Source code for mordred.TopoPSA

from collections import defaultdict

from rdkit.Chem import BondType, rdMolDescriptors

from ._base import Descriptor

__all__ = ("TopoPSA",)


[docs] class TopoPSA(Descriptor): r"""topological polar surface area descriptor(NO only: rdkit wrapper). :type no_only: bool :param no_only: * True: N,O only TPSA * False: all(N,O,S,P) TPSA References * :doi:`10.1021/jm000942e` """ since = "1.0.0" __slots__ = ("_no_only",)
[docs] def description(self): return "topological polar surface area{}".format( " (use only nitrogen and oxygen)" if self._no_only else "" )
@classmethod def preset(cls, version): yield cls(True) yield cls(False) def __str__(self): return "TopoPSA(NO)" if self._no_only else "TopoPSA" def parameters(self): return (self._no_only,) def __init__(self, no_only=True): self._no_only = no_only def calculate(self): tpsa = rdMolDescriptors.CalcTPSA(self.mol) if self._no_only: return tpsa for atom in self.mol.GetAtoms(): atomic_num = atom.GetAtomicNum() if atomic_num == 15: tpsa += self._get_phosphorus_contrib(atom) elif atomic_num == 16: tpsa += self._get_sulfur_contrib(atom) return tpsa @staticmethod def _hydrogen_count(atom): return atom.GetTotalNumHs() + sum( 1 for a in atom.GetNeighbors() if a.GetAtomicNum() == 1 ) @staticmethod def _bond_type_count(atom): cnt = defaultdict(int) for bond in atom.GetBonds(): if bond.GetIsAromatic(): cnt[BondType.AROMATIC] += 1 else: cnt[bond.GetBondType()] += 1 return dict(cnt) @classmethod def _get_phosphorus_contrib(cls, atom): nH = cls._hydrogen_count(atom) cnt = cls._bond_type_count(atom) if atom.GetFormalCharge() != 0 or atom.GetIsAromatic(): return 0.0 if nH == 1 and cnt == {BondType.SINGLE: 3, BondType.DOUBLE: 1}: return 23.47 elif nH == 0: if cnt == {BondType.SINGLE: 3}: return 13.59 elif cnt == {BondType.SINGLE: 1, BondType.DOUBLE: 1}: return 34.14 elif cnt == {BondType.SINGLE: 3, BondType.DOUBLE: 1}: return 9.81 return 0.0 @classmethod def _get_sulfur_contrib(cls, atom): nH = cls._hydrogen_count(atom) cnt = cls._bond_type_count(atom) if atom.GetFormalCharge() != 0: return 0.0 if atom.GetIsAromatic(): if nH == 0: if cnt == {BondType.AROMATIC: 2}: return 28.24 elif cnt == {BondType.AROMATIC: 2, BondType.DOUBLE: 1}: return 21.70 else: if nH == 1 and cnt == {BondType.SINGLE: 2}: return 38.80 elif nH == 0: if cnt == {BondType.SINGLE: 2}: return 25.30 elif cnt == {BondType.DOUBLE: 1}: return 32.09 elif cnt == {BondType.SINGLE: 2, BondType.DOUBLE: 1}: return 19.21 elif cnt == {BondType.SINGLE: 2, BondType.DOUBLE: 2}: return 8.38 return 0.0 rtype = float