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

Issues (942)

skchem/forcefields/base.py (6 issues)

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Informational 6

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

"""
## skchem.forcefields.base

Module specifying base class for forcefields.
"""
import warnings
from abc import ABCMeta, abstractmethod

import pandas as pd
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem.rdDistGeom import EmbedMolecule
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from ..utils import Suppressor
from ..base import Transformer
from ..filters.base import TransformFilter


class ForceField(Transformer, TransformFilter):
    # TODO: Multiple conformer generation handling.


    """ Base forcefield class.

    Filter drops those that fail to be optimized.

     """

    __metaclass__ = ABCMeta

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

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

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

    @property
    def columns(self):
        return pd.Index(['structure'])

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

        success = EmbedMolecule(mol)
        if success == -1:
            msg = 'Failed to Embed Molecule {}'.format(mol.name)
            if self.error_on_fail:
                raise RuntimeError(msg)
            elif self.warn_on_fail:
                warnings.warn(msg)
            return None

        if self.add_hs:
            return mol.add_hs(add_coords=True)
        else:
            return mol

    def _transform_mol(self, mol):

        mol = mol.copy()

        with Suppressor():
            if self.preembed:
                mol = self.embed(mol)

            if mol is None:  # embedding failed
                return None

            res = self._optimize(mol)

        if res == -1:
            msg = 'Failed to optimize molecule \'{}\' using {}'.format(
                mol.name, self.__class__)
            if self.error_on_fail:
                raise RuntimeError(msg)
            elif self.warn_on_fail:
                warnings.warn(msg)
            return None

        return mol

    @abstractmethod
    def _optimize(self, mol):
        pass


class RoughEmbedding(ForceField):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    def _optimize(self, mol):
        return mol


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.base
8
9		Module specifying base class for forcefields.
10		"""
11	1	import warnings
12	1	from abc import ABCMeta, abstractmethod
13
14	1	import pandas as pd
		0 ignored issues – show Configuration introduced 2016-07-11 22:49 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...
15	1	from rdkit.Chem.rdDistGeom import EmbedMolecule
		0 ignored issues – show Configuration introduced 2016-07-11 22:49 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
16
17	1	from ..utils import Suppressor
18	1	from ..base import Transformer
19	1	from ..filters.base import TransformFilter
20
21
22	1	class ForceField(Transformer, TransformFilter):
23		# TODO: Multiple conformer generation handling.
		0 ignored issues – show Coding Style introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report Show Similar Issues like this `TODO` and `FIXME` comments should generally be avoided. Loading history...
24
25		""" Base forcefield class.
26
27		Filter drops those that fail to be optimized.
28
29		"""
30
31	1	__metaclass__ = ABCMeta
32
33	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 Show Similar Issues like this Too many arguments (7/5) Loading history...
34		add_hs=True, n_jobs=1, verbose=True):
35
36		self.add_hs = add_hs
37		self.warn_on_fail = warn_on_fail
38		self.error_on_fail = error_on_fail
39		self.preembed = preembed
40		super(ForceField, self).__init__(verbose=verbose, n_jobs=n_jobs)
41
42	1	@property
43		def columns(self):
44		return pd.Index(['structure'])
45
46	1	def embed(self, mol):
		0 ignored issues – show Coding Style introduced 2016-07-11 22:49 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
47
48		success = EmbedMolecule(mol)
49		if success == -1:
50		msg = 'Failed to Embed Molecule {}'.format(mol.name)
51		if self.error_on_fail:
52		raise RuntimeError(msg)
53		elif self.warn_on_fail:
54		warnings.warn(msg)
55		return None
56
57		if self.add_hs:
58		return mol.add_hs(add_coords=True)
59		else:
60		return mol
61
62	1	def _transform_mol(self, mol):
63
64		mol = mol.copy()
65
66		with Suppressor():
67		if self.preembed:
68		mol = self.embed(mol)
69
70		if mol is None: # embedding failed
71		return None
72
73		res = self._optimize(mol)
74
75		if res == -1:
76		msg = 'Failed to optimize molecule \'{}\' using {}'.format(
77		mol.name, self.__class__)
78		if self.error_on_fail:
79		raise RuntimeError(msg)
80		elif self.warn_on_fail:
81		warnings.warn(msg)
82		return None
83
84		return mol
85
86	1	@abstractmethod
87		def _optimize(self, mol):
88		pass
89
90
91	1	class RoughEmbedding(ForceField):
		0 ignored issues – show Coding Style introduced 2016-07-11 22:49 UTC by Report Bug Copy Issue Report Show Similar Issues like this 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...
92	1	def _optimize(self, mol):
93		return mol
94

Issues (942)

skchem/forcefields/base.py (6 issues)

Labels

Severity

Introduced By

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

richlewis42 / scikit-chem

Issues (942)

skchem/forcefields/base.py (6 issues)

Labels

Severity

Introduced By

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

Duplication Side-by-Side

Filter issues like

2. Missing init.py files

2. Missing init.py files