Source code for mordred.CPSA

r"""charged partial surface area descriptor.

References
    * :doi:`10.1021/ac00220a013`

"""
import numpy as np

from ._base import Descriptor
from ._util import atoms_to_numpy
from .surface_area import SurfaceArea
from ._atomic_property import AtomicProperty, vdw_radii

__all__ = (
    "PNSA",
    "PPSA",
    "DPSA",
    "FNSA",
    "FPSA",
    "WNSA",
    "WPSA",
    "RNCG",
    "RPCG",
    "RNCS",
    "RPCS",
    "TASA",
    "TPSA",
    "RASA",
    "RPSA",
)


class CPSABase(Descriptor):
    __slots__ = ()
    require_3D = True

    @classmethod
    def preset(cls, version):
        yield cls()

    def parameters(self):
        return ()

    def __str__(self):
        return self.__class__.__name__

    rtype = float


class VersionCPSABase(CPSABase):
    __slots__ = ("_version",)

    @classmethod
    def preset(cls, version):
        return map(cls, cls.versions)

    def parameters(self):
        return (self._version,)

    versions = [1, 2, 3, 4, 5]

    def __init__(self, version=1):
        self._version = version

    def __str__(self):
        return "{}{}".format(self.__class__.__name__, self._version)


class AtomicSurfaceArea(CPSABase):
    __slots__ = "_solvent_radius", "_level"

    def parameters(self):
        return self._solvent_radius, self._level

    def __init__(self, solvent_radius=1.4, level=5):
        self._solvent_radius = solvent_radius
        self._level = level

    def calculate(self):
        rs = atoms_to_numpy(
            lambda a: vdw_radii[a.GetAtomicNum()] + self._solvent_radius, self.mol
        )

        with self.rethrow_zerodiv():
            sa = SurfaceArea(rs, self.coord, self._level)
        return np.array(sa.surface_area())

    rtype = None


class TotalSurfaceArea(CPSABase):
    __slots__ = ()

    def dependencies(self):
        return {"ASA": AtomicSurfaceArea()}

    def calculate(self, ASA):
        return np.sum(ASA)


class AtomicCharge(CPSABase):
    __slots__ = ()
    require_3D = False

    def dependencies(self):
        return {"charges": AtomicProperty(self.explicit_hydrogens, "c")}

    def calculate(self, charges):
        return charges

    rtype = None


[docs] class PNSA(VersionCPSABase): r"""partial negative surface area descriptor. .. math:: {\rm PNSA}_1 = \sum_{a-} {\rm SA}_a^- where :math:`\sum_{a-}` means sum over negative charged atoms, :math:`{\rm SA}_a^-` is atomic partial surface area. :type version: int :param version: one of :py:attr:`versions` """ since = "1.0.0" __slots__ = ()
[docs] def description(self): return "partial negative surface area (version {})".format(self._version)
def dependencies(self): return {"SA": AtomicSurfaceArea(), "charges": AtomicCharge()} @staticmethod def _mask(charges): return charges < 0.0 def calculate(self, SA, charges): mask = self._mask(charges) if self._version == 1: f = 1.0 elif self._version == 2: f = np.sum(charges[mask]) elif self._version == 3: f = charges[mask] elif self._version == 4: f = np.sum(charges[mask]) / self.mol.GetNumAtoms() elif self._version == 5: with self.rethrow_zerodiv(): f = np.sum(charges[mask]) / np.sum(mask) return np.sum(f * SA[mask])
[docs] class PPSA(PNSA): r"""partial positive surface area descriptor. :type version: int :param version: one of :py:attr:`versions` """ since = "1.0.0" __slots__ = ()
[docs] def description(self): return "partial positive surface area (version {})".format(self._version)
@staticmethod def _mask(charges): return charges > 0.0
[docs] class DPSA(VersionCPSABase): r"""difference in charged partial surface area descriptor. :type version: int :param version: one of :py:attr:`versions` """ since = "1.0.0" __slots__ = ()
[docs] def description(self): return "difference in charged partial surface area (version {})".format( self._version )
def dependencies(self): return {"PNSA": PNSA(self._version), "PPSA": PPSA(self._version)} def calculate(self, PPSA, PNSA): return PPSA - PNSA
[docs] class FNSA(VersionCPSABase): r"""fractional charged partial negative surface area descriptor. :type version: int :param version: one of :py:attr:`versions` """ since = "1.0.0" __slots__ = ()
[docs] def description(self): return "fractional charged partial negative surface area (version {})".format( self._version ) # noqa: E501
def _SA(self): return PNSA(self._version) def dependencies(self): return {"ASA": AtomicSurfaceArea(), "SA": self._SA()} def calculate(self, SA, ASA): return SA / np.sum(ASA)
[docs] class FPSA(FNSA): r"""fractional charged partial positive surface area descriptor. :type version: int :param version: one of :py:attr:`versions` """ since = "1.0.0" __slots__ = ()
[docs] def description(self): return "fractional charged partial positive surface area (version {})".format( self._version ) # noqa: E501
def _SA(self): return PPSA(self._version)
[docs] class WNSA(FNSA): r"""surface weighted charged partial negative surface area descriptor. :type version: int :param version: one of :py:attr:`versions` """ since = "1.0.0" __slots__ = ()
[docs] def description(self): return "surface weighted charged partial negative surface area (version {})".format( self._version ) # noqa: E501
def calculate(self, SA, ASA): return SA * np.sum(ASA) / 1000.0
[docs] class WPSA(FPSA): r"""surface weighted charged partial positive surface area descriptor. :type version: int :param version: one of :py:attr:`versions` """ since = "1.0.0" __slots__ = ()
[docs] def description(self): return "surface weighted charged partial positive surface area (version {})".format( self._version ) # noqa: E501
def calculate(self, SA, ASA): return SA * np.sum(ASA) / 1000.0
[docs] class RNCG(CPSABase): r"""relative negative charge descriptor.""" since = "1.0.0" __slots__ = () require_3D = False
[docs] def description(self): return "relative negative charge"
@staticmethod def _mask(charges): return charges < 0.0 def dependencies(self): return {"charges": AtomicCharge()} def calculate(self, charges): charges = charges[self._mask(charges)] if len(charges) == 0: return 0.0 Qmax = charges[np.argmax(np.abs(charges))] return Qmax / np.sum(charges)
[docs] class RPCG(RNCG): r"""relative positive charge descriptor.""" since = "1.0.0" __slots__ = ()
[docs] def description(self): return "relative positive charge"
@staticmethod def _mask(charges): return charges > 0.0
[docs] class RNCS(CPSABase): r"""relative negative charge surface area descriptor.""" since = "1.0.0" __slots__ = () _RCG = RNCG()
[docs] def description(self): return "relative negative charge surface area"
def dependencies(self): return {"RCG": self._RCG, "SA": AtomicSurfaceArea(), "charges": AtomicCharge()} @staticmethod def _mask(charges): return charges < 0 def calculate(self, RCG, SA, charges): mask = self._mask(charges) charges = charges[mask] if len(charges) == 0: return 0.0 SAmax = SA[mask][np.argmax(np.abs(charges))] return SAmax / RCG rtype = float
[docs] class RPCS(RNCS): r"""relative positive charge surface area descriptor.""" since = "1.0.0" __slots__ = ()
[docs] def description(self): return "relative positive charge surface area"
@staticmethod def _mask(charges): return charges > 0 _RCG = RPCG()
[docs] class TASA(CPSABase): r"""total hydrophobic surface area descriptor.""" since = "1.0.0" __slots__ = ()
[docs] def description(self): return "total hydrophobic surface area"
@staticmethod def _mask(charges): return np.abs(charges) < 0.2 def dependencies(self): return {"SA": AtomicSurfaceArea(), "charges": AtomicCharge()} def calculate(self, SA, charges): return np.sum(SA[self._mask(charges)])
[docs] class TPSA(TASA): r"""total polar surface area descriptor.""" since = "1.0.0" __slots__ = ()
[docs] def description(self): return "total polar surface area"
@staticmethod def _mask(charges): return np.abs(charges) >= 0.2
[docs] class RASA(CPSABase): r"""relative hydrophobic surface area descriptor.""" since = "1.0.0" __slots__ = () _TxSA = TASA()
[docs] def description(self): return "relative hydrophobic surface area"
def dependencies(self): return {"SASA": AtomicSurfaceArea(), "TxSA": self._TxSA} def calculate(self, TxSA, SASA): return TxSA / np.sum(SASA)
[docs] class RPSA(RASA): r"""relative polar surface area descriptor."""
[docs] def description(self): return "relative polar surface area"
since = "1.0.0" __slots__ = () _TxSA = TPSA()