Mol.__eq__() - Code Metrics - Inspection of "added to_smiles functions" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 1baf98...c0c140 )

by Rich

created 2016-06-07 13:25 UTC

Mol.eq() A

↳ Parent: Mol

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Importance

Changes	1
Bugs	1	Features	1

Metric	Value
cc	2
c	1
b	1
f	1
dl	0
loc	5
rs	9.4285

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

"""
## skchem.core.mol

Defining molecules in scikit-chem.
"""

import rdkit.Chem
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
import rdkit.Chem.inchi
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem.rdDepictor import Compute2DCoords
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem.rdMolDescriptors import CalcMolFormula, CalcExactMolWt
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

import json

from . import Atom, Bond, Conformer

from .base import ChemicalObject, AtomView, PropertyView
from ..utils import Suppressor


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

    """Class representing a Molecule in scikit-chem.

    Mol objects inherit directly from rdkit Mol objects.  Therefore, they
    contain atom and bond information, and may also include properties and
    atom bookmarks.

    Example:
        Constructors are implemented as class methods with the `from_` prefix.

        ```python
        m = Mol.from_smiles('c1ccccc1')
        ```

        Serializers are implemented as instance methods with the `to_` prefix.

        ```python
        m.to_smiles()
        ```

    """

    def __init__(self, *args, **kwargs):

        """
        The default constructor.

        Note:
            This will be rarely used, as it can only create an empty molecule.

        Args:
            *args: Arguments to be passed to the rdkit Mol constructor.
            **kwargs: Arguments to be passed to the rdkit Mol constructor.
        """
        super(Mol, self).__init__(*args, **kwargs)
        self.__two_d = None #set in constructor

    @property
    def name(self):

        """ str: The name of the molecule.

        Raises:
            KeyError"""

        try:
            return self.GetProp('_Name')

        except KeyError:
            return None

    @name.setter
    def name(self, value):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

        if value is None:
            self.ClearProp('_Name')

        else:
            self.SetProp('_Name', value)


    @property
    def atoms(self):

        """ List[skchem.Atom]: An iterable over the atoms of the molecule. """

        if not hasattr(self, '_atoms'):
            self._atoms = AtomView(self)
class Foo:
    def __init__(self, x=None):
        self.x = x
        return self._atoms

    @property
    def bonds(self):

        """ List[skchem.Bond]: An iterable over the bonds of the molecule. """

        return [Bond.from_super(self.GetBondWithIdx(i)) \

                for i in range(self.GetNumBonds())]


    @property
    def mass(self):

        """ float: the mass of the molecule. """

        return CalcExactMolWt(self)

    @property
    def props(self):

        """ PropertyView: A dictionary of the properties of the molecule. """

        if not hasattr(self, '_props'):
            self._props = PropertyView(self)
class Foo:
    def __init__(self, x=None):
        self.x = x
        return self._props

    @property
    def conformers(self):

        """ List[Conformer]: conformers of the molecule. """

        return [Conformer.from_super(self.GetConformer(i)) \

            for i in range(len(self.GetConformers()))]


    def to_formula(self):

        """ str: the chemical formula of the molecule.

        Raises:
            RuntimeError"""

        # formula may be undefined if atoms are uncertainly typed
        # e.g. if the molecule was initialize through SMARTS
        try:
            return CalcMolFormula(self)
        except RuntimeError:
            raise ValueError('Formula is undefined for {}'.format(self))

    def _two_d(self):

        """ Return a conformer with coordinates in two dimension. """

        if not hasattr(self, '__two_d'):
            self.__two_d = Compute2DCoords(self)
        return self.conformers[self.__two_d]

    def to_dict(self, kind="chemdoodle"):

        """ A dictionary representation of the molecule.

        Args:
            kind (str):
                The type of representation to use.  Only `chemdoodle` is
                currently supported.
                Defaults to 'Chemdoodle'.

        Returns:
            dict:
                dictionary representation of the molecule."""

        if kind == "chemdoodle":
            return self._to_dict_chemdoodle()

        else:
            raise NotImplementedError

    def _to_dict_chemdoodle(self):

        """ Chemdoodle dict representation of the molecule.

        Documentation of the format may be found on the [chemdoodle website](https://web.chemdoodle.com/docs/chemdoodle-json-format/)"""


        atom_positions = [p.to_dict() for p in self._two_d().atom_positions]
        atom_elements = [a.element for a in self.atoms]

        for i, atom_position in enumerate(atom_positions):
            atom_position['l'] = atom_elements[i]

        bonds = [b.to_dict() for b in self.bonds]

        return {"m": [{"a": atom_positions, "b": bonds}]}

    def to_json(self, kind='chemdoodle'):

        """ Serialize a molecule using JSON.

        Args:
            kind (str):
                The type of serialization to use.  Only `chemdoodle` is
                currently supported.

        Returns:
            str: the json string. """

        return json.dumps(self.to_dict(kind=kind))

    def to_inchi_key(self):

        """ The InChI key of the molecule.

        Returns:
            str: the InChI key.

        Raises:
            RuntimeError"""

        if not rdkit.Chem.inchi.INCHI_AVAILABLE:
            raise ImportError("InChI module not available.")

        res = rdkit.Chem.InchiToInchiKey(self.to_inchi())


        if res is None:
            raise RuntimeError("The molecule could not be encoded as InChI key.")

        return res

    def to_binary(self):

        """  Serialize the molecule to binary encoding.

        Args:
            None

        Returns:
            bytes: the molecule in bytes.

        Notes:
            Due to limitations in RDKit, not all data is serialized.  Notably,
            properties are not, so e.g. compound names are not saved."""

        return self.ToBinary()


    @classmethod
    def from_binary(cls, binary):

        """ Decode a molecule from a binary serialization.

        Args:
            binary: The bytes string to decode.

        Returns:
            skchem.Mol: The molecule encoded in the binary."""

        return cls(binary)

    def __repr__(self):
        try:
            formula = self.to_formula()
        except ValueError:
            # if we can't generate the formula, just say it is unknown
            formula = 'unknown'

        return '<{klass} name="{name}" formula="{formula}" at {address}>'.format(
            klass=self.__class__.__name__,
            name=self.name,
            formula=formula,
            address=hex(id(self)))

    def __contains__(self, item):
        if isinstance(item, Mol):
            return self.HasSubstructMatch(item)

        else:
            raise NotImplementedError('No way to check if {} contains {}'.format(self, item))

    def __eq__(self, item):
        if isinstance(item, self.__class__):
            return (self in item) and (item in self)
        else:
            return False

    def _repr_javascript(self):

        """ Rich printing in javascript. """

        return self.to_json()

    def __str__(self):
        return '<Mol: {}>'.format(self.to_smiles())


def bind_constructor(constructor_name, name_to_bind=None):

    """ Bind an (rdkit) constructor to the class """

    @classmethod
    def constructor(_, in_arg, name=None, *args, **kwargs):

        """ The constructor to be bound. """

        m = getattr(rdkit.Chem, 'MolFrom' + constructor_name)(in_arg, *args, **kwargs)

        if m is None:
            raise ValueError('Failed to parse molecule, {}'.format(in_arg))
        m = Mol.from_super(m)

        m.name = name
        return m

    setattr(Mol, 'from_{}'.format(constructor_name).lower() \
        if name_to_bind is None else name_to_bind, constructor)

def bind_serializer(serializer_name, name_to_bind=None):

    """ Bind an (rdkit) serializer to the class """

    def serializer(self, *args, **kwargs):

        """ The serializer to be bound. """
        return getattr(rdkit.Chem, 'MolTo' + serializer_name)(self, *args, **kwargs)

    setattr(Mol, 'to_{}'.format(serializer_name).lower() \
        if name_to_bind is None else name_to_bind, serializer)

CONSTRUCTORS = ['Inchi', 'Smiles', 'Mol2Block', 'Mol2File', 'MolBlock', \
                    'MolFile', 'PDBBlock', 'PDBFile', 'Smarts', 'TPLBlock', 'TPLFile']
SERIALIZERS = ['Inchi', 'Smiles', 'MolBlock', 'MolFile', 'PDBBlock', 'Smarts', 'TPLBlock', 'TPLFile']


list(map(bind_constructor, CONSTRUCTORS))

list(map(bind_serializer, SERIALIZERS))



Push — master ( 1baf98...c0c140 )

Mol.eq() A

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

1			#! /usr/bin/env python
2			#
3			# Copyright (C) 2015-2016 Rich Lewis <[email protected]>
4			# License: 3-clause BSD
5
6			"""
7			## skchem.core.mol
8
9			Defining molecules in scikit-chem.
10			"""
11
12			import rdkit.Chem
			0 ignored issues – show Configuration introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report 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...
13			import rdkit.Chem.inchi
			0 ignored issues – show Configuration introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The import `rdkit.Chem.inchi` 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...
14			from rdkit.Chem.rdDepictor import Compute2DCoords
			0 ignored issues – show Configuration introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The import `rdkit.Chem.rdDepictor` 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...
15			from rdkit.Chem.rdMolDescriptors import CalcMolFormula, CalcExactMolWt
			0 ignored issues – show Configuration introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The import `rdkit.Chem.rdMolDescriptors` 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
17			import json
18
19			from . import Atom, Bond, Conformer
			0 ignored issues – show Unused Code introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The import `Atom` seems to be unused. Loading history...
20			from .base import ChemicalObject, AtomView, PropertyView
21			from ..utils import Suppressor
			0 ignored issues – show Unused Code introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report Unused Suppressor imported from utils Loading history...
22
23			class Mol(rdkit.Chem.rdchem.Mol, ChemicalObject):
24
25			"""Class representing a Molecule in scikit-chem.
26
27			Mol objects inherit directly from rdkit Mol objects. Therefore, they
28			contain atom and bond information, and may also include properties and
29			atom bookmarks.
30
31			Example:
32			Constructors are implemented as class methods with the `from_` prefix.
33
34			```python
35			m = Mol.from_smiles('c1ccccc1')
36			```
37
38			Serializers are implemented as instance methods with the `to_` prefix.
39
40			```python
41			m.to_smiles()
42			```
43
44			"""
45
46			def __init__(self, args, *kwargs):
47
48			"""
49			The default constructor.
50
51			Note:
52			This will be rarely used, as it can only create an empty molecule.
53
54			Args:
55			*args: Arguments to be passed to the rdkit Mol constructor.
56			**kwargs: Arguments to be passed to the rdkit Mol constructor.
57			"""
58			super(Mol, self).__init__(args, *kwargs)
59			self.__two_d = None #set in constructor
60
61			@property
62			def name(self):
63
64			""" str: The name of the molecule.
65
66			Raises:
67			KeyError"""
68
69			try:
70			return self.GetProp('_Name')
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `GetProp`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
71			except KeyError:
72			return None
73
74			@name.setter
75			def name(self, value):
			0 ignored issues – show Coding Style introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report This method should have a docstring. The coding style of this project requires that you add a docstring to this code element. Below, you find an example for methods: class SomeClass: def some_method(self): """Do x and return foo.""" If you would like to know more about docstrings, we recommend to read PEP-257: Docstring Conventions. Loading history...
76
77			if value is None:
78			self.ClearProp('_Name')
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `ClearProp`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
79			else:
80			self.SetProp('_Name', value)
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `SetProp`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
81
82			@property
83			def atoms(self):
84
85			""" List[skchem.Atom]: An iterable over the atoms of the molecule. """
86
87			if not hasattr(self, '_atoms'):
88			self._atoms = AtomView(self)
			0 ignored issues – show Coding Style introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The attribute `_atoms` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
89			return self._atoms
90
91			@property
92			def bonds(self):
93
94			""" List[skchem.Bond]: An iterable over the bonds of the molecule. """
95
96			return [Bond.from_super(self.GetBondWithIdx(i)) \
			0 ignored issues – show Bug introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `GetBondWithIdx`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
97			for i in range(self.GetNumBonds())]
			0 ignored issues – show Bug introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `GetNumBonds`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
98
99			@property
100			def mass(self):
101
102			""" float: the mass of the molecule. """
103
104			return CalcExactMolWt(self)
105
106			@property
107			def props(self):
108
109			""" PropertyView: A dictionary of the properties of the molecule. """
110
111			if not hasattr(self, '_props'):
112			self._props = PropertyView(self)
			0 ignored issues – show Coding Style introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The attribute `_props` was defined outside `__init__`. It is generally a good practice to initialize all attributes to default values in the `__init__` method: class Foo: def __init__(self, x=None): self.x = x Loading history...
113			return self._props
114
115			@property
116			def conformers(self):
117
118			""" List[Conformer]: conformers of the molecule. """
119
120			return [Conformer.from_super(self.GetConformer(i)) \
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `GetConformer`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
121			for i in range(len(self.GetConformers()))]
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `GetConformers`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
122
123			def to_formula(self):
124
125			""" str: the chemical formula of the molecule.
126
127			Raises:
128			RuntimeError"""
129
130			# formula may be undefined if atoms are uncertainly typed
131			# e.g. if the molecule was initialize through SMARTS
132			try:
133			return CalcMolFormula(self)
134			except RuntimeError:
135			raise ValueError('Formula is undefined for {}'.format(self))
136
137			def _two_d(self):
138
139			""" Return a conformer with coordinates in two dimension. """
140
141			if not hasattr(self, '__two_d'):
142			self.__two_d = Compute2DCoords(self)
143			return self.conformers[self.__two_d]
144
145			def to_dict(self, kind="chemdoodle"):
146
147			""" A dictionary representation of the molecule.
148
149			Args:
150			kind (str):
151			The type of representation to use. Only `chemdoodle` is
152			currently supported.
153			Defaults to 'Chemdoodle'.
154
155			Returns:
156			dict:
157			dictionary representation of the molecule."""
158
159			if kind == "chemdoodle":
160			return self._to_dict_chemdoodle()
161
162			else:
163			raise NotImplementedError
164
165			def _to_dict_chemdoodle(self):
166
167			""" Chemdoodle dict representation of the molecule.
168
169			Documentation of the format may be found on the [chemdoodle website](https://web.chemdoodle.com/docs/chemdoodle-json-format/)"""
			0 ignored issues – show Coding Style introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (136/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
170
171			atom_positions = [p.to_dict() for p in self._two_d().atom_positions]
172			atom_elements = [a.element for a in self.atoms]
173
174			for i, atom_position in enumerate(atom_positions):
175			atom_position['l'] = atom_elements[i]
176
177			bonds = [b.to_dict() for b in self.bonds]
178
179			return {"m": [{"a": atom_positions, "b": bonds}]}
180
181			def to_json(self, kind='chemdoodle'):
182
183			""" Serialize a molecule using JSON.
184
185			Args:
186			kind (str):
187			The type of serialization to use. Only `chemdoodle` is
188			currently supported.
189
190			Returns:
191			str: the json string. """
192
193			return json.dumps(self.to_dict(kind=kind))
194
195			def to_inchi_key(self):
196
197			""" The InChI key of the molecule.
198
199			Returns:
200			str: the InChI key.
201
202			Raises:
203			RuntimeError"""
204
205			if not rdkit.Chem.inchi.INCHI_AVAILABLE:
206			raise ImportError("InChI module not available.")
207
208			res = rdkit.Chem.InchiToInchiKey(self.to_inchi())
			0 ignored issues – show Bug introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `to_inchi`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
209
210			if res is None:
211			raise RuntimeError("The molecule could not be encoded as InChI key.")
212
213			return res
214
215			def to_binary(self):
216
217			""" Serialize the molecule to binary encoding.
218
219			Args:
220			None
221
222			Returns:
223			bytes: the molecule in bytes.
224
225			Notes:
226			Due to limitations in RDKit, not all data is serialized. Notably,
227			properties are not, so e.g. compound names are not saved."""
228
229			return self.ToBinary()
			0 ignored issues – show Bug introduced 2016-05-24 17:01 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `ToBinary`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
230
231			@classmethod
232			def from_binary(cls, binary):
233
234			""" Decode a molecule from a binary serialization.
235
236			Args:
237			binary: The bytes string to decode.
238
239			Returns:
240			skchem.Mol: The molecule encoded in the binary."""
241
242			return cls(binary)
243
244			def __repr__(self):
245			try:
246			formula = self.to_formula()
247			except ValueError:
248			# if we can't generate the formula, just say it is unknown
249			formula = 'unknown'
250
251			return '<{klass} name="{name}" formula="{formula}" at {address}>'.format(
252			klass=self.__class__.__name__,
253			name=self.name,
254			formula=formula,
255			address=hex(id(self)))
256
257			def __contains__(self, item):
258			if isinstance(item, Mol):
259			return self.HasSubstructMatch(item)
			0 ignored issues – show Bug introduced 2016-05-15 15:29 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `HasSubstructMatch`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
260			else:
261			raise NotImplementedError('No way to check if {} contains {}'.format(self, item))
262
263			def __eq__(self, item):
264			if isinstance(item, self.__class__):
265			return (self in item) and (item in self)
266			else:
267			return False
268
269			def _repr_javascript(self):
270
271			""" Rich printing in javascript. """
272
273			return self.to_json()
274
275			def __str__(self):
276			return '<Mol: {}>'.format(self.to_smiles())
			0 ignored issues – show Bug introduced 2016-01-19 16:21 UTC by Report Bug Copy Issue Report The Instance of `Mol` does not seem to have a member named `to_smiles`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
277
278			def bind_constructor(constructor_name, name_to_bind=None):
279
280			""" Bind an (rdkit) constructor to the class """
281
282			@classmethod
283			def constructor(_, in_arg, name=None, args, *kwargs):
284
285			""" The constructor to be bound. """
286
287			m = getattr(rdkit.Chem, 'MolFrom' + constructor_name)(in_arg, args, *kwargs)
			0 ignored issues – show Coding Style Naming introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The name `m` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
288			if m is None:
289			raise ValueError('Failed to parse molecule, {}'.format(in_arg))
290			m = Mol.from_super(m)
			0 ignored issues – show Coding Style Naming introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The name `m` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
291			m.name = name
292			return m
293
294			setattr(Mol, 'from_{}'.format(constructor_name).lower() \
295			if name_to_bind is None else name_to_bind, constructor)
296
297			def bind_serializer(serializer_name, name_to_bind=None):
298
299			""" Bind an (rdkit) serializer to the class """
300
301			def serializer(self, args, *kwargs):
302
303			""" The serializer to be bound. """
304			return getattr(rdkit.Chem, 'MolTo' + serializer_name)(self, args, *kwargs)
305
306			setattr(Mol, 'to_{}'.format(serializer_name).lower() \
307			if name_to_bind is None else name_to_bind, serializer)
308
309			CONSTRUCTORS = ['Inchi', 'Smiles', 'Mol2Block', 'Mol2File', 'MolBlock', \
310			'MolFile', 'PDBBlock', 'PDBFile', 'Smarts', 'TPLBlock', 'TPLFile']
311			SERIALIZERS = ['Inchi', 'Smiles', 'MolBlock', 'MolFile', 'PDBBlock', 'Smarts', 'TPLBlock', 'TPLFile']
			0 ignored issues – show Coding Style introduced 2016-06-07 13:27 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (101/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history...
312
313			list(map(bind_constructor, CONSTRUCTORS))
			0 ignored issues – show introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report Used builtin function 'map' Loading history...
314			list(map(bind_serializer, SERIALIZERS))
			0 ignored issues – show introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report Used builtin function 'map' Loading history...
315

richlewis42 / scikit-chem

Push — master ( 1baf98...c0c140 )

Mol.__eq__() A

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

Duplication Side-by-Side

Filter issues like

Mol.eq() A

2. Missing init.py files

2. Missing init.py files

2. Missing init.py files

2. Missing init.py files