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fix a bug about case like (CH2)5 #20

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fix a bug about case like (CH2)5 #20

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81 changes: 46 additions & 35 deletions molscribe/chemistry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

import rdkit
import rdkit.Chem as Chem

from rdkit.Chem import AllChem
rdkit.RDLogger.DisableLog('rdApp.*')

from SmilesPE.pretokenizer import atomwise_tokenizer
Expand Down Expand Up @@ -360,7 +360,10 @@ def get_smiles_from_symbol(symbol, mol, atom, bonds):

total_bonds = int(sum([bond.GetBondTypeAsDouble() for bond in bonds]))
formula_list = _expand_carbon(_parse_formula(symbol))
smiles, bonds_left, num_trails, success = _condensed_formula_list_to_smiles(formula_list, total_bonds, None)
if len(bonds)!=2:
smiles, bonds_left, num_trails, success = _condensed_formula_list_to_smiles(formula_list, total_bonds, None)
else:
smiles, bonds_left, num_trails, success = _condensed_formula_list_to_smiles(formula_list, 1, None)
if success:
return smiles
return None
Expand Down Expand Up @@ -442,39 +445,47 @@ def _need_expand(mol, mappings):
atom.SetIsotope(0)
continue

# remove bonds connected to abbreviation/condensed formula
adjacent_indices = [bond.GetOtherAtomIdx(i) for bond in bonds]
for adjacent_idx in adjacent_indices:
mol_w.RemoveBond(i, adjacent_idx)

adjacent_atoms = [mol_w.GetAtomWithIdx(adjacent_idx) for adjacent_idx in adjacent_indices]
for adjacent_atom, bond in zip(adjacent_atoms, bonds):
adjacent_atom.SetNumRadicalElectrons(int(bond.GetBondTypeAsDouble()))

# get indices of atoms of main body that connect to substituent
bonding_atoms_w = adjacent_indices
# assume indices are concated after combine mol_w and mol_r
bonding_atoms_r = [mol_w.GetNumAtoms()]
for atm in mol_r.GetAtoms():
if atm.GetNumRadicalElectrons() and atm.GetIdx() > 0:
bonding_atoms_r.append(mol_w.GetNumAtoms() + atm.GetIdx())

# combine main body and substituent into a single molecule object
combo = Chem.CombineMols(mol_w, mol_r)

# connect substituent to main body with bonds
mol_w = Chem.RWMol(combo)
# if len(bonding_atoms_r) == 1: # substituent uses one atom to bond to main body
for atm in bonding_atoms_w:
bond_order = mol_w.GetAtomWithIdx(atm).GetNumRadicalElectrons()
mol_w.AddBond(atm, bonding_atoms_r[0], order=BOND_TYPES[bond_order])

# reset radical electrons
for atm in bonding_atoms_w:
mol_w.GetAtomWithIdx(atm).SetNumRadicalElectrons(0)
for atm in bonding_atoms_r:
mol_w.GetAtomWithIdx(atm).SetNumRadicalElectrons(0)
atoms_to_remove.append(i)
if "(" in symbol and len(bonds)==2:#(CH2)5
connected_info = [(neighbor.GetIdx(), mol_w.GetBondBetweenAtoms(i, neighbor.GetIdx()).GetBondType()) for neighbor in atom.GetNeighbors()]
combined = Chem.RWMol(AllChem.CombineMols(mol_w, mol_r))
combined.AddBond(connected_info[0][0], mol_w.GetNumAtoms(), connected_info[0][1])
combined.AddBond(connected_info[1][0], mol_w.GetNumAtoms()+mol_r.GetNumAtoms()-1, connected_info[1][1])
mol_w = combined
atoms_to_remove.append(i)
else:
# remove bonds connected to abbreviation/condensed formula
adjacent_indices = [bond.GetOtherAtomIdx(i) for bond in bonds]
for adjacent_idx in adjacent_indices:
mol_w.RemoveBond(i, adjacent_idx)

adjacent_atoms = [mol_w.GetAtomWithIdx(adjacent_idx) for adjacent_idx in adjacent_indices]
for adjacent_atom, bond in zip(adjacent_atoms, bonds):
adjacent_atom.SetNumRadicalElectrons(int(bond.GetBondTypeAsDouble()))

# get indices of atoms of main body that connect to substituent
bonding_atoms_w = adjacent_indices
# assume indices are concated after combine mol_w and mol_r
bonding_atoms_r = [mol_w.GetNumAtoms()]
for atm in mol_r.GetAtoms():
if atm.GetNumRadicalElectrons() and atm.GetIdx() > 0:
bonding_atoms_r.append(mol_w.GetNumAtoms() + atm.GetIdx())

# combine main body and substituent into a single molecule object
combo = Chem.CombineMols(mol_w, mol_r)

# connect substituent to main body with bonds
mol_w = Chem.RWMol(combo)
# if len(bonding_atoms_r) == 1: # substituent uses one atom to bond to main body
for atm in bonding_atoms_w:
bond_order = mol_w.GetAtomWithIdx(atm).GetNumRadicalElectrons()
mol_w.AddBond(atm, bonding_atoms_r[0], order=BOND_TYPES[bond_order])

# reset radical electrons
for atm in bonding_atoms_w:
mol_w.GetAtomWithIdx(atm).SetNumRadicalElectrons(0)
for atm in bonding_atoms_r:
mol_w.GetAtomWithIdx(atm).SetNumRadicalElectrons(0)
atoms_to_remove.append(i)

# Remove atom in the end, otherwise the id will change
# Reverse the order and remove atoms with larger id first
Expand Down