+        elif (solventname == "octanol") or (solventname == "cccccccc") or (solventname == "c8"): solventname = "octanol"
+        elif (solventname == "phenol") or (solventname == "phoh") or (solventname == "oc1ccccc1") or (solventname == "c1ccc(cc1)o"): solventname = "phenol"
+        elif (solventname == "thf") or (solventname == "tetrahydrofuran"): solventname = "thf"
+        elif (solventname == "toluene") or (solventname == "phme") or (solventname == "cc1ccccc1"): solventname = "toluene"
+        elif (solventname == "octanol wet") or (solventname == "octanolwet") or (solventname == "wet octanol") or (solventname == "wetoctanol"): solventname = "octanol wet"
+
+    if (densityfile + "blahblah" == "blahblah") and (calcdensity == "1"): 
+        densityfile = geometryfile.replace(".xyz","").replace(".sdf","").replace(".mol2","").replace(".pdb","") + "_dens"
+
+    def RunQMOptg():
+        proc = subprocess.Popen([exe,geometryfile,charge,Telec,solvation,solventname,optimisegeometry,newgeometryfile,thermo,energythresh,gradientthresh,calcdensity,densityfile,electronicreactivity,orbitalreactivity,KoopmanIP,IP,EA,electronegativity,hardness], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        out,err = proc.communicate()
+        return out,err
+    out,err = RunQMOptg()
+
+    if err.decode("utf-8") + "blahblah" != "blahblah": print("error:",err)
+    else:
+        #process data from output file
+        outputfile = out.decode("utf-8").split("\n")
+        #print(out.decode("utf-8"))
+        etotal = 0.0
+        gsolvation = 0.0
+        fetchvibr = False
+        vibrations = []
+        fetchthermo = False
+        temperature = []
+        entropy = []
+        enthalpy = []
+        gibbs = []
+        internalenergy = []
+        helmholtz = []
+        cp = []
+        cv = []
+        fetchatomicprops = False
+        atmlist = []
+        charges = []
+        polarisabilities = []
+        totalpol = 0.0
+        fetchelecreact = False
+        fetchorbreact = False
+        eFukuiElctrophilie = []
+        eFukuiNucleophilie = []
+        eFukuiRadical = []
+        eSoftnessElctrophilie = []
+        eSoftnessNucleophilie = []
+        eSoftnessRadical = []
+        oFukuiElctrophilie = []
+        oFukuiNucleophilie = []
+        oFukuiRadical = []
+        oSoftnessElctrophilie = []
+        oSoftnessNucleophilie = []
+        oSoftnessRadical = []
+        ipkoopman = 0.0
+        ip = 0.0
+        ea = 0.0
+        eneg = 0.0
+        hard = 0.0
+        out_dict = {}
+        for iline in range(len(outputfile)):
+            line = outputfile[iline]
+            #check whether array data is available
+            if line.startswith(">all vibrational frequencies"): 
+                fetchvibr = True
+                continue
+            elif line.startswith("<all vibrational frequencies"): 
+                fetchvibr = False
+                continue
+            elif line.startswith(">Thermodynamics"): 
+                fetchthermo = True
+                continue
+            elif line.startswith("<Thermodynamics"): 
+                fetchthermo = False
+                continue
+            elif line.startswith(">atom;charge;pol"): 
+                fetchatomicprops = True
+                continue
+            elif line.startswith("<atom;charge;pol"): 
+                fetchatomicprops = False
+                continue
+            elif line.startswith(">Electronic Reactivity indices"): 
+                fetchelecreact = True
+                continue
+            elif line.startswith("<Electronic Reactivity indices"): 
+                fetchelecreact = False
+                continue
+            elif line.startswith(">Orbital Reactivity indices"): 
+                fetchorbreact = True
+                continue
+            elif line.startswith("<Orbital Reactivity indices"): 
+                fetchorbreact = False
+                continue
+            #fetch data
+            if line.startswith("Total Energy = "): 
+                etotal = float(line.replace("Total Energy = ",""))
+                out_dict['etotal']=etotal
+            elif line.startswith("Gsolv = "): 
+                gsolvation = float(line.replace("Gsolv = ",""))
+                out_dict['gsolvation']=gsolvation
+            elif "Total Polarizability" in line: 
+                totalpol = float(line.replace("Total Polarizability","").replace(" ",""))
+                out_dict['totalpol']=totalpol                
+            elif line.startswith("Ionization Potential (Koopman):"): 
+                ipkoopman = float(line.replace("Ionization Potential (Koopman):","").replace("   eV",""))
+                out_dict['ipkoopman']=ipkoopman
+            elif line.startswith("Ionization Potential (Definition): "): 
+                ip = float(line.replace("Ionization Potential (Definition): ","").replace("   eV",""))
+                out_dict['ip']=ip
+            elif line.startswith("Electron Affinity (Definition): "): 
+                ea = float(line.replace("Electron Affinity (Definition): ","").replace("   eV",""))
+                out_dict['ea']=ea
+            elif line.startswith("Electronegativity: "): 
+                eneg = float(line.replace("Electronegativity: ","").replace("   eV",""))
+                out_dict['eneg']=eneg
+            elif line.startswith("Hardness: "): 
+                hard = float(line.replace("Hardness: ","").replace("   eV",""))
+                out_dict['hard']=hard
+            elif fetchvibr: 
+                vibrations.append(float(line))
+                out_dict['vibrations']=vibrations
+            elif fetchthermo: 
+                data = line.split(";")
+                temperature.append(float(data[0]))
+                entropy.append(float(data[1]))
+                enthalpy.append(float(data[2]))
+                gibbs.append(float(data[3]))
+                internalenergy.append(float(data[4]))
+                helmholtz.append(float(data[5]))
+                cp.append(float(data[6]))
+                cv.append(float(data[7]))
+                out_dict['fetchthermo']={"temperature":temperature,
+                "entropy":entropy,
+                "enthalpy":enthalpy,
+                "gibbs":gibbs,
+                "internalenergy":internalenergy,
+                "helmholtz":helmholtz,
+                "cp":cp,
+                "cv":cv
+                }
+            elif fetchatomicprops:
+                data = line.split(";")
+                atmlist.append(int(data[0]))
+                charges.append(float(data[1]))
+                polarisabilities.append(float(data[2]))
+                out_dict['fetchatomicprops']={"atmlist":atmlist,
+                "charges":charges,
+                "polarisabilities":polarisabilities
+                }
+            elif fetchelecreact:
+                data = line.strip().rstrip().replace("  "," ").split(" ")
+                eFukuiElctrophilie.append(float(data[0]))
+                eFukuiNucleophilie.append(float(data[1]))
+                eFukuiRadical.append(float(data[2]))
+                eSoftnessElctrophilie.append(float(data[3]))
+                eSoftnessNucleophilie.append(float(data[4]))
+                eSoftnessRadical.append(float(data[5]))
+                out_dict['fetchelecreact']=fetchelecreact
+            elif fetchorbreact:
+                data = line.strip().rstrip().replace("  "," ").split(" ")
+                oFukuiElctrophilie.append(float(data[0]))
+                oFukuiNucleophilie.append(float(data[1]))
+                oFukuiRadical.append(float(data[2]))
+                oSoftnessElctrophilie.append(float(data[3]))
+                oSoftnessNucleophilie.append(float(data[4]))
+                oSoftnessRadical.append(float(data[5]))
+                out_dict['fetchorbreact']=fetchorbreact
+        #print(argv)
+        #print(out_dict)
+        if not newgeometryfile.endswith(".xyz"): 
+            newgeometryfile += ".xyz"
+        out_dict["xyz"] = ReadXYZ(newgeometryfile)
+        return out_dict
+        #data collected; if there is a whether, then variable is boolean
+        #geometryfile               the geometry of the molecule
+        #charge                     the total charge
+        #solventname                the name of the solvent
+        #optimisegeometry           whether geometry was optimised
+        #newgeometryfile            the name of the file containing optimised geometry
+        #thermo                     whether thermodynamics was done
+        #calcdensity                whether the electronic density was calculated
+        #densityfile                the name of the file containing electronic density
+        #electronicreactivity       whether electronic reactivity data was calculated
+        #orbitalreactivity          whether orbital reacticity data was calculated
+        #KoopmanIP                  whether the Koopman ionisation potential was calculated
+        #IP                         whether the ionisation potential was calculated
+        #EA                         whether electron affinity was calculated
+        #electronegativity          whether electronegativity was calculated
+        #hardness                   whether hardness was calculated
+        #etotal                     the molecule's total energy in Hartree
+        #gsolvation                 solvation Gibbs free energy in Hartree
+        #vibrations                 array containing vibrational frequencies in cm-1
+        #temperature                array containing temperatures
+        #entropy                    array containing entropies
+        #enthalpy                   array containing enthalpies
+        #gibbs                      array containing Gibbs free energies
+        #internalenergy             array containing internal energies
+        #helmholtz                  array containing Helmholts energies
+        #cp                         array containing heat capacities at constant pressure
+        #cv                         array containing heat capacities at constant volume
+        #atmlist                    list of atoms
+        #charges                    partial charges in electrons
+        #polarisabilities           atomic polarisabilities in bohr
+        #totalpol                   total polarisability in cubic bohr
+        #eFukuiElctrophilie         Fukui index for electrophilicity (calculated from charges)
+        #eFukuiNucleophilie         Fukui index for nucleophilicity (calculated from charges)
+        #eFukuiRadical              Fukui index for radical reactivity (calculated from charges)
+        #eSoftnessElctrophilie      softness index for electrophilicity (calculated from charges)
+        #eSoftnessNucleophilie      softness index for nucleophilicity (calculated from charges)
+        #eSoftnessRadical           softness index for radical reactivity (calculated from charges)
+        #oFukuiElctrophilie         Fukui index for electrophilicity (calculated from frontier orbitals)
+        #oFukuiNucleophilie         Fukui index for nucleophilicity (calculated from frontier orbitals)
+        #oFukuiRadical              Fukui index for radical reactivity (calculated from frontier orbitals)
+        #oSoftnessElctrophilie      softness index for electrophilicity (calculated from frontier orbitals)
+        #oSoftnessNucleophilie      softness index for nucleophilicity (calculated from frontier orbitals)
+        #oSoftnessRadical           softness index for radical reactivity (calculated from frontier orbitals)
+        #ipkoopman                  Koopman ionisation potential in eV
+        #ip                         ionisation potential in eV
+        #ea                         electron affinity in eV
+        #eneg                       electronegativity in eV
+        #hard                       hardness in eV
+
+if __name__=="__main__":
+    out_dict = run_gfn2(sys.argv)
+
+    print(out_dict)

ulysses

@@ -0,0 +1 @@
+Subproject commit 75e16c3c06a85831c076ca54b530c45dfcc9fb9d