UFF.__init__() - Code Metrics - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

UFF.init() A
last analyzed 2016-09-01 14:43 UTC

↳ Parent: UFF

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	1.125

Importance

Changes	3
Bugs	0	Features	3

Metric	Value
c	3
b	0
f	3
dl	0
loc	19
ccs	1
cts	2
cp	0.5
rs	9.4285
cc	1
crap	1.125

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

"""
## skchem.forcefields.uff

Module specifying the universal force field.
"""
from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from .base import ForceField


class UFF(ForceField):

    """ Universal Force Field transformer. """

    def __init__(self, preembed=True, warn_on_fail=True, error_on_fail=False,

                 add_hs=True, n_jobs=1, verbose=True):

        """ Initialize a UFF object.

        Args:
            preembed (bool):
                Whether to embed before optimizing.
            warn_on_fail (bool):
                Whether to warn if a molecule fails to optimise.
            error_on_fail (bool):
                Whether to raise an error if a molecule fails to optimise.
            add_hs (bool):
                Whether to automatically add hydrogens.
        """

        super(UFF, self).__init__(preembed=preembed, warn_on_fail=warn_on_fail,
                                  error_on_fail=error_on_fail, add_hs=add_hs,
                                  verbose=verbose, n_jobs=n_jobs)

    def _optimize(self, mol):
        try:
            return UFFOptimizeMolecule(mol)
        except RuntimeError:
            return None


UFF.init() A
last analyzed 2016-09-01 14:43 UTC

Complexity

Size

Duplication

Code Coverage

Importance

1. Missing Dependencies

2. Missing init.py files

1		#! /usr/bin/env python
2		#
3		# Copyright (C) 2016 Rich Lewis <[email protected]>
4		# License: 3-clause BSD
5
6	1	"""
7		## skchem.forcefields.uff
8
9		Module specifying the universal force field.
10		"""
11	1	from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule
		0 ignored issues – show Configuration introduced 2016-07-10 23:48 UTC by Report Bug Copy Issue Report The import `rdkit.Chem.rdForceFieldHelpers` 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...
12
13	1	from .base import ForceField
14
15
16	1	class UFF(ForceField):
17
18		""" Universal Force Field transformer. """
19
20	1	def __init__(self, preembed=True, warn_on_fail=True, error_on_fail=False,
		0 ignored issues – show best-practice introduced 2016-08-18 20:05 UTC by Report Bug Copy Issue Report Too many arguments (7/5) Loading history...
21		add_hs=True, n_jobs=1, verbose=True):
22
23		""" Initialize a UFF object.
24
25		Args:
26		preembed (bool):
27		Whether to embed before optimizing.
28		warn_on_fail (bool):
29		Whether to warn if a molecule fails to optimise.
30		error_on_fail (bool):
31		Whether to raise an error if a molecule fails to optimise.
32		add_hs (bool):
33		Whether to automatically add hydrogens.
34		"""
35
36		super(UFF, self).__init__(preembed=preembed, warn_on_fail=warn_on_fail,
37		error_on_fail=error_on_fail, add_hs=add_hs,
38		verbose=verbose, n_jobs=n_jobs)
39
40	1	def _optimize(self, mol):
41		try:
42		return UFFOptimizeMolecule(mol)
43		except RuntimeError:
44		return None
		0 ignored issues – show Coding Style introduced 2016-07-18 17:48 UTC by Report Bug Copy Issue Report Final newline missing Loading history...

richlewis42 / scikit-chem

UFF.__init__() A last analyzed 2016-09-01 14:43 UTC

Complexity

Size

Duplication

Code Coverage

Importance

1. Missing Dependencies

2. Missing __init__.py files

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UFF.init() A
last analyzed 2016-09-01 14:43 UTC

2. Missing init.py files