StructureMethods

Complexity

Total Complexity

9

Size/Duplication

Total Lines	32
Duplicated Lines	0 %

Test Coverage

Coverage

27.27%

Importance

Changes	3
Bugs	0	Features	1

5 Methods

Rating	Name	Duplication	Size	Complexity
A	__init__()	0	2	1
A	remove_hs()	0	2	2
A	add_hs()	0	2	2
A	atoms()	0	3	2
A	visualize()	0	15	2

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

""" # skchem.pandas.structure_methods

 Tools for adding a default attribute to pandas objects."""

from sklearn.manifold import TSNE, MDS

The import sklearn.manifold could not be resolved.

from sklearn.decomposition import PCA

The import sklearn.decomposition could not be resolved.

from matplotlib import pyplot as plt

The import matplotlib could not be resolved.

Unused pyplot imported from matplotlib as plt

import pandas as pd

The import pandas could not be resolved.

from pandas.core.base import NoNewAttributesMixin, AccessorProperty

The import pandas.core.base could not be resolved.

from pandas.core.series import Series

The import pandas.core.series could not be resolved.

from pandas.core.index import Index

The import pandas.core.index could not be resolved.

from .. import core
from .. import descriptors

DIM_RED = {
    'tsne': TSNE,
    'pca': PCA,
    'mds': MDS
}


class StructureMethods(NoNewAttributesMixin):

    """ Accessor for calling chemical methods on series of molecules. """

    def __init__(self, data):
        self._data = data

    def add_hs(self, **kwargs):

This method should have a docstring.

        return self._data.apply(lambda m: m.add_hs(**kwargs))

Usage of * or ** arguments should usually be done with care.

    def remove_hs(self, **kwargs):

This method should have a docstring.

        return self._data.apply(lambda m: m.remove_hs(**kwargs))

Usage of * or ** arguments should usually be done with care.

    def visualize(self, fper='morgan', dim_red='tsne', dim_red_kw={}, **kwargs):

The default value {} might cause unintended side-effects.

This method should have a docstring.

        if isinstance(dim_red, str):
            dim_red = DIM_RED.get(dim_red.lower())(**dim_red_kw)

Usage of * or ** arguments should usually be done with care.

        fper = descriptors.get(fper)
        fper.verbose = False
        feats = fper.transform(self._data)
        feats = feats.fillna(feats.mean())
        twod = pd.DataFrame(dim_red.fit_transform(feats))

The Instance of str does not seem to have a member named fit_transform.

        ax = twod.plot.scatter(x=0, y=1, **kwargs)

The name ax does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

        ax.set_xticklabels([])
        ax.set_xlabel('')
        ax.set_yticklabels([])
        ax.set_ylabel('')

    @property
    def atoms(self):

This method should have a docstring.

        return self._data.apply(lambda m: m.atoms)


def only_contains_mols(ser):

This function should have a docstring.

    return ser.apply(lambda s: isinstance(s, core.Mol)).all()


class StructureAccessorMixin(object):

    """ Mixin to bind chemical methods to objects. """

    def _make_structure_accessor(self):
        if isinstance(self, Index):
            raise AttributeError('Can only use .mol accessor with molecules,'
                                 'which use np.object_ in scikit-chem.')
        if not only_contains_mols(self):
            raise AttributeError('Can only use .mol accessor with '
                                 'Series that only contain mols.')

        return StructureMethods(self)
    mol = AccessorProperty(StructureMethods, _make_structure_accessor)

Series.__bases__ += StructureAccessorMixin,