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Mason.py
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# -*- coding: utf-8 -*-
"""
Created on Wed Feb 17 12:18:29 2021
@author: Shusen Chen
"""
from openbabel import openbabel as ob
import random
import os
import configparser
def GetTemplateAndLigandLib(config):
#read files and alloc memory to store template and ligands
# initialize template
conv = ob.OBConversion()
mol = ob.OBMol()
conv.SetInFormat(config['IODir']['Template'].split('.')[-1])
conv.ReadFile(mol, config['IODir']['Template'])
core = mol.GetAtom(int(config['Properties']['coreNum']))
core.SetFormalCharge(int(config['Properties']['charge']))
core.SetSpinMultiplicity(int(config['Properties']['multiplicity']))
# initialize ligands
ligandLib = {}
for filename in os.listdir(config['IODir']['LigandLibDir']):
if '.mol' in filename:
ligand = ob.OBMol()
conv.SetInFormat("mol")
conv.ReadFile(ligand, config['IODir']['LigandLibDir'] + filename)
ligandLib[filename.split(".")[0]] = ligand
return mol, ligandLib
def Init(configFile):
config = configparser.ConfigParser()
config.read(configFile)
template, ligandLib = GetTemplateAndLigandLib(config)
if not os.path.exists(config['IODir']['Output']):
os.makedirs(config['IODir']['Output'])
#generate the combinations of ligands from ligand library
originLigandCombs = {"": []}
originLigandCombs = LigandIter(originLigandCombs, ligandLib,\
int(config['common']['coordNum']))
ligandCombs = {}
ligandCombsNameSplit = []
for name in originLigandCombs:
temp = name.split("_")[1:]
temp.sort()
if temp not in ligandCombsNameSplit:
ligandCombsNameSplit.append(temp)
ligandCombs[name] = originLigandCombs[name]
return template, ligandCombs, config
def LigandIter(ligandCombs, ligandLib, coordNum):
ligandMaxCoordNum = 0
ligandMinCoordNum = 10
for name in ligandLib:
ligandCoordNum = len(ligandLib[name].GetTitle().split(","))
if ligandCoordNum < ligandMinCoordNum:
ligandMinCoordNum = ligandCoordNum
if ligandCoordNum > ligandMaxCoordNum:
ligandMaxCoordNum = ligandCoordNum
# print(ligandMinCoordNum, ligandMaxCoordNum)
if coordNum < ligandMinCoordNum:
# print("type1")
return ligandCombs
newLigandCombs = {}
for i in range(ligandMinCoordNum, min(coordNum, ligandMaxCoordNum) + 1):
# print("iter1 ligandCoord =", i)
tempLigandCombs = {}
for name in ligandLib:
# print("iter2", name)
if len(ligandLib[name].GetTitle().split(",")) == i:
for item in ligandCombs:
# print("******************")
# print("coordNum = ", coordNum)
# print("item = ", item)
# print("name = ", name)
newitem = item + "_" + name
tempLigandCombs[newitem] = []
# for a in ligandCombs:
# print("ligandCombs", a)
tempLigandCombs[newitem] = list(ligandCombs[item])
tempLigandCombs[newitem].append(ligandLib[name])
# for a in ligandCombs:
# print("ligandCombs", a)
# for a in tempLigandCombs:
# print("tempLigandCombs", a)
# print("*************")
# print(len(newitem))
# coordNum -= i
newLigandCombs.update(LigandIter(tempLigandCombs, ligandLib, coordNum - i))
# print(len(newligands2added))
# print("Type 2")
return newLigandCombs
def AddLigand2Mol(mol, ligand, constraints, config):
#add ligand(OBmol) to mol(OBMol) with constraints by freezing all atoms in mol
#define which atoms to be connected
molNConnect = int(config['Properties']['coreNum'])
ligandNConnects = [int(i) for i in ligand.GetTitle().split(',')]
# print(ligandNConnects)
#params which affect the running time, the less the faster
randomRepeatTimes = int(config['forcefield']['randomRepeatTimes'])
randomPlacementScale = float(config['forcefield']['randomPlacementScale'])
stepsPerAtom = int(randomPlacementScale)
#initial
vector = ob.vector3()
minE = float('inf')
tempLigand = ob.OBMol(ligand)
minmol = ob.OBMol()
forcefield = ob.OBForceField.FindForceField(config['forcefield']['ff4AddLigand'])
#randomly translating ligand coords to avoid crush
for i in range(randomRepeatTimes):
tempmol = ob.OBMol(mol)
vector.Set(random.random() - .5, random.random() - .5, random.random() - .5)
vector *= (2 * randomPlacementScale)
tempLigand.Translate(vector)
tempmol += tempLigand
for ligandNConnect in ligandNConnects:
tempmol.AddBond(molNConnect, mol.NumAtoms() + ligandNConnect, 1)
#set forcefield with constraints
forcefield.SetConstraints(constraints)
forcefield.Setup(tempmol, constraints)
# print(tempmol.NumAtoms())
forcefield.ConjugateGradients(stepsPerAtom * tempmol.NumAtoms())
forcefield.GetCoordinates(tempmol)
if forcefield.Energy() < minE:
minE = forcefield.Energy()
minmol.Clear()
minmol = tempmol
else:
tempmol.Clear()
tempLigand.Clear()
return minmol
def AddLigands2Mol(mol, ligands, config):
# add several ligands(list of OBmols) to mol(OBmol)
# read config to setup forcefield and steps
stepsPerAtom = int(config['forcefield']['stepsPerAtom'])
# set constrains for the atoms from mol
constraints = ob.OBFFConstraints()
for i in range(mol.NumAtoms()):
constraints.AddAtomConstraint(i + 1)
if config['forcefield']['ff4WholeMol'] != 'NO':
# print("preforming whole molecule optimazation...")
forcefield = ob.OBForceField.FindForceField(config['forcefield']['ff4WholeMol'])
forcefield.SetConstraints(constraints)
#add ligand one by one with crude optimization
minE = float('inf')
minmol = ob.OBMol()
for i in range(int(config['forcefield']['randomRepeatTimesWholeMol'])):
tempmol = ob.OBMol(mol)
# print(i)
for ligand in ligands:
tempmol = AddLigand2Mol(tempmol, ligand, constraints, config)
## constraints.AddAtomConstraint(mol.NumAtoms() - ligand.NumAtoms() + 1)
# Optimizing with more expensive method here
forcefield.Setup(tempmol, constraints)
# print((mol.NumAtoms() + ligand.NumAtoms()))
# print(forcefield.Energy())
forcefield.SteepestDescent(stepsPerAtom * tempmol.NumAtoms())
# print(forcefield.Energy())
forcefield.GetCoordinates(tempmol)
forcefield.Setup(tempmol, constraints)
forcefield.WeightedRotorSearch(tempmol.NumAtoms(), stepsPerAtom * tempmol.NumAtoms())
forcefield.GetCoordinates(tempmol)
forcefield.Setup(tempmol, constraints)
# print(forcefield.Energy())
forcefield.ConjugateGradients(stepsPerAtom * tempmol.NumAtoms())
# print(forcefield.Energy())
forcefield.GetCoordinates(tempmol)
if forcefield.Energy() < minE:
minE = forcefield.Energy()
minmol.Clear()
minmol = tempmol
else:
tempmol.Clear()
return minmol
# def WriteNewTSS(name, template, ligandCombs, config):
# conv = ob.OBConversion()
# conv.SetInFormat("mol")
# mol = AddLigands2Mol(template, ligandCombs[name], config)
# conv.WriteFile(mol, config['IODir']['Output'] + \
# template.GetAtom(int(config['Properties']['coreNum'])).GetType()\
# + name + ".mol")
# mol.Clear()