Conformer.canonicalize() - Code Metrics - Inspection of "added extra core functionality" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( ea74a1...6ddd48 )

by Rich

created 2016-08-30 21:23 UTC

Conformer.canonicalize() A

↳ Parent: Conformer

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	3
CRAP Score	1

Importance

Changes

Metric	Value
c	0
b	0
f	0
dl	0
loc	6
ccs	3
cts	3
cp	1
rs	9.4285
cc	1
crap	1

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

"""
## skchem.core.conformer

Defining conformers in scikit-chem.
"""

import warnings

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.rdDistGeom import EmbedMolecule, EmbedMultipleConfs
# .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 .base import ChemicalObject, ChemicalObjectView


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

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

    @property
    def owner(self):

        """ skchem.Mol: the owning molecule. """
        from .mol import Mol
        return Mol.from_super(self.GetOwningMol())


    @property
    def positions(self):

        """ np.ndarray: the atom positions in the conformer.

        Note:
            This is a copy of the data, not the data itself.  You cannot
            allocate to a slice of this.
        """

        # cant slice this array sadly.

        return np.array([self.GetAtomPosition(i) for i in range(len(self))])


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

        assert val.shape[0] == len(self), 'Positions must be given only for ' \
                                          'atoms in the molecule.'
        assert 1 < val.shape[1] <= 3, 'Positions must be 2 or 3 dimensional.'

        if val.shape[1] == 2:
            val = np.hstack((val, np.zeros((len(val), 1))))

        self.Set3D(bool((val[:, 2] != 0).any()))


        return [self.SetAtomPosition(i, v) for i, v in enumerate(val)]


    @property
    def centre_of_mass(self):

        """ np.array: the centre of mass of the comformer. """

        atomic_mass = self.owner.atoms.atomic_mass
        return atomic_mass.dot(self.positions) / atomic_mass.sum()

    @property
    def geometric_centre(self):

        """ np.array: the geometric centre of the conformer. """

        return self.positions.mean(axis=0)

    def centre_representation(self, centre_of_mass=True):

        """ Centre representation to the center of mass.

        Args:
            centre_of_mass (bool):
                Whether to use the masses of atoms to calculate the centre of
                mass, or just use the mean position coordinate.

        Returns:
            Conformer
        """

        if centre_of_mass:
            self.positions -= self.centre_of_mass
        else:
            self.positions -= self.geometric_centre

    def _inertia_tensor(self):

        """ Calculate the inertia tensor. """

        mass = self.owner.atoms.atomic_mass
        pos = self.positions

        return np.array([[((pos[:, (i % 3) - 1] ** 2 +
                            pos[:, (j % 3) - 2] ** 2 if (i == j)
                            else - pos[:, i] * pos[:, j]) * mass).sum()
                          for i in range(3)] for j in range(3)])

    def align_with_principal_axes(self):

        """ Align the reference frame with the principal axes of inertia. """

        eig_val, eig_vects = np.linalg.eigh(self._inertia_tensor())

        self.positions = self.positions.dot(eig_vects)

    def canonicalize(self):

        """ Center the reference frame at the centre of mass and """

        self.centre_representation(centre_of_mass=True)
        self.align_with_principal_axes()

    @property
    def id(self):


        """ The ID of the conformer. """

        return self.GetId()


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

        warnings.warn('Setting the conformer value directly '
                      'may cause issues.', UserWarning)
        self.SetId(int(value))


    @property
    def is_3d(self):

        """ bool: whether the conformer is three dimensional. """

        return self.Is3D()


    @is_3d.setter
    def is_3d(self, val):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

        pos = self.positions
        pos[:, 2] = 0
        self.positions = pos

    def __len__(self):

        return self.GetNumAtoms()


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

            address=hex(id(self)))


class ConformerView(ChemicalObjectView):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    def __getitem__(self, index):

        res = super(ConformerView, self).__getitem__(index)
        if res is None:
            try:
                return Conformer.from_super(
                    self.owner.GetConformer(int(index)))
            except ValueError:
                raise IndexError(
                        'Conformer id {} not available (choose one '

                        'of {}).'.format(index, tuple(self.id)))
        else:
            return res

    def __setitem__(self, key, value):

        assert isinstance(value, Conformer), 'Only `Conformer`s can be added.'
        assert len(value) == len(self.owner.atoms), \
            '`Conformers` must have the same number of atoms as the `Mol`.'
        self.owner.RemoveConformer(int(key))
        with warnings.catch_warnings():
            warnings.simplefilter('ignore')
            value.id = key
        self.owner.AddConformer(value)

    def __delitem__(self, key):

        self.owner.RemoveConformer(key)

    def __iter__(self):
        return ConformerIterator(self)

    def __len__(self):

        return self.owner.GetNumConformers()

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

        assert isinstance(value, rdkit.Chem.Conformer)
        self[max(self.id) + 1] = value

    def append_2d(self, **kwargs):

        """ Append a 2D conformer. """

        kwargs['clearConfs'] = False
        Compute2DCoords(self.owner, **kwargs)

    def append_3d(self, n_conformers=1, **kwargs):

        """ Append (a) 3D conformer(s), roughly embedded but not optimized.

        Args:
            n_conformers (int):
                The number of conformers to append.
            Further kwargs are passed to `EmbedMultipleConfs`.

        """

        kwargs.setdefault('numConfs', n_conformers)
        kwargs['clearConfs'] = False
        EmbedMultipleConfs(self.owner, **kwargs)

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

        return np.array([conformer.positions for conformer in self])

    @property
    def is_3d(self):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

        return np.array([conformer.is_3d for conformer in self])

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

        return np.array([conf.GetId() for conf in self.owner.GetConformers()])


class ConformerIterator(object):

    """  Iterator for chemical object views.  """

    def __init__(self, view):
        """ Create an iterator from a chemical object view. """
        self.view = view
        self._ids = view.id
        self._current = 0
        self._high = len(view)

    def __next__(self):
        if self._current >= self._high:
            raise StopIteration
        else:
            self._current += 1
            return self.view[self._ids[self._current - 1]]

    # py2 compat
    next = __next__


Push — master ( ea74a1...6ddd48 )

Conformer.canonicalize() A

Complexity

Size

Duplication

Code Coverage

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	1	"""
7		## skchem.core.conformer
8
9		Defining conformers in scikit-chem.
10		"""
11
12	1	import warnings
13
14	1	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...
15	1	from rdkit.Chem.rdDepictor import Compute2DCoords
		0 ignored issues – show Configuration introduced 2016-08-25 14:00 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...
16	1	from rdkit.Chem.rdDistGeom import EmbedMolecule, EmbedMultipleConfs
		0 ignored issues – show Configuration introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The import `rdkit.Chem.rdDistGeom` 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... Unused Code introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report Unused EmbedMolecule imported from rdkit.Chem.rdDistGeom Loading history...
17
18	1	import numpy as np
		0 ignored issues – show Configuration introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report 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...
19
20	1	from .base import ChemicalObject, ChemicalObjectView
21
22
23	1	class Conformer(rdkit.Chem.rdchem.Conformer, ChemicalObject):
24
25		""" Class representing a Conformer in scikit-chem. """
26
27	1	@property
28		def owner(self):
29
30		""" skchem.Mol: the owning molecule. """
31	1	from .mol import Mol
32	1	return Mol.from_super(self.GetOwningMol())
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `GetOwningMol`. 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...
33
34	1	@property
35		def positions(self):
36
37		""" np.ndarray: the atom positions in the conformer.
38
39		Note:
40		This is a copy of the data, not the data itself. You cannot
41		allocate to a slice of this.
42		"""
43
44		# cant slice this array sadly.
45
46	1	return np.array([self.GetAtomPosition(i) for i in range(len(self))])
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `GetAtomPosition`. 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
48	1	@positions.setter
49		def positions(self, val):
		0 ignored issues – show Coding Style introduced 2016-08-25 14:00 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...
50
51	1	assert val.shape[0] == len(self), 'Positions must be given only for ' \
52		'atoms in the molecule.'
53	1	assert 1 < val.shape[1] <= 3, 'Positions must be 2 or 3 dimensional.'
54
55	1	if val.shape[1] == 2:
56	1	val = np.hstack((val, np.zeros((len(val), 1))))
57
58	1	self.Set3D(bool((val[:, 2] != 0).any()))
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `Set3D`. 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...
59
60	1	return [self.SetAtomPosition(i, v) for i, v in enumerate(val)]
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `SetAtomPosition`. 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...
61
62	1	@property
63		def centre_of_mass(self):
64
65		""" np.array: the centre of mass of the comformer. """
66
67	1	atomic_mass = self.owner.atoms.atomic_mass
68	1	return atomic_mass.dot(self.positions) / atomic_mass.sum()
69
70	1	@property
71		def geometric_centre(self):
72
73		""" np.array: the geometric centre of the conformer. """
74
75	1	return self.positions.mean(axis=0)
76
77	1	def centre_representation(self, centre_of_mass=True):
78
79		""" Centre representation to the center of mass.
80
81		Args:
82		centre_of_mass (bool):
83		Whether to use the masses of atoms to calculate the centre of
84		mass, or just use the mean position coordinate.
85
86		Returns:
87		Conformer
88		"""
89
90	1	if centre_of_mass:
91	1	self.positions -= self.centre_of_mass
92		else:
93	1	self.positions -= self.geometric_centre
94
95	1	def _inertia_tensor(self):
96
97		""" Calculate the inertia tensor. """
98
99	1	mass = self.owner.atoms.atomic_mass
100	1	pos = self.positions
101
102	1	return np.array([[((pos[:, (i % 3) - 1] ** 2 +
103		pos[:, (j % 3) - 2] ** 2 if (i == j)
104		else - pos[:, i] * pos[:, j]) * mass).sum()
105		for i in range(3)] for j in range(3)])
106
107	1	def align_with_principal_axes(self):
108
109		""" Align the reference frame with the principal axes of inertia. """
110
111	1	eig_val, eig_vects = np.linalg.eigh(self._inertia_tensor())
		0 ignored issues – show Unused Code introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The variable `eig_val` seems to be unused. Loading history...
112	1	self.positions = self.positions.dot(eig_vects)
113
114	1	def canonicalize(self):
115
116		""" Center the reference frame at the centre of mass and """
117
118	1	self.centre_representation(centre_of_mass=True)
119	1	self.align_with_principal_axes()
120
121	1	@property
122		def id(self):
		0 ignored issues – show Coding Style Naming introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The name `id` does not conform to the attribute naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
123
124		""" The ID of the conformer. """
125
126	1	return self.GetId()
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `GetId`. This check looks for calls to members that are non-existent. These calls will fail. The member could have been renamed or removed. Loading history...
127
128	1	@id.setter
129		def id(self, value):
		0 ignored issues – show Coding Style Naming introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The name `id` does not conform to the attribute naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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... Coding Style introduced 2016-08-25 14:00 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...
130
131	1	warnings.warn('Setting the conformer value directly '
132		'may cause issues.', UserWarning)
133	1	self.SetId(int(value))
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `SetId`. 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...
134
135	1	@property
136		def is_3d(self):
137
138		""" bool: whether the conformer is three dimensional. """
139
140	1	return self.Is3D()
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `Is3D`. 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...
141
142	1	@is_3d.setter
143		def is_3d(self, val):
		0 ignored issues – show Coding Style introduced 2016-08-25 14:00 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... Unused Code introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The argument `val` seems to be unused. Loading history...
144
145	1	pos = self.positions
146	1	pos[:, 2] = 0
147	1	self.positions = pos
148
149	1	def __len__(self):
150
151	1	return self.GetNumAtoms()
		0 ignored issues – show Bug introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The Instance of `Conformer` 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...
152
153	1	def __repr__(self):
154	1	return '<{klass} id="{id}" at {address}>'.format(
155		klass=self.__class__.__name__,
156		id=self.GetId(),
		0 ignored issues – show Bug introduced 2016-08-16 15:32 UTC by Report Bug Copy Issue Report The Instance of `Conformer` does not seem to have a member named `GetId`. 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...
157		address=hex(id(self)))
158
159
160	1	class ConformerView(ChemicalObjectView):
		0 ignored issues – show Coding Style introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report This class 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...
161
162	1	def __getitem__(self, index):
163
164	1	res = super(ConformerView, self).__getitem__(index)
165	1	if res is None:
166	1	try:
167	1	return Conformer.from_super(
168		self.owner.GetConformer(int(index)))
169	1	except ValueError:
170	1	raise IndexError(
171		'Conformer id {} not available (choose one '
		0 ignored issues – show Coding Style introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report Wrong hanging indentation. 'Conformer id {} not available (choose one ' \| ^ Loading history...
172		'of {}).'.format(index, tuple(self.id)))
173		else:
174	1	return res
175
176	1	def __setitem__(self, key, value):
177
178	1	assert isinstance(value, Conformer), 'Only `Conformer`s can be added.'
179	1	assert len(value) == len(self.owner.atoms), \
180		'`Conformers` must have the same number of atoms as the `Mol`.'
181	1	self.owner.RemoveConformer(int(key))
182	1	with warnings.catch_warnings():
183	1	warnings.simplefilter('ignore')
184	1	value.id = key
185	1	self.owner.AddConformer(value)
186
187	1	def __delitem__(self, key):
188
189	1	self.owner.RemoveConformer(key)
190
191	1	def __iter__(self):
192	1	return ConformerIterator(self)
193
194	1	def __len__(self):
195
196	1	return self.owner.GetNumConformers()
197
198	1	def append(self, value):
		0 ignored issues – show Coding Style introduced 2016-08-25 14:00 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...
199
200	1	assert isinstance(value, rdkit.Chem.Conformer)
201	1	self[max(self.id) + 1] = value
202
203	1	def append_2d(self, **kwargs):
204
205		""" Append a 2D conformer. """
206
207	1	kwargs['clearConfs'] = False
208	1	Compute2DCoords(self.owner, **kwargs)
209
210	1	def append_3d(self, n_conformers=1, **kwargs):
211
212		""" Append (a) 3D conformer(s), roughly embedded but not optimized.
213
214		Args:
215		n_conformers (int):
216		The number of conformers to append.
217		Further kwargs are passed to `EmbedMultipleConfs`.
218
219		"""
220
221	1	kwargs.setdefault('numConfs', n_conformers)
222	1	kwargs['clearConfs'] = False
223	1	EmbedMultipleConfs(self.owner, **kwargs)
224
225	1	@property
226		def positions(self):
		0 ignored issues – show Coding Style introduced 2016-08-25 14:00 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...
227
228	1	return np.array([conformer.positions for conformer in self])
229
230	1	@property
231		def is_3d(self):
		0 ignored issues – show Coding Style introduced 2016-08-25 14:00 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...
232
233	1	return np.array([conformer.is_3d for conformer in self])
234
235	1	@property
236		def id(self):
		0 ignored issues – show Coding Style Naming introduced 2016-08-25 14:00 UTC by Report Bug Copy Issue Report The name `id` does not conform to the attribute 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... Coding Style introduced 2016-08-25 14:00 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...
237
238	1	return np.array([conf.GetId() for conf in self.owner.GetConformers()])
239
240
241	1	class ConformerIterator(object):
242
243		""" Iterator for chemical object views. """
244
245	1	def __init__(self, view):
246		""" Create an iterator from a chemical object view. """
247	1	self.view = view
248	1	self._ids = view.id
249	1	self._current = 0
250	1	self._high = len(view)
251
252	1	def __next__(self):
253	1	if self._current >= self._high:
254	1	raise StopIteration
255		else:
256	1	self._current += 1
257	1	return self.view[self._ids[self._current - 1]]
258
259		# py2 compat
260		next = __next__
261

richlewis42 / scikit-chem

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Conformer.canonicalize() A

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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

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