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Copy pathDescriptors_monomer.py
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Descriptors_monomer.py
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import sys
import numpy as np
import pandas as pd
import rdkit.Chem,rdkit.Chem.AllChem as rdkit
from rdkit import Chem
from rdkit.Chem import rdqueries
from rdkit.Chem import RWMol
from rdkit.Chem import Lipinski
from rdkit import RDLogger
import stk
def Count_number(molecular,index):
q = rdqueries.AtomNumEqualsQueryAtom(index)
return len(molecular.GetAtomsMatchingQuery(q))
def Index_atom(atom):
if atom=='H':
index=1
elif atom=='B':
index=5
elif atom=='C':
index=6
elif atom=='N':
index=7
elif atom=='O':
index=8
elif atom=='F':
index=9
elif atom=='Si':
index=14
elif atom=='P':
index=15
elif atom=='S':
index=16
elif atom=='Cl':
index=17
elif atom=='Se':
index=34
elif atom=='Br':
index=35
elif atom=='As':
index=33
elif atom=='I':
index=53
return index
def Count_Aromatic(molecular):
return Lipinski.NumAromaticRings(molecular)
def Count_Noaromatic(molecular):
return Lipinski.NumAliphaticRings(molecular)
# VDW and MW
def Get_molecular(molecular):
m=molecular.replace("[*]", "").replace("()", "")
m1= rdkit.MolFromSmiles(m)
m1= rdkit.AddHs(m1)
return m1
# monomer length
def Group(smi):
moment=smi.replace("I", "[3H]")
moment=moment.replace("[*]", "I")
moment=moment.replace("*", "I")
return moment
def Line_polymer(monomer,number):
bb=stk.BuildingBlock(monomer,[stk.IodoFactory()])
polymer= stk.ConstructedMolecule(
topology_graph=stk.polymer.Linear((bb, ), 'A', number),)
return polymer.to_rdkit_mol()
def polymer_Optimize(polymer):
rdkit.SanitizeMol(polymer)
rdkit.MMFFOptimizeMolecule(polymer)
return polymer
def Get_Connect(polymer):
Connect_index=0
atom_Num=[]
for atom in polymer.GetAtoms():
Num=atom.GetAtomicNum()
atom_Num.append(Num)
for i in range (0,len(atom_Num)):
if (atom_Num[i-1]==1 and atom_Num[i]>1 and i>0):
Connect_index=i
return Connect_index
def Get_NoHydrogen_Connect(smiles):
smiles=smiles.replace("[*]", "")
smiles=smiles.replace("()", "")
mol=rdkit.MolFromSmiles(smiles)
Atoms=[]
for atom in mol.GetAtoms():
Atoms.append(atom.GetIdx())
return (len (Atoms)+1)
def Cal_distance(monomer,index1,index2):
x1,y1,z1=monomer.GetConformer().GetAtomPosition(index1)
x2,y2,z2=monomer.GetConformer().GetAtomPosition(index2)
distance=np.sqrt((x1-x2)**2+(y1-y2)**2+(z1-z2)**2)
return distance
# Some predefined functions for making mainchain
def set_linker_flag(mol, reverse=False):
"""
poly.set_linker_flag
Args:
mol: RDkit Mol object
reverse: Reversing head and tail (boolean)
Returns:
boolean
"""
flag = False
mol.SetIntProp('head_idx', -1)
mol.SetIntProp('tail_idx', -1)
mol.SetIntProp('head_ne_idx', -1)
mol.SetIntProp('tail_ne_idx', -1)
for atom in mol.GetAtoms():
atom.SetBoolProp('linker', False)
atom.SetBoolProp('head', False)
atom.SetBoolProp('tail', False)
atom.SetBoolProp('head_neighbor', False)
atom.SetBoolProp('tail_neighbor', False)
if (atom.GetSymbol() == "H" and atom.GetIsotope() == 3) or atom.GetSymbol() == "*":
atom.SetBoolProp('linker', True)
if not flag:
mol.SetIntProp('head_idx', atom.GetIdx())
mol.SetIntProp('tail_idx', atom.GetIdx())
flag = True
else:
if reverse:
mol.SetIntProp('head_idx', atom.GetIdx())
else:
mol.SetIntProp('tail_idx', atom.GetIdx())
if not flag: return False
mol_head_idx = mol.GetIntProp('head_idx')
mol.GetAtomWithIdx(mol_head_idx).SetBoolProp('head', True)
mol_tail_idx = mol.GetIntProp('tail_idx')
mol.GetAtomWithIdx(mol_tail_idx).SetBoolProp('tail', True)
head_ne_idx = mol.GetAtomWithIdx(mol_head_idx).GetNeighbors()[0].GetIdx()
mol.SetIntProp('head_ne_idx', head_ne_idx)
mol.GetAtomWithIdx(head_ne_idx).SetBoolProp('head_neighbor', True)
tail_ne_idx = mol.GetAtomWithIdx(mol_tail_idx).GetNeighbors()[0].GetIdx()
mol.SetIntProp('tail_ne_idx', tail_ne_idx)
mol.GetAtomWithIdx(tail_ne_idx).SetBoolProp('tail_neighbor', True)
return True
def set_terminal_idx(mol):
count = 0
for atom in mol.GetAtoms():
resinfo = atom.GetPDBResidueInfo()
if resinfo is None: continue
resname = resinfo.GetResidueName()
if resname == 'TU0':
for na in atom.GetNeighbors():
if na.GetPDBResidueInfo() is None: continue
elif na.GetPDBResidueInfo().GetResidueName() != 'TU0':
mol.SetIntProp('terminal_idx1', atom.GetIdx())
mol.SetIntProp('terminal_ne_idx1', na.GetIdx())
count += 1
elif resname == 'TU1':
for na in atom.GetNeighbors():
if na.GetPDBResidueInfo() is None: continue
elif na.GetPDBResidueInfo().GetResidueName() != 'TU1':
mol.SetIntProp('terminal_idx2', atom.GetIdx())
mol.SetIntProp('terminal_ne_idx2', na.GetIdx())
count += 1
return count
def set_mainchain_flag(mol):
for atom in mol.GetAtoms():
atom.SetBoolProp('main_chain', False)
linker_result = set_linker_flag(mol)
terminal_result = set_terminal_idx(mol)
if not linker_result and terminal_result == 0:
return False
if terminal_result > 0:
if mol.GetIntProp('terminal_ne_idx1') == mol.GetIntProp('terminal_ne_idx2'):
path = [mol.GetIntProp('terminal_ne_idx1')]
else:
path = Chem.GetShortestPath(mol, mol.GetIntProp('terminal_ne_idx1'), mol.GetIntProp('terminal_ne_idx2'))
elif mol.GetIntProp('head_idx') == mol.GetIntProp('tail_idx'):
path = Chem.GetShortestPath(mol, mol.GetIntProp('head_idx'), mol.GetIntProp('head_ne_idx'))
else:
path = Chem.GetShortestPath(mol, mol.GetIntProp('head_idx'), mol.GetIntProp('tail_idx'))
for idx in path:
atom = mol.GetAtomWithIdx(idx)
atom.SetBoolProp('main_chain', True)
for batom in atom.GetNeighbors():
if batom.GetTotalDegree() == 1:
batom.SetBoolProp('main_chain', True)
rings = Chem.GetSymmSSSR(mol)
m_rings = []
for ring in rings:
dup = list(set(path) & set(ring))
if len(dup) > 0:
m_rings.append(ring)
for idx in ring:
atom = mol.GetAtomWithIdx(idx)
atom.SetBoolProp('main_chain', True)
for batom in atom.GetNeighbors():
if batom.GetTotalDegree() == 1:
batom.SetBoolProp('main_chain', True)
for m_ring in m_rings:
for ring in rings:
dup = list(set(m_ring) & set(ring))
if len(dup) > 0:
for idx in ring:
atom = mol.GetAtomWithIdx(idx)
atom.SetBoolProp('main_chain', True)
for batom in atom.GetNeighbors():
if batom.GetTotalDegree() == 1:
batom.SetBoolProp('main_chain', True)
return True
#vander Waals volume
def cal_VDW (smiles):
mol= rdkit.MolFromSmiles(smiles)
mol= rdkit.AddHs(mol)
num_C=Count_number(mol,Index_atom('C'))
num_H=Count_number(mol,Index_atom('H'))
num_N=Count_number(mol,Index_atom('N'))
num_O=Count_number(mol,Index_atom('O'))
num_Cl=Count_number(mol,Index_atom('Cl'))
num_Br=Count_number(mol,Index_atom('Br'))
num_F=Count_number(mol,Index_atom('F'))
num_I=Count_number(mol,Index_atom('I'))
num_S=Count_number(mol,Index_atom('S'))
num_P=Count_number(mol,Index_atom('P'))
num_As=Count_number(mol,Index_atom('As'))
num_B=Count_number(mol,Index_atom('B'))
num_Aromatic=Count_Aromatic(mol)
num_Noaromatic=Count_Noaromatic(mol)
All_Bonds=num_C*20.58+num_H*7.24+num_N*15.60+num_O*14.71+num_Cl*22.45+num_Br*26.52+num_F*13.31+num_I*32.52+num_S*24.43+num_P*24.43+num_As*26.52+num_B*40.48
N_B=num_C+num_H+num_N+num_O+num_Cl+num_Br+num_F+num_I+num_S+num_P+num_As+num_B+num_Aromatic+num_Noaromatic-1
R_A=num_Aromatic
R_NR=num_Noaromatic
V_vdw=All_Bonds-5.92*N_B-14.7*R_A-3.8*R_NR
return np.round (V_vdw,2)
#Molecular weight
def cal_MW (smiles):
mol= rdkit.MolFromSmiles(smiles)
mol= rdkit.AddHs(mol)
num_C=Count_number(mol,Index_atom('C'))
num_H=Count_number(mol,Index_atom('H'))
num_N=Count_number(mol,Index_atom('N'))
num_O=Count_number(mol,Index_atom('O'))
num_Cl=Count_number(mol,Index_atom('Cl'))
num_Br=Count_number(mol,Index_atom('Br'))
num_F=Count_number(mol,Index_atom('F'))
num_I=Count_number(mol,Index_atom('I'))
num_S=Count_number(mol,Index_atom('S'))
num_P=Count_number(mol,Index_atom('P'))
num_As=Count_number(mol,Index_atom('As'))
num_B=Count_number(mol,Index_atom('B'))
MW=num_C*12.01+num_H*1.01+num_N*14.01+num_O*16.00+num_Cl*35.45+num_Br*79.90+num_F*19.00+num_I*126.90+num_S*32.07+num_P*30.97+num_As*74.92+num_B*10.81
return MW
#monomer length
def Cal_length (smi,number):
polymer=Line_polymer(Group(smi),number)
polymer=polymer_Optimize(polymer)
secong_index=Get_Connect(polymer)
if secong_index!=0:
index=secong_index
else:
index=Get_NoHydrogen_Connect(smi)
length=Cal_distance(polymer,1,index)
return np.round (length,2)
# extract mainchain
def extract_mainchain(smiles):
main_smi = None
if smiles.count('*') != 2:
print('Illegal number of connecting points in SMILES. %s' % smiles)
return main_smi
smi = smiles.replace('[*]', '[3H]')
smi = smi.replace('*', '[3H]')
try:
mol = Chem.MolFromSmiles(smi)
mol = Chem.AddHs(mol)
except:
print('Cannot convert to Mol object from %s' % smiles)
return main_smi
set_mainchain_flag(mol)
for atom in mol.GetAtoms():
if atom.GetBoolProp('main_chain'):
for na in atom.GetNeighbors():
if not na.GetBoolProp('main_chain'):
bidx = mol.GetBondBetweenAtoms(atom.GetIdx(), na.GetIdx()).GetIdx()
mol = Chem.FragmentOnBonds(mol, [bidx], addDummies=False)
RDLogger.DisableLog('rdApp.*')
try:
fsmi = [Chem.MolToSmiles(Chem.MolFromSmiles(x)) for x in Chem.MolToSmiles(mol).split('.')]
except:
print('Cannot convert to fragmented Mol')
RDLogger.EnableLog('rdApp.*')
return main_smi
RDLogger.EnableLog('rdApp.*')
for s in fsmi:
if '[3H]' in s:
try:
main_smi = Chem.MolToSmiles(Chem.MolFromSmiles(s.replace('[3H]', '*')))
except:
print('Cannot convert to canonical SMILES from %s' % smi)
return main_smi
#Molecular weight of Backbone/Molecular weight of Monomer
def cal_MWratio (smi):
Backbone_smi=extract_mainchain(smi)
MW_ratio=cal_MW (Backbone_smi)/cal_MW (smi)
return np.round (MW_ratio,3)
if __name__ == '__main__':
filename = sys.argv[1]
df=pd.read_csv(path+str(filename))
SMI=df["SMILES"]
df['VDW'] = df['SMILES'].map(lambda x: cal_VDW (x))
df['MW'] = df['SMILES'].map(lambda x: cal_MW (x))
df['Monomer_length'] = df['SMILES'].map(lambda x: Cal_length (x,2))
df['MW_ratio'] = df['SMILES'].map(lambda x: cal_MWratio (x))
df.to_csv("./dataset/Descriptors/VII_Descriptors_monomer.csv",index=None)