BondView

Complexity

Total Complexity

6

Size/Duplication

Total Lines	21
Duplicated Lines	0 %

Test Coverage

Coverage

0%

Importance

Changes	1
Bugs	0	Features	0

4 Methods

Rating	Name	Duplication	Size	Complexity
A	order()	0	3	2
A	__getitem__()	0	6	2
A	index()	0	3	1
A	__len__()	0	2	1

#! /usr/bin/env python
#
# Copyright (C) 2015-2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD

"""
## skchem.core.bond

Defining chemical bonds in scikit-chem.
"""

import pandas as pd

The import pandas could not be resolved.

import rdkit.Chem

The import rdkit.Chem could not be resolved.

from . import Atom
from .base import ChemicalObject, PropertyView, ChemicalObjectView

class Bond(rdkit.Chem.rdchem.Bond, ChemicalObject):

    """
    Class representing a chemical bond in scikit-chem.

    """

    @property
    def props(self):

        """ PropertyView: rdkit properties of the atom. """

        if not hasattr(self, '_props'):
            self._props = PropertyView(self)

The attribute _props was defined outside __init__.

        return PropertyView(self)

    @property
    def order(self):

        """ int: the order of the bond. """

        return self.GetBondTypeAsDouble()

The Instance of Bond does not seem to have a member named GetBondTypeAsDouble.

    @property
    def atoms(self):

        """ list[Atom]: list of atoms involved in the bond. """

        return [Atom.from_super(self.GetBeginAtom()), Atom.from_super(self.GetEndAtom())]

The Instance of Bond does not seem to have a member named GetBeginAtom.

The Instance of Bond does not seem to have a member named GetEndAtom.

    def draw(self):

        """ str: Draw the bond in ascii. """

        return '{}{}{}'.format(self.atoms[0].element, \
            '-' if self.order == 1 else self.GetSmarts(), \

The Instance of Bond does not seem to have a member named GetSmarts.

            self.atoms[1].element)

    def to_dict(self):

        """ dict: Convert to a dictionary representation. """

        return {"b": self.GetBeginAtomIdx(), "e": self.GetEndAtomIdx(), "o": self.order}

The Instance of Bond does not seem to have a member named GetBeginAtomIdx.

The Instance of Bond does not seem to have a member named GetEndAtomIdx.

    def __repr__(self):
        return '<{klass} type="{bond}" at {address}>'.format(klass=self.__class__.__name__, \
            bond=self.draw(), \
            address=hex(id(self)))

    def __str__(self):
        return self.draw()


class BondView(ChemicalObjectView):

    """ Bond interface wrapper """
    def __getitem__(self, index):
        from .bond import Bond

Bond is re-defining a name which is already available in the outer-scope (previously defined on line 18).

This module seems to import itself.

        if index >= len(self):
            raise IndexError('Index {} out of range for molecule with {} bonds.'.format(index, len(self)))

This line is too long as per the coding-style (106/100).

        else:
            return Bond.from_super(self.owner.GetBondWithIdx(index))


    def __len__(self):
        return self.owner.GetNumBonds()

    @property
    def order(self):

This method should have a docstring.

        return pd.RangeIndex((bond.order for bond in self), index=self.index)

    @property
    def index(self):

This method should have a docstring.

        return pd.RangeIndex(len(self), name='bond_idx')