Mol.__init__() - Code Metrics - Inspection of "updated pylintrc" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 2bc047...202252 )

by Rich

created 2016-04-14 16:47 UTC

Mol.init() A

↳ Parent: Mol

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Metric	Value
cc	1
dl	0
loc	3
rs	10

#! /usr/bin/env python
#
# Copyright (C) 2007-2009 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
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
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

import json

from skchem.core import ChemicalObject, Atom, Bond, Conformer

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

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

    def __init__(self, *args, **kwargs):
        super(Mol, self).__init__(*args, **kwargs)
        self.__two_d = None #set in constructor

    @property
    def name(self):

        """ Return the name of the molecule. """

        try:
            return self.GetProp('_Name')

        except KeyError:
            return None

    @name.setter
    def name(self, value):

        """ Set the name of the molecule. """

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

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


    @property
    def atoms(self):

        """ return an iterable over the atoms of the molecule. """

        return [Atom.from_super(self.GetAtomWithIdx(i)) for i in range(self.GetNumAtoms())]


    @atoms.setter
    def atoms(self, value):

        """ Set the atoms of a molecule.  Not implemented. """

        raise NotImplementedError

    @property
    def bonds(self):

        """ Return an iterable over the bonds of the molecule. """

        return [Bond.from_super(self.GetBondWithIdx(i)) for i in range(self.GetNumBonds())]


    @bonds.setter
    def bonds(self, value):

        """ Set the bonds of the molecule. Not implemented. """

        raise NotImplementedError

    # use a view to easily set properties?
    @property
    def props(self):

        """ Return a dictionary of the properties of the molecule. """

        return {i: self.GetProp(i) for i in self.GetPropNames()}


    @props.setter
    def props(self, value):

        """ Set the properties of the molecule. Not implemented. """

        raise NotImplementedError

    @property
    def atom_props(self):

        """ Return a dict of lists of properties on atoms of the molecule. """

        if not hasattr(self, '_atom_prop_names'):
            res = set()
            for atom in self.atoms:
                res = res.union(set(atom.props.keys()))
            self._atom_prop_names = list(res)
class Foo:
    def __init__(self, x=None):
        self.x = x
        return {prop: [atom.props.get(prop, None) for atom in self.atoms]
                                        for prop in self._atom_prop_names}


    @property
    def conformers(self):

        """ Return a list of conformers of the molecule. """

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

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


    @conformers.setter
    def conformers(self, value):

        """ Set the conformers of the molecule.  Not implemented. """

        raise NotImplementedError

    def to_formula(self):

        """ Return the chemical formula of the molecule. """

        return CalcMolFormula(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"):

        """
        Return a dictionary representation of the molecule.

        TODO

        """

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

        else:
            raise NotImplementedError

    def _to_dict_chemdoodle(self):

        """ Return a chemdoodle dict representation of the molecule. """

        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'):

        """ Return a JSON representation of the molecule. """

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

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

        """ Return the INCHI key of the molecule. """

        return rdkit.Chem.InchiToInchiKey(self.to_inchi(), *args, **kwargs)


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

    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', 'PDBBlock', 'Smarts', 'TPLBlock', 'TPLFile']

list(map(bind_constructor, CONSTRUCTORS))

list(map(bind_serializer, SERIALIZERS))



Push — master ( 2bc047...202252 )

Mol.init() A

Complexity

Size

Duplication

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) 2007-2009 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			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...
14			from rdkit.Chem.rdMolDescriptors import CalcMolFormula
			0 ignored issues – show Configuration introduced 2016-01-19 16:21 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...
15
16			import json
17
18			from skchem.core import ChemicalObject, Atom, Bond, Conformer
19
20			class Mol(rdkit.Chem.rdchem.Mol, ChemicalObject):
21
22			"""
23			Class representing a Molecule in scikit-chem.
24			"""
25
26			def __init__(self, args, *kwargs):
27			super(Mol, self).__init__(args, *kwargs)
28			self.__two_d = None #set in constructor
29
30			@property
31			def name(self):
32
33			""" Return the name of the molecule. """
34
35			try:
36			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...
37			except KeyError:
38			return None
39
40			@name.setter
41			def name(self, value):
42
43			""" Set the name of the molecule. """
44
45			if value is None:
46			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...
47			else:
48			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...
49
50			@property
51			def atoms(self):
52
53			""" return an iterable over the atoms of the molecule. """
54
55			return [Atom.from_super(self.GetAtomWithIdx(i)) for i in range(self.GetNumAtoms())]
			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 `GetAtomWithIdx`. 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... 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 `GetNumAtoms`. 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...
56
57			@atoms.setter
58			def atoms(self, value):
59
60			""" Set the atoms of a molecule. Not implemented. """
61
62			raise NotImplementedError
63
64			@property
65			def bonds(self):
66
67			""" Return an iterable over the bonds of the molecule. """
68
69			return [Bond.from_super(self.GetBondWithIdx(i)) for i in range(self.GetNumBonds())]
			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 `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... 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 `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...
70
71			@bonds.setter
72			def bonds(self, value):
73
74			""" Set the bonds of the molecule. Not implemented. """
75
76			raise NotImplementedError
77
78			# use a view to easily set properties?
79			@property
80			def props(self):
81
82			""" Return a dictionary of the properties of the molecule. """
83
84			return {i: self.GetProp(i) for i in self.GetPropNames()}
			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... 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 `GetPropNames`. 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...
85
86			@props.setter
87			def props(self, value):
88
89			""" Set the properties of the molecule. Not implemented. """
90
91			raise NotImplementedError
92
93			@property
94			def atom_props(self):
95
96			""" Return a dict of lists of properties on atoms of the molecule. """
97
98			if not hasattr(self, '_atom_prop_names'):
99			res = set()
100			for atom in self.atoms:
101			res = res.union(set(atom.props.keys()))
102			self._atom_prop_names = list(res)
			0 ignored issues – show Coding Style introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The attribute `_atom_prop_names` 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...
103			return {prop: [atom.props.get(prop, None) for atom in self.atoms]
104			for prop in self._atom_prop_names}
			0 ignored issues – show Coding Style introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report Wrong continued indentation. for prop in self._atom_prop_names} \| ^ Loading history...
105
106			@property
107			def conformers(self):
108
109			""" Return a list of conformers of the molecule. """
110
111			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...
112			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...
113
114			@conformers.setter
115			def conformers(self, value):
116
117			""" Set the conformers of the molecule. Not implemented. """
118
119			raise NotImplementedError
120
121			def to_formula(self):
122
123			""" Return the chemical formula of the molecule. """
124
125			return CalcMolFormula(self)
126
127			def _two_d(self):
128
129			""" Return a conformer with coordinates in two dimension. """
130
131			if not hasattr(self, '__two_d'):
132			self.__two_d = Compute2DCoords(self)
133			return self.conformers[self.__two_d]
134
135			def to_dict(self, kind="chemdoodle"):
136
137			"""
138			Return a dictionary representation of the molecule.
139
140			TODO
141
142			"""
143
144			if kind == "chemdoodle":
145			return self._to_dict_chemdoodle()
146
147			else:
148			raise NotImplementedError
149
150			def _to_dict_chemdoodle(self):
151
152			""" Return a chemdoodle dict representation of the molecule. """
153
154			atom_positions = [p.to_dict() for p in self._two_d().atom_positions]
155			atom_elements = [a.element for a in self.atoms]
156
157			for i, atom_position in enumerate(atom_positions):
158			atom_position['l'] = atom_elements[i]
159
160			bonds = [b.to_dict() for b in self.bonds]
161
162			return {"m": [{"a": atom_positions, "b": bonds}]}
163
164			def to_json(self, kind='chemdoodle'):
165
166			""" Return a JSON representation of the molecule. """
167
168			return json.dumps(self.to_dict(kind=kind))
169
170			def to_inchi_key(self, args, *kwargs):
171
172			""" Return the INCHI key of the molecule. """
173
174			return rdkit.Chem.InchiToInchiKey(self.to_inchi(), args, *kwargs)
			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_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...
175
176			def __repr__(self):
177			return '<{klass} name="{name}" formula="{formula}" at {address}>'.format(
178			klass=self.__class__.__name__,
179			name=self.name,
180			formula=self.to_formula(),
181			address=hex(id(self)))
182
183			def _repr_javascript(self):
184
185			""" Rich printing in javascript. """
186
187			return self.to_json()
188
189			def __str__(self):
190			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...
191
192			def bind_constructor(constructor_name, name_to_bind=None):
193
194			""" Bind an (rdkit) constructor to the class """
195
196			@classmethod
197			def constructor(_, in_arg, name=None, args, *kwargs):
198
199			""" The constructor to be bound. """
200
201			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}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
202			if m is None:
203			raise ValueError('Failed to parse molecule, {}'.format(in_arg))
204			m = Mol.from_super(m)
			0 ignored issues – show Coding Style Naming introduced 2016-04-14 16:48 UTC by Report Bug Copy Issue Report The name `m` does not conform to the variable naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
205			m.name = name
206			return m
207
208			setattr(Mol, 'from_{}'.format(constructor_name).lower() \
209			if name_to_bind is None else name_to_bind, constructor)
210
211			def bind_serializer(serializer_name, name_to_bind=None):
212
213			""" Bind an (rdkit) serializer to the class """
214
215			def serializer(self, args, *kwargs):
216
217			""" The serializer to be bound. """
218			return getattr(rdkit.Chem, 'MolTo' + serializer_name)(self, args, *kwargs)
219
220			setattr(Mol, 'to_{}'.format(serializer_name).lower() \
221			if name_to_bind is None else name_to_bind, serializer)
222
223			CONSTRUCTORS = ['Inchi', 'Smiles', 'Mol2Block', 'Mol2File', 'MolBlock', \
224			'MolFile', 'PDBBlock', 'PDBFile', 'Smarts', 'TPLBlock', 'TPLFile']
225			SERIALIZERS = ['Inchi', 'Smiles', 'MolBlock', 'PDBBlock', 'Smarts', 'TPLBlock', 'TPLFile']
226
227			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...
228			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...
229

richlewis42 / scikit-chem

Push — master ( 2bc047...202252 )

Mol.__init__() A

Complexity

Size

Duplication

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

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Mol.init() A

2. Missing init.py files

2. Missing init.py files

2. Missing init.py files