ForceField.optimize() - Code Metrics - Inspection of "small refactors" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 01edc4...2b1c29 )

by Rich

created 2016-07-18 17:47 UTC

ForceField.optimize() C

↳ Parent: ForceField

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Importance

Changes	2
Bugs	0	Features	2

Metric	Value
c	2
b	0
f	2
dl	0
loc	22
rs	5.7894
cc	7

#! /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
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 .. import core
from ..utils import NamedProgressBar, Suppressor

class ForceField(object):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    def __init__(self, embed=True, warn_on_fail=True, error_on_fail=False, drop_failed=True, add_hs=True):


        self.add_hs = add_hs
        self.drop_failed = drop_failed
        self.warn_on_fail = warn_on_fail
        self.error_on_fail = error_on_fail
        self.preembed = embed

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

        # TODO: likely need to handle which conformer here


        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

    def _optimize(self, mol):
        raise NotImplementedError

    def transform(self, obj):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        if isinstance(obj, core.Mol):
            return self.optimize(obj)
        elif isinstance(obj, pd.Series):
            bar = NamedProgressBar(name=self.__class__.__name__)

            res = pd.Series([self.optimize(mol) for mol in bar(obj)], index=obj.index, name=obj.name)

            if self.drop_failed:
                res = res[res.notnull()]
            return res
        elif isinstance(obj, pd.DataFrame):
            res = self.transform(obj.structure)
            res = res.to_frame().join(obj.drop('structure', axis=1))
            return res
        elif isinstance(obj, (tuple, list)):
            return self.transform(pd.Series(obj, [mol.name for mol in obj]))
        else:
            raise NotImplementedError

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			"""
7			## skchem.forcefields.base
8
9			Module specifying base class for forcefields.
10			"""
11			import warnings
12			import pandas as pd
			0 ignored issues – show Configuration introduced 2016-07-11 22:49 UTC by Report Bug Copy Issue Report 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...
13			from rdkit.Chem.rdDistGeom import EmbedMolecule
			0 ignored issues – show Configuration introduced 2016-07-11 22:49 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...
14
15			from .. import core
16			from ..utils import NamedProgressBar, Suppressor
17
18			class ForceField(object):
			0 ignored issues – show Coding Style introduced 2016-07-10 23:48 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...
19			def __init__(self, embed=True, warn_on_fail=True, error_on_fail=False, drop_failed=True, add_hs=True):
			0 ignored issues – show Coding Style introduced 2016-07-11 22:49 UTC by Report Bug Copy Issue Report This line is too long as per the coding-style (106/100). This check looks for lines that are too long. You can specify the maximum line length. Loading history... best-practice introduced 2016-07-11 22:49 UTC by Report Bug Copy Issue Report Too many arguments (6/5) Loading history...
20
21			self.add_hs = add_hs
22			self.drop_failed = drop_failed
23			self.warn_on_fail = warn_on_fail
24			self.error_on_fail = error_on_fail
25			self.preembed = embed
26
27			def embed(self, mol):
			0 ignored issues – show Coding Style introduced 2016-07-11 22:49 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...
28
29			success = EmbedMolecule(mol)
30			if success == -1:
31			msg = 'Failed to Embed Molecule {}'.format(mol.name)
32			if self.error_on_fail:
33			raise RuntimeError(msg)
34			elif self.warn_on_fail:
35			warnings.warn(msg)
36			return None
37
38			if self.add_hs:
39			return mol.add_hs(add_coords=True)
40			else:
41			return mol
42
43
44			def optimize(self, mol):
			0 ignored issues – show Coding Style introduced 2016-07-10 23:48 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...
45
46			# TODO: likely need to handle which conformer here
			0 ignored issues – show Coding Style introduced 2016-07-11 22:49 UTC by Report Bug Copy Issue Report `TODO` and `FIXME` comments should generally be avoided. Loading history...
47
48			with Suppressor():
49			if self.preembed:
50			mol = self.embed(mol)
51
52			if mol is None: # embedding failed
53			return None
54
55			res = self._optimize(mol)
56
57			if res == -1:
58			msg = 'Failed to optimize molecule \'{}\' using {}'.format(mol.name, self.__class__)
59			if self.error_on_fail:
60			raise RuntimeError(msg)
61			elif self.warn_on_fail:
62			warnings.warn(msg)
63			return None
64
65			return mol
66
67			def _optimize(self, mol):
68			raise NotImplementedError
69
70			def transform(self, obj):
			0 ignored issues – show Coding Style introduced 2016-07-11 22:49 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...
71			if isinstance(obj, core.Mol):
72			return self.optimize(obj)
73			elif isinstance(obj, pd.Series):
74			bar = NamedProgressBar(name=self.__class__.__name__)
			0 ignored issues – show introduced 2016-07-11 22:49 UTC by Report Bug Copy Issue Report Black listed name "bar" Loading history...
75			res = pd.Series([self.optimize(mol) for mol in bar(obj)], index=obj.index, name=obj.name)
			0 ignored issues – show Coding Style introduced 2016-07-13 10:33 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... Bug introduced 2016-07-13 13:49 UTC by Report Bug Copy Issue Report `bar` does not seem to be callable. Loading history...
76			if self.drop_failed:
77			res = res[res.notnull()]
78			return res
79			elif isinstance(obj, pd.DataFrame):
80			res = self.transform(obj.structure)
81			res = res.to_frame().join(obj.drop('structure', axis=1))
82			return res
83			elif isinstance(obj, (tuple, list)):
84			return self.transform(pd.Series(obj, [mol.name for mol in obj]))
85			else:
86			raise NotImplementedError
87
88			class RoughEmbedding(ForceField):
			0 ignored issues – show Coding Style introduced 2016-07-11 22:49 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...
89			def _optimize(self, mol):
90			return mol
91

Push — master ( 01edc4...2b1c29 )

ForceField.optimize() C

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing init.py files

1. Missing Dependencies

2. Missing init.py files

richlewis42 / scikit-chem

Push — master ( 01edc4...2b1c29 )

ForceField.optimize() C

Complexity

Size

Duplication

Importance

1. Missing Dependencies

2. Missing __init__.py files

1. Missing Dependencies

2. Missing __init__.py files

Duplication Side-by-Side

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2. Missing init.py files

2. Missing init.py files