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SMILES with metal added
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@cchang373
cchang373 committed Sep 25, 2021
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208 changes: 208 additions & 0 deletions molecule_rxn/add_metal.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 4 09:27:38 2020
@author: cchang373
"""
from rdkit import Chem
from json import load,dump
import rdkit

def add_single_metal(smi, metal_atom):
mol = Chem.MolFromSmiles(smi)
smi = Chem.MolToSmiles(mol)
mol = Chem.MolFromSmiles(smi)
mol_H = Chem.AddHs(mol)
for num, atom_object in enumerate(mol_H.GetAtoms()):
if atom_object.GetSymbol() != 'H' and atom_object.GetSymbol() != metal_atom:
count_bond = 0
saturate = 4 if atom_object.GetSymbol() == 'C' else 2
for bonds in mol_H.GetBonds():
if num in [bonds.GetBeginAtomIdx(), bonds.GetEndAtomIdx()]:
count_bond += 1 if bonds.GetBondType() == rdkit.Chem.rdchem.BondType.SINGLE else 2
if saturate > count_bond:
string_add = '('+metal_atom+')'
count_heavy = 0
for idx, char in enumerate(smi):
if count_heavy == num and (char == 'C' or char == 'O'):
element = 'C' if char == 'C' else 'O'
if count_heavy != 0 and smi[idx-1] == '[':
try:
a = int(smi[idx+2])
smi_Pt = smi[:idx+4] + string_add + smi[idx+4:]
except:
smi_Pt = smi[:idx+3] + string_add + smi[idx+3:] if smi[idx+1]=='H' else smi[:idx+2]+string_add+smi[idx+2:]
elif count_heavy != 0 and smi[idx-1] != '[':
smi_Pt = smi[:idx+1]+string_add+smi[idx+1:]
elif count_heavy == 0 and idx != 0:
try:
a = int(smi[idx+2])
smi_Pt = smi[:idx+4] + string_add + smi[idx+4:]
except:
smi_Pt = smi[:idx+3] + string_add + smi[idx+3:] if smi[idx+1] == 'H' else smi[:idx+2]+string_add+smi[idx+2:]
elif count_heavy == 0 and idx == 0:
smi_Pt = smi[:idx+1]+string_add+smi[idx+1:]
mol_Pt = Chem.MolFromSmiles(smi_Pt)
smi_Pt = Chem.MolToSmiles(mol_Pt)
return smi_Pt
if char == 'C' or char == 'O' or char == 'P' or char == 'A' or char == 'R':
count_heavy += 1
return

class smi_single():
def __init__(self):
self.single_smi = []
def smi_single(self,smi_list):
new_smi = []
for smi in smi_list:
if 'O=' in smi or '=O' in smi:
mol=Chem.MolFromSmiles(smi)
smi=Chem.MolToSmiles(mol)
mol=Chem.MolFromSmiles(smi)
mol_H=Chem.AddHs(mol)
for num, atom_object in enumerate(mol_H.GetAtoms()):
if atom_object.GetSymbol() =='C' and 'O' in [x.GetSymbol() for x in atom_object.GetNeighbors()]:
bonds=atom_object.GetBonds()
for bond in bonds:
if bond.GetBondType() == rdkit.Chem.rdchem.BondType.DOUBLE:
if mol_H.GetAtomWithIdx(bond.GetBeginAtomIdx()).GetSymbol() == 'O' or mol_H.GetAtomWithIdx(bond.GetEndAtomIdx()).GetSymbol() == 'O':
O_num = bond.GetBeginAtomIdx() if mol_H.GetAtomWithIdx(bond.GetBeginAtomIdx()).GetSymbol() == 'O' else bond.GetEndAtomIdx()
C_num = num
H_count = len([x.GetSymbol() for x in atom_object.GetNeighbors()if x.GetSymbol() == 'H'])
if H_count == 0:
H_add = ''
elif H_count == 1:
H_add = 'H'
else:
H_add = 'H' + str(H_count)
count_C, count_O = 0,0
for idx,char in enumerate(smi):
if count_C == C_num and char == 'C':
try:
h=smi[idx-1:idx+2]
if h == '[C]' or smi[idx-1:idx+3] == '[CH]':
smi_C = smi
break
else:
smi_C = smi[:idx]+'[C'+H_add+']'+smi[idx+1:]
break
except:
smi_C = smi[:idx]+'[C'+H_add+']'+smi[idx+1:]
break
if char == 'C' or char == 'O' or char == 'P':
count_C += 1
for idx,char in enumerate(smi_C):
if count_O == O_num and char == 'O':
try:
h = smi_C[idx+1]
if smi_C[idx+1] == '=':
smi_O = smi_C[:idx]+'[O]'+smi_C[idx+2:]
else:
smi_O = smi_C[:idx-1]+'[O]'+smi_C[idx+1:]
except:
smi_O = smi_C[:idx-1]+'[O]'+smi_C[idx+1:]
break
if char in 'COPRA':
count_O += 1
mol_O = Chem.MolFromSmiles(smi_O)
smi_O = Chem.MolToSmiles(mol_O)
if smi_O not in self.single_smi:
self.single_smi.append(smi_O)
new_smi.append(smi_O)
#print(new_smi)
if len(new_smi) == 0:
return self.single_smi
else:
return self.smi_single(new_smi)
return
#print(smi_single().smi_single(['[CH]OC(C)=O']))

class add_metal():
def __init__(self):
self.smis_Pt = []
#self.smis_Pt_list = []
#self.l1 = 0
#self.l2 = 0
def add_metal(self,smi,metal):
#print('flag: ',self.smis_Pt)
mol = Chem.MolFromSmiles(smi)
smi = Chem.MolToSmiles(mol)
mol = Chem.MolFromSmiles(smi)
mol_H = Chem.AddHs(mol)
for num, atom_object in enumerate(mol_H.GetAtoms()):
if atom_object.GetSymbol() != 'H' and atom_object.GetSymbol() != metal:
count_bond = 0
saturate = 4 if atom_object.GetSymbol() == 'C' else 2
for bonds in mol_H.GetBonds():
if num in [bonds.GetBeginAtomIdx(), bonds.GetEndAtomIdx()]:
count_bond += 1 if bonds.GetBondType() == rdkit.Chem.rdchem.BondType.SINGLE else 2
if saturate > count_bond:
string_add = ('(['+metal+'])') * (saturate-count_bond)
count_heavy = 0
for idx, char in enumerate(smi):
if count_heavy == num and (char == 'C' or char == 'O'):
if count_heavy != 0 and smi[idx-1] == '[':
try:
a = int(smi[idx+2])
smi_Pt = smi[:idx+4] + string_add + smi[idx+4:]
#print('flag 1: ', smi_Pt)
except:
smi_Pt = smi[:idx+3] + string_add + smi[idx+3:] if smi[idx+1]=='H' else smi[:idx+2]+string_add+smi[idx+2:]
#print('flag 2: ', smi_Pt)
elif count_heavy != 0 and smi[idx-1] != '[':
smi_Pt = smi[:idx+1]+string_add+smi[idx+1:]
#print('flag 3: ', smi_Pt)
elif count_heavy == 0 and idx != 0:
try:
a = int(smi[idx+2])
smi_Pt = smi[:idx+4] + string_add + smi[idx+4:]
#print('flag 4: ', smi_Pt)
except:
smi_Pt = smi[:idx+3] + string_add + smi[idx+3:] if smi[idx+1] == 'H' else smi[:idx+2]+string_add+smi[idx+2:]
#print('flag 5: ', idx, smi_Pt, smi)
elif count_heavy == 0 and idx == 0:
smi_Pt = smi[:idx+1]+string_add+smi[idx+1:]
#print('flag 6: ', smi_Pt)
mol_Pt = Chem.MolFromSmiles(smi_Pt)
smi_Pt = Chem.MolToSmiles(mol_Pt)
if smi_Pt not in self.smis_Pt:
self.smis_Pt.append(smi_Pt)
break
if char == 'C' or char == 'O' or char in 'PRA':
count_heavy += 1

return self.smis_Pt

print(add_metal().add_metal('[O]C[C]','Rh'))

class add_metal_all():
def __init__(self):
self.smis_Pt_list=[]
#self.l1=0
#self.l2=0

def add_metal_all(self,smi_list,metal):
new_list = []
#l1=len(self.smis_Pt_list)
#print('l1: ',l1)
for smi in smi_list:
smi_n_list = add_metal().add_metal(smi, metal)
#print(smi_n_list,smi)
if len(smi_n_list) == 0:
continue
for smi_n in smi_n_list:
if smi_n not in self.smis_Pt_list:
self.smis_Pt_list.append(smi_n)
new_list.append(smi_n)

#l2=len(self.smis_Pt_list)
if len(new_list) == 0:
#print('l1 end: ',l)
#print('finished: ',self.smis_Pt_list)
return self.smis_Pt_list
else:
#print('still looping: ',self.smis_Pt_list)
return self.add_metal_all(new_list, metal)
print(add_metal_all().add_metal_all(['[O]C[C]'],'Rh'))

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