Source code for mordred._base.descriptor

from abc import ABCMeta, abstractmethod
from inspect import isabstract
from contextlib import contextmanager

import six
import numpy as np


class MissingValueException(Exception):
    "internally used exception"

    __slots__ = ('error',)

    def __init__(self, error):
        self.error = error


[docs]class Descriptor(six.with_metaclass(ABCMeta, object)):
    r"""abstract base class of descriptors."""

    __slots__ = '_context',

    explicit_hydrogens = True
    kekulize = False
    require_connected = False
    require_3D = False

    def __reduce_ex__(self, version):
        return self.__class__, self.parameters()

    @abstractmethod
[docs]    def parameters(self):
        '''get __init__ arguments of this descriptor instance.

        (abstract method)
        '''
        raise NotImplementedError('not implemented Descriptor.parameters method')

    @property
    def as_argument(self):
        '''argument representation of descriptor'''
        return self

    @staticmethod
    def _pretty(v):
        v = getattr(v, 'as_argument', v)
        return repr(v)

    def __repr__(self):
        return '{}({})'.format(
            self.__class__,
            ', '.join(self._pretty(a) for a in self.parameters())
        )

    def __hash__(self):
        return hash((self.__class__, self.parameters()))

    def __compare_by_reduce(meth):
        def compare(self, other):
            l = self.__class__, self.parameters()
            r = other.__class__, other.parameters()
            return getattr(l, meth)(r)

        return compare

    __eq__ = __compare_by_reduce('__eq__')
    __ne__ = __compare_by_reduce('__ne__')

    __lt__ = __compare_by_reduce('__lt__')
    __gt__ = __compare_by_reduce('__gt__')
    __le__ = __compare_by_reduce('__le__')
    __ge__ = __compare_by_reduce('__ge__')

    rtype = None

    @classmethod
[docs]    def preset(cls):
        r"""generate preset descriptor instances.

        :rtype: iterable
        """
        return ()

[docs]    def dependencies(self):
        r"""descriptor dependencies.

        :rtype: {:py:class:`str`: (:py:class:`Descriptor` or :py:class:`None`)} or :py:class:`None`
        """
        pass

    @abstractmethod
[docs]    def calculate(self, mol):
        r"""calculate descriptor value.

        (abstract method)
        """
        raise NotImplementedError('not implemented Descriptor.calculate method')

    @classmethod
[docs]    def is_descriptor_class(cls, desc):
        r"""check calculatable descriptor class or not.

        :rtype: :py:class:`bool`
        """
        return (
            isinstance(desc, type) and
            issubclass(desc, cls) and
            not isabstract(desc)
        )

    @property
    def mol(self):
        '''get molecule'''
        return self._context.get_mol(self)

    @property
    def coord(self):
        '''get 3D coordinate'''
        if not self.require_3D:
            self.fail(AttributeError('use 3D coordinate in 2D descriptor'))

        return self._context.get_coord(self)

    @contextmanager
[docs]    def rethrow_zerodiv(self):
        '''treat zero div as known exception'''
        with np.errstate(divide='raise', invalid='raise'):
            try:
                yield
            except (FloatingPointError, ZeroDivisionError) as e:
                self.fail(ZeroDivisionError(*e.args))

[docs]    def fail(self, exception):
        '''raise known exception and return missing value'''
        raise MissingValueException(exception)

    @contextmanager
[docs]    def rethrow_na(self, exception):
        '''treat any exceptions as known exception'''
        try:
            yield
        except exception as e:
            self.fail(e)