Update motif_sample.py

motif_sample.py

@@ -5,7 +5,6 @@ import random
 import torch
 import numpy as np
 import math
-from vina import Vina
 from openbabel import pybel
 import subprocess
 import multiprocessing as mp
@@ -21,7 +20,6 @@ from rdkit import RDConfig
 from rdkit.Chem.Descriptors import MolLogP, qed
 from copy import deepcopy
 import tempfile
-import AutoDockTools
 import contextlib
 from torch_scatter import scatter_add, scatter_mean
 from rdkit.Geometry import Point3D
@@ -57,97 +55,6 @@ def supress_stdout(func):
     return wrapper
 
 
-class PrepLig(object):
-    def __init__(self, input_mol, mol_format):
-        if mol_format == 'smi':
-            self.ob_mol = pybel.readstring('smi', input_mol)
-        elif mol_format == 'sdf':
-            self.ob_mol = next(pybel.readfile(mol_format, input_mol))
-        else:
-            raise ValueError(f'mol_format {mol_format} not supported')
-
-    def addH(self, polaronly=False, correctforph=True, PH=7):
-        self.ob_mol.OBMol.AddHydrogens(polaronly, correctforph, PH)
-        obutils.writeMolecule(self.ob_mol.OBMol, 'tmp_h.sdf')
-
-    def gen_conf(self):
-        sdf_block = self.ob_mol.write('sdf')
-        rdkit_mol = Chem.MolFromMolBlock(sdf_block, removeHs=False)
-        AllChem.EmbedMolecule(rdkit_mol, Chem.rdDistGeom.ETKDGv3())
-        self.ob_mol = pybel.readstring('sdf', Chem.MolToMolBlock(rdkit_mol))
-        obutils.writeMolecule(self.ob_mol.OBMol, 'conf_h.sdf')
-
-    @supress_stdout
-    def get_pdbqt(self, lig_pdbqt=None):
-        preparator = MoleculePreparation()
-        preparator.prepare(self.ob_mol.OBMol)
-        if lig_pdbqt is not None:
-            preparator.write_pdbqt_file(lig_pdbqt)
-            return
-        else:
-            return preparator.write_pdbqt_string()
-
-
-class PrepProt(object):
-    def __init__(self, pdb_file):
-        self.prot = pdb_file
-
-    def del_water(self, dry_pdb_file):  # optional
-        with open(self.prot) as f:
-            lines = [l for l in f.readlines() if l.startswith('ATOM') or l.startswith('HETATM')]
-            dry_lines = [l for l in lines if not 'HOH' in l]
-
-        with open(dry_pdb_file, 'w') as f:
-            f.write(''.join(dry_lines))
-        self.prot = dry_pdb_file
-
-    def addH(self, prot_pqr):  # call pdb2pqr
-        self.prot_pqr = prot_pqr
-        subprocess.Popen(['pdb2pqr30', '--ff=AMBER', self.prot, self.prot_pqr],
-                         stderr=subprocess.DEVNULL, stdout=subprocess.DEVNULL).communicate()
-
-    def get_pdbqt(self, prot_pdbqt):
-        prepare_receptor = os.path.join(AutoDockTools.__path__[0], 'Utilities24/prepare_receptor4.py')
-        subprocess.Popen(['python3', prepare_receptor, '-r', self.prot_pqr, '-o', prot_pdbqt],
-                         stderr=subprocess.DEVNULL, stdout=subprocess.DEVNULL).communicate()
-
-
-def calculate_vina(number, pro_path, lig_path):
-    lig_path = os.path.join(lig_path, str(number)+'.sdf')
-    size_factor = 1.2
-    buffer = 5.
-    # openmm_relax(pro_path)
-    # relax_sdf(lig_path)
-    mol = Chem.MolFromMolFile(lig_path, sanitize=True)
-    pos = mol.GetConformer(0).GetPositions()
-    center = np.mean(pos, 0)
-    ligand_pdbqt = './data/tmp/' + str(number) + '_lig.pdbqt'
-    protein_pqr = './data/tmp/' + str(number) + '_pro.pqr'
-    protein_pdbqt = './data/tmp/' + str(number) + '_pro.pdbqt'
-    lig = PrepLig(lig_path, 'sdf')
-    lig.addH()
-    lig.get_pdbqt(ligand_pdbqt)
-
-    prot = PrepProt(pro_path)
-    prot.addH(protein_pqr)
-    prot.get_pdbqt(protein_pdbqt)
-
-    v = Vina(sf_name='vina', seed=0, verbosity=0)
-    v.set_receptor(protein_pdbqt)
-    v.set_ligand_from_file(ligand_pdbqt)
-    x, y, z = (pos.max(0) - pos.min(0)) * size_factor + buffer
-    v.compute_vina_maps(center=center, box_size=[x, y, z])
-    energy = v.score()
-    print('Score before minimization: %.3f (kcal/mol)' % energy[0])
-    energy_minimized = v.optimize()
-    print('Score after minimization : %.3f (kcal/mol)' % energy_minimized[0])
-    v.dock(exhaustiveness=64, n_poses=32)
-    score = v.energies(n_poses=1)[0][0]
-    print('Score after docking : %.3f (kcal/mol)' % score)
-
-    return score
-
-
 def get_feat(mol):
     fdefName = os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef')
     factory = ChemicalFeatures.BuildFeatureFactory(fdefName)