Issues in atom.py (master) - Issues in master - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

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skchem/features/atom.py (69 issues)

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#! /usr/bin/env python
#
# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
# License: 3-clause BSD

"""
## skchem.descriptors.atom

Module specifying atom based descriptor generators.
"""

import functools
from abc import ABCMeta

import pandas as pd
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
import numpy as np
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from rdkit import Chem
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem import Crippen
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem import Lipinski
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem import rdMolDescriptors, rdPartialCharges
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem.rdchem import HybridizationType
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from ..core import Mol
from ..resource import PERIODIC_TABLE, ORGANIC
from ..base import AtomTransformer, Featurizer
from ..utils import nanarray


def element(a):


    """ Return the element """

    return a.GetSymbol()


def is_element(a, symbol='C'):


    """ Is the atom of a given element """
    return element(a) == symbol

element_features = {'is_{}'.format(e): functools.partial(is_element, symbol=e)

                    for e in ORGANIC}


def is_h_acceptor(a):


    """ Is an H acceptor? """

    m = a.GetOwningMol()

    idx = a.GetIdx()
    return idx in [i[0] for i in Lipinski._HAcceptors(m)]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent


def is_h_donor(a):


    """ Is an H donor? """

    m = a.GetOwningMol()

    idx = a.GetIdx()
    return idx in [i[0] for i in Lipinski._HDonors(m)]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent


def is_hetero(a):


    """ Is a heteroatom? """

    m = a.GetOwningMol()

    idx = a.GetIdx()
    return idx in [i[0] for i in Lipinski._Heteroatoms(m)]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent


def atomic_number(a):


    """ Atomic number of atom """

    return a.GetAtomicNum()


def atomic_mass(a):


    """ Atomic mass of atom """

    return a.atomic_mass


def explicit_valence(a):


    """ Explicit valence of atom """
    return a.GetExplicitValence()


def implicit_valence(a):


    """ Implicit valence of atom """

    return a.GetImplicitValence()


def valence(a):


    """ returns the valence of the atom """

    return explicit_valence(a) + implicit_valence(a)


def formal_charge(a):


    """ Formal charge of atom """

    return a.GetFormalCharge()


def is_aromatic(a):


    """ Boolean if atom is aromatic"""

    return a.GetIsAromatic()


def num_implicit_hydrogens(a):


    """ Number of implicit hydrogens """

    return a.GetNumImplicitHs()


def num_explicit_hydrogens(a):


    """ Number of explicit hydrodgens """

    return a.GetNumExplicitHs()


def num_hydrogens(a):


    """ Number of hydrogens """

    return num_implicit_hydrogens(a) + num_explicit_hydrogens(a)


def is_in_ring(a):


    """ Whether the atom is in a ring """

    return a.IsInRing()


def crippen_log_p_contrib(a):


    """ Hacky way of getting logP contribution. """

    idx = a.GetIdx()
    m = a.GetOwningMol()

    return Crippen._GetAtomContribs(m)[idx][0]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent


def crippen_molar_refractivity_contrib(a):


    """ Hacky way of getting molar refractivity contribution. """

    idx = a.GetIdx()
    m = a.GetOwningMol()

    return Crippen._GetAtomContribs(m)[idx][1]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent


def tpsa_contrib(a):


    """ Hacky way of getting total polar surface area contribution. """

    idx = a.GetIdx()
    m = a.GetOwningMol()

    return rdMolDescriptors._CalcTPSAContribs(m)[idx]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent


def labute_asa_contrib(a):


    """ Hacky way of getting accessible surface area contribution. """

    idx = a.GetIdx()
    m = a.GetOwningMol()

    return rdMolDescriptors._CalcLabuteASAContribs(m)[0][idx]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent


def gasteiger_charge(a, force_calc=False):


    """ Hacky way of getting gasteiger charge """

    res = a.props.get('_GasteigerCharge', None)
    if res and not force_calc:
        return float(res)
    else:
        m = a.GetOwningMol()

        rdPartialCharges.ComputeGasteigerCharges(m)
        return float(a.props['_GasteigerCharge'])


def pauling_electronegativity(a):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return a.pauling_electronegativity


def first_ionization(a):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return PERIODIC_TABLE.loc[a.atomic_number, 'first_ionisation_energy']


def group(a):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return PERIODIC_TABLE.loc[a.atomic_number, 'group']


def period(a):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return PERIODIC_TABLE.loc[a.atomic_number, 'period']


def is_hybridized(a, hybrid_type=HybridizationType.SP3):


    """ Hybridized as type hybrid_type, default SP3 """

    return str(a.GetHybridization()) == str(hybrid_type)

hybridization_features = {'is_' + n + '_hybridized': functools.partial(

    is_hybridized, hybrid_type=n)
                          for n in HybridizationType.names}

ATOM_FEATURES = {
    'atomic_number': atomic_number,
    'atomic_mass': atomic_mass,
    'formal_charge': formal_charge,
    'gasteiger_charge': gasteiger_charge,
    'pauling_electronegativity': pauling_electronegativity,
    'first_ionisation': first_ionization,
    'group': group,
    'period': period,
    'valence': valence,
    'is_aromatic': is_aromatic,
    'num_hydrogens': num_hydrogens,
    'is_in_ring': is_in_ring,
    'log_p_contrib': crippen_log_p_contrib,
    'molar_refractivity_contrib': crippen_molar_refractivity_contrib,
    'is_h_acceptor': is_h_acceptor,
    'is_h_donor': is_h_donor,
    'is_heteroatom': is_hetero,
    'total_polar_surface_area_contrib': tpsa_contrib,
    'total_labute_accessible_surface_area': labute_asa_contrib,
}
ATOM_FEATURES.update(element_features)
ATOM_FEATURES.update(hybridization_features)


class AtomFeaturizer(AtomTransformer, Featurizer):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    def __init__(self, features='all', n_jobs=1, verbose=True):
        self._features = None
        self.features = features

        super(AtomFeaturizer, self).__init__(n_jobs=n_jobs, verbose=verbose)

    @property
    def name(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return 'atom_feat'

    @property
    def features(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return self._features

    @features.setter

    def features(self, features):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        if isinstance(features, str):
            if features == 'all':
                features = ATOM_FEATURES
            else:
                features = {features: ATOM_FEATURES[features]}
        elif isinstance(features, list):
            features = {feature: ATOM_FEATURES[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)
        self._features.index.name = 'atom_features'

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

    def _transform_atom(self, atom):
        return self.features.apply(lambda f: f(atom)).values


    def _transform_mol(self, mol):
        return np.array([self.transform(a) for a in mol.atoms])


class DistanceTransformer(AtomTransformer, Featurizer):

    """ Base class implementing Distance Matrix transformers.

    Concrete classes inheriting from this should implement `_transform_mol`.
    """

    __metaclass__ = ABCMeta

    @property
    def minor_axis(self):
        return pd.RangeIndex(self.max_atoms, name='atom_idx')

    def _transform_atom(self, atom):
        return NotImplemented

    def transform(self, mols):
        res = super(DistanceTransformer, self).transform(mols)
        if isinstance(mols, Mol):
            res = res.iloc[:len(mols.atoms), :len(mols.atoms)]
        return res


class SpacialDistanceTransformer(DistanceTransformer):


    """ Transformer class for generating 3D distance matrices.  """

    # TODO: handle multiple conformers


    def __init__(self, n_jobs=1, verbose=True):

        """ Initialize a SpacialDistanceTransformer.

        Args:
            n_jobs (int):
                The number of processes to run the featurizer in.
            verbose (bool):
                Whether to output a progress bar.
        """
        super(SpacialDistanceTransformer, self).__init__(n_jobs=n_jobs,
                                                         verbose=verbose)

    @property
    def name(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return 'spacial_dist'

    def _transform_mol(self, mol):
        res = nanarray((len(mol.atoms), self.max_atoms))
        res[:, :len(mol.atoms)] = Chem.Get3DDistanceMatrix(mol)
        return res


class GraphDistanceTransformer(DistanceTransformer):


    """ Transformer class for generating Graph distance matrices. """

    def __init__(self, n_jobs=1, verbose=True):

        """ Initialize a GraphDistanceTransformer.

        Args:
            n_jobs (int):
                The number of processes to run the featurizer in.
            verbose (bool):
                Whether to output a progress bar.
        """

        super(GraphDistanceTransformer, self).__init__(n_jobs=n_jobs,
                                                       verbose=verbose)

    @property
    def name(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        return 'graph_dist'

    def _transform_mol(self, mol):
        res = nanarray((len(mol.atoms), self.max_atoms))
        res[:len(mol.atoms), :len(mol.atoms)] = Chem.GetDistanceMatrix(mol)
        return res


Issues (942)

skchem/features/atom.py (69 issues)

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1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

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1. Missing Dependencies

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1		#! /usr/bin/env python
2		#
3		# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
4		# License: 3-clause BSD
5
6	1	"""
7		## skchem.descriptors.atom
8
9		Module specifying atom based descriptor generators.
10		"""
11
12	1	import functools
13	1	from abc import ABCMeta
14
15	1	import pandas as pd
		0 ignored issues – show Configuration introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `pandas` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
16	1	import numpy as np
		0 ignored issues – show Configuration introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `numpy` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
17
18	1	from rdkit import Chem
		0 ignored issues – show Configuration introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `rdkit` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
19	1	from rdkit.Chem import Crippen
		0 ignored issues – show Configuration introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `rdkit.Chem` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
20	1	from rdkit.Chem import Lipinski
		0 ignored issues – show Configuration introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `rdkit.Chem` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
21	1	from rdkit.Chem import rdMolDescriptors, rdPartialCharges
		0 ignored issues – show Configuration introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `rdkit.Chem` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
22	1	from rdkit.Chem.rdchem import HybridizationType
		0 ignored issues – show Configuration introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report Show Similar Issues like this The import `rdkit.Chem.rdchem` could not be resolved. This can be caused by one of the following: 1. Missing Dependencies This error could indicate a configuration issue of Pylint. Make sure that your libraries are available by adding the necessary commands. # .scrutinizer.yml before_commands: - sudo pip install abc # Python2 - sudo pip3 install abc # Python3 Tip: We are currently not using virtualenv to run pylint, when installing your modules make sure to use the command for the correct version. 2. Missing __init__.py files This error could also result from missing `__init__.py` files in your module folders. Make sure that you place one file in each sub-folder. Loading history...
23
24	1	from ..core import Mol
25	1	from ..resource import PERIODIC_TABLE, ORGANIC
26	1	from ..base import AtomTransformer, Featurizer
27	1	from ..utils import nanarray
28
29
30	1	def element(a):
		0 ignored issues – show Coding Style Naming introduced 2016-08-25 16:29 UTC by Report Bug Copy Issue Report Show Similar Issues like this The name `a` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
31
32		""" Return the element """

richlewis42 / scikit-chem

Issues (942)

skchem/features/atom.py (69 issues)

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2. Missing __init__.py files

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2. Missing __init__.py files

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2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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