def extract_side_chains(mol, remove_duplicates=False, mark='[*]'):
""" Extract side chains from a smiles string. Core is handled as Murcko scaffold.
:param mol: {str} smiles string of a molecule.
:param remove_duplicates: {bool} Keep or remove duplicates.
:param mark: character to mark attachment points.
:return: smiles strings of side chains in a list, attachment points replaced by [R].
"""
pos = range(0, 20)
set_pos = ['[' + str(x) + '*]' for x in pos]
m1 = MolFromSmiles(mol)
try:
core = MurckoScaffold.GetScaffoldForMol(m1)
side_chain = ReplaceCore(m1, core)
smi = MolToSmiles(side_chain, isomericSmiles=True
) # isomericSmiles adds a number to the dummy atoms.
except:
return list()
for i in pos:
smi = smi.replace(''.join(set_pos[i]), mark)
if remove_duplicates:
return list(set(smi.split('.')))
else:
return smi.split('.')
def retrieve_fragments(mol):
substructures_smiles = MolToSmiles(mol)
sidechains = []
sidechains_smiles_list = substructures_smiles.split(".")
for sidechain_smiles in sidechains_smiles_list:
sidechain = MolFromSmiles(sidechain_smiles)
if sidechain_smiles != "":
sidechains.append(sidechain)
return sidechains, sidechains_smiles_list
