UFF - Code Metrics - Inspection of "add 3d structure distance calculator" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 4cde57...24f8d3 )

by Rich

created 2016-07-10 23:46 UTC

UFF A

↳ Parent: Project

Complexity

Total Complexity

Size/Duplication

Total Lines	18
Duplicated Lines	0 %

Importance

Changes	1
Bugs	0	Features	1

Metric	Value
wmc	5
c	1
b	0
f	1
dl	0
loc	18
rs	10

2 Methods

Rating	Name	Duplication	Size	Complexity
A	__init__()	0	2	1
A	optimize()	0	13	4

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

"""
## skchem.forcefields.uff

Module specifying the universal force field.
"""
import warnings

from .base import ForceField
from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3


class UFF(ForceField):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    def __init__(self):
class SomeParent:
    def __init__(self):
        self.x = 1

class SomeChild(SomeParent):
    def __init__(self):
        # Initialize the super class
        SomeParent.__init__(self)
        pass

    def optimize(self, mol):
        res = UFFOptimizeMolecule(mol)

        if res == -1:
            msg = 'Failed to optimize molecule \'{}\' using MMFF'.format(mol.name)
            if self.error_on_fail:
                raise RuntimeError(msg)
            elif self.warn_on_fail:
                warnings.warn(msg)
            else:
                pass

        return mol


Push — master ( 4cde57...24f8d3 )

UFF A

Complexity

Size/Duplication

Importance

2 Methods

1. Missing Dependencies

2. Missing init.py files

1			#! /usr/bin/env python
2			#
3			# Copyright (C) 2015 Rich Lewis <[email protected]>
4			# License: 3-clause BSD
5
6			"""
7			## skchem.forcefields.uff
8
9			Module specifying the universal force field.
10			"""
11			import warnings
12
13			from .base import ForceField
14			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...
15
16
17			class UFF(ForceField):
			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...
18
19			def __init__(self):
			0 ignored issues – show Bug introduced 2016-07-10 23:48 UTC by Report Bug Copy Issue Report The `__init__` method of the super-class `ForceField` is not called. It is generally advisable to initialize the super-class by calling its `__init__` method: class SomeParent: def __init__(self): self.x = 1 class SomeChild(SomeParent): def __init__(self): # Initialize the super class SomeParent.__init__(self) Loading history...
20			pass
21
22			def optimize(self, mol):
23			res = UFFOptimizeMolecule(mol)
24
25			if res == -1:
26			msg = 'Failed to optimize molecule \'{}\' using MMFF'.format(mol.name)
27			if self.error_on_fail:
28			raise RuntimeError(msg)
29			elif self.warn_on_fail:
30			warnings.warn(msg)
31			else:
32			pass
33
34			return mol
			0 ignored issues – show Coding Style introduced 2016-07-10 23:48 UTC by Report Bug Copy Issue Report Final newline missing Loading history...

richlewis42 / scikit-chem

Push — master ( 4cde57...24f8d3 )

UFF A

Complexity

Size/Duplication

Importance

2 Methods

1. Missing Dependencies

2. Missing __init__.py files

Duplication Side-by-Side

Filter issues like

2. Missing init.py files