Source code for mordred.TopoPSA

from collections import defaultdict

from rdkit.Chem import BondType, rdMolDescriptors

from ._base import Descriptor

__all__ = ("TopoPSA",)


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`

    """

    __slots__ = ("_no_only",)

    def description(self):
        return "topological polar surface area{}".format(
            " (use only nitrogen and oxygen)" if self._no_only else "",
        )

    @classmethod
    def preset(cls):
        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