richlewis42 / scikit-chem

skchem/features/physicochemical.py

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

"""
## skchem.descriptors.physicochemical

Physicochemical descriptors and associated functions are defined.

"""

from rdkit.Chem import Descriptors

The import rdkit.Chem could not be resolved.

import pandas as pd

The import pandas could not be resolved.

import numpy as np

The import numpy could not be resolved.

from ..base import Transformer, Featurizer
from ..utils import camel_to_snail

DESCRIPTORS = {camel_to_snail(s): f for (s, f) in Descriptors.descList}


class PhysicochemicalFeaturizer(Transformer, Featurizer):

    """ Physicochemical descriptor generator using RDKit descriptor """

    def __init__(self, features='all', **kwargs):

        """ Create a physicochemical descriptor generator.

        Args:
            descriptors (list<(str, func)> or 'all'):
                Descriptors to calculate, or if 'all', use all descriptors."""

        super(PhysicochemicalFeaturizer, self).__init__(**kwargs)

        self.features = features

    @property
    def features(self):

This method should have a docstring.

        return self._features

    @features.setter

This code seems to be duplicated in your project.

    def features(self, features):

This method should have a docstring.

        if features == 'all':
            features = DESCRIPTORS
        elif isinstance(features, str):
            features = {features: DESCRIPTORS[features]}
        elif isinstance(features, list):
            features = {feature: DESCRIPTORS[feature] for feature in features}
        elif isinstance(features, (dict, pd.Series)):
            features = features
        else:
            raise NotImplementedError('Cannot use features {}'.format(features))

        self._features = pd.Series(features)

The attribute _features was defined outside __init__.

        self._features.index.name = 'physicochemical_features'

    @property
    def name(self):

This method should have a docstring.

This method could be written as a function/class method.

        return 'physchem'

    @property
    def columns(self):
        return self.features.index

    def _transform_mol(self, mol):
        res = []
        for (n, f) in self.features.iteritems():

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

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

The variable n seems to be unused.

            try:
                res.append(f(mol))
            except ValueError:
                return res.append(np.NaN)

        return np.array(res)