def num_bond_in_ring(mol: Chem.rdchem.Mol):
"""
Check the number of the bonds that are in the ring, count vector.
"""
count = 0
n_atoms = mol.GetNumAtoms()
for a1 in range(n_atoms):
for a2 in range(a1 + 1, n_atoms):
bond = mol.GetBondBetweenAtoms(a1, a2)
if bond is None:
continue
elif bond.IsInRing():
count += 1
return [count]
def trim_side_chain(mol: Chem.rdchem.Mol, core, unwanted_side_chains):
"""Trim list of side chain from a molecule."""
mol = Chem.AddHs(mol)
match = mol.GetSubstructMatch(core)
map2idx = {}
map2nei = {}
unwanted2map = {}
for patt in unwanted_side_chains:
unwanted2map[patt] = [
a.GetAtomMapNum() for a in patt.GetAtoms() if a.GetAtomMapNum()
]
unwanted_mapping = list(
itertools.chain.from_iterable(unwanted2map.values()))
for atom in core.GetAtoms():
num = atom.GetAtomMapNum()
if num and num in unwanted_mapping:
mol_atom_idx = match[atom.GetIdx()]
map2idx[mol_atom_idx] = num
nei_atoms = mol.GetAtomWithIdx(mol_atom_idx).GetNeighbors()
map2nei[mol_atom_idx] = [
n.GetIdx() for n in nei_atoms if n.GetIdx() in match
]
emol = Chem.EditableMol(mol)
for atom_idx, atom_map in map2idx.items():
dummy = Chem.rdchem.Atom("*")
dummy.SetAtomMapNum(atom_map)
nei_idx = map2nei.get(atom_idx, [None])[0]
if nei_idx:
bond = mol.GetBondBetweenAtoms(atom_idx, nei_idx)
emol.RemoveBond(atom_idx, nei_idx)
new_ind = emol.AddAtom(dummy)
emol.AddBond(nei_idx, new_ind, bond.GetBondType())
mol = emol.GetMol()
mol = Chem.RemoveHs(mol)
query_param = AdjustQueryParameters()
query_param.makeDummiesQueries = False
query_param.adjustDegree = False
query_param.aromatizeIfPossible = True
for patt, _ in unwanted2map.items():
cur_frag = dm.fix_mol(patt)
mol = Chem.DeleteSubstructs(mol, cur_frag, onlyFrags=True)
return dm.keep_largest_fragment(mol)
