SpaceDistanceCalculator - 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

SpaceDistanceCalculator A

↳ Parent: Project

Complexity

Total Complexity

Size/Duplication

Total Lines	24
Duplicated Lines	0 %

Importance

Changes	1
Bugs	0	Features	1

Metric	Value
wmc	5
c	1
b	0
f	1
dl	0
loc	24
rs	10

2 Methods

Rating	Name	Duplication	Size	Complexity
A	_transform_mol()	0	16	4
A	__init__()	0	5	1

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

"""
## skchem.descriptors.atom

Module specifying atom based descriptor generators.
"""

import pandas as pd
# .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
import progressbar
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from rdkit import Chem
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem import Crippen
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem import Lipinski
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem import rdMolDescriptors, rdPartialCharges
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3
from rdkit.Chem.rdchem import HybridizationType
# .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

import functools
import warnings

from .. import core
from ..data import PERIODIC_TABLE
from ..filters import OrganicFilter
from .. import forcefields

def element(a):


    """ Return the element """

    return a.GetSymbol()

def is_element(a, symbol='C'):


    """ Is the atom of a given element """
    return element(a) == symbol

element_features = {'is_{}'.format(e): functools.partial(is_element, symbol=e) for e in OrganicFilter.organic}


def is_h_acceptor(a):


    """ Is an H acceptor? """

    m = a.GetOwningMol()

    idx = a.GetIdx()
    return idx in [i[0] for i in Lipinski._HAcceptors(m)]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

def is_h_donor(a):


    """ Is an H donor? """

    m = a.GetOwningMol()

    idx = a.GetIdx()
    return idx in [i[0] for i in Lipinski._HDonors(m)]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

def is_hetero(a):


    """ Is a heteroatom? """

    m = a.GetOwningMol()

    idx = a.GetIdx()
    return idx in [i[0] for i in Lipinski._Heteroatoms(m)]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

def atomic_number(a):


    """ Atomic number of atom """

    return a.GetAtomicNum()

def atomic_mass(a):


    """ Atomic mass of atom """

    return a.mass

def explicit_valence(a):


    """ Explicit valence of atom """
    return a.GetExplicitValence()

def implicit_valence(a):


    """ Implicit valence of atom """

    return a.GetImplicitValence()

def valence(a):


    """ returns the valence of the atom """

    return explicit_valence(a) + implicit_valence(a)

def formal_charge(a):


    """ Formal charge of atom """

    return a.GetFormalCharge()

def is_aromatic(a):


    """ Boolean if atom is aromatic"""

    return a.GetIsAromatic()

def num_implicit_hydrogens(a):


    """ Number of implicit hydrogens """

    return a.GetNumImplicitHs()

def num_explicit_hydrogens(a):


    """ Number of explicit hydrodgens """

    return a.GetNumExplicitHs()

def num_hydrogens(a):


    """ Number of hydrogens """

    return num_implicit_hydrogens(a) + num_explicit_hydrogens(a)

def is_in_ring(a):


    """ Whether the atom is in a ring """

    return a.IsInRing()

def crippen_log_p_contrib(a):


    """ Hacky way of getting logP contribution. """

    idx = a.GetIdx()
    m = a.GetOwningMol()

    return Crippen._GetAtomContribs(m)[idx][0]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

def crippen_molar_refractivity_contrib(a):


    """ Hacky way of getting molar refractivity contribution. """

    idx = a.GetIdx()
    m = a.GetOwningMol()

    return Crippen._GetAtomContribs(m)[idx][1]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

def tpsa_contrib(a):


    """ Hacky way of getting total polar surface area contribution. """

    idx = a.GetIdx()
    m = a.GetOwningMol()

    return rdMolDescriptors._CalcTPSAContribs(m)[idx]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

def labute_asa_contrib(a):


    """ Hacky way of getting accessible surface area contribution. """

    idx = a.GetIdx()
    m = a.GetOwningMol()

    return rdMolDescriptors._CalcLabuteASAContribs(m)[0][idx]
class MyParent:
    def __init__(self):
        self._x = 1;
        self.y = 2;

class MyChild(MyParent):
    def some_method(self):
        return self._x    # Ok, since accessed from a child class

class AnotherClass:
    def some_method(self, instance_of_my_child):
        return instance_of_my_child._x   # Would be flagged as AnotherClass is not
                                         # a child class of MyParent

def gasteiger_charge(a, force_calc=False):


    """ Hacky way of getting gasteiger charge """

    res = a.props.get('_GasteigerCharge', None)
    if res and not force_calc:
        return float(res)
    else:
        idx = a.GetIdx()

        m = a.GetOwningMol()

        rdPartialCharges.ComputeGasteigerCharges(m)
        return float(a.props['_GasteigerCharge'])

def electronegativity(a):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return PERIODIC_TABLE.loc[a.atomic_number, 'pauling_electronegativity']

def first_ionization(a):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return PERIODIC_TABLE.loc[a.atomic_number, 'first_ionisation_energy']

def group(a):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return PERIODIC_TABLE.loc[a.atomic_number, 'group']

def period(a):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    return PERIODIC_TABLE.loc[a.atomic_number, 'period']

def is_hybridized(a, hybrid_type=HybridizationType.SP3):


    """ Hybridized as type hybrid_type, default SP3 """

    return str(a.GetHybridization()) is hybrid_type

hybridization_features = {'is_' + n + '_hybridized': functools.partial(is_hybridized, hybrid_type=n) for n in HybridizationType.names}


atom_features = {

    'atomic_number': atomic_number,
    'atomic_mass': atomic_mass,
    'formal_charge': formal_charge,
    'gasteiger_charge': gasteiger_charge,
    'electronegativity': electronegativity,
    'first_ionisation': first_ionization,
    'group': group,
    'period': period,
    'valence': valence,
    'is_aromatic': is_aromatic,
    'num_hydrogens': num_hydrogens,
    'is_in_ring': is_in_ring,
    'log_p_contrib': crippen_log_p_contrib,
    'molar_refractivity_contrib': crippen_molar_refractivity_contrib,
    'is_h_acceptor': is_h_acceptor,
    'is_h_donor': is_h_donor,
    'is_heteroatom': is_hetero,
    'total_polar_surface_area_contrib': tpsa_contrib,
    'total_labute_accessible_surface_area': labute_asa_contrib,
}
atom_features.update(element_features)
atom_features.update(hybridization_features)

class AtomFeatureCalculator(object):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    def __init__(self, features='all', max_atoms=75):
        if features == 'all':
            features = atom_features
        self.features = pd.Series(features)
        self.max_atoms = max_atoms

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

    def transform(self, obj):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        if isinstance(obj, core.Atom):
            return self._transform_atom(obj)
        elif isinstance(obj, core.Mol):
            return self._transform_mol(obj)
        elif isinstance(obj, pd.Series):
            return self._transform_series(obj)
        elif isinstance(obj, pd.DataFrame):
            return self._transform_series(obj.structure)
        elif isinstance(obj, (tuple, list)):
            return self._transform_series(obj)
        else:
            raise NotImplementedError

    def _transform_atom(self, atom):
        return self.features.apply(lambda f: f(atom))

    def _transform_mol(self, mol):
        return pd.DataFrame(self.transform(a) for a in mol.atoms)

    def _transform_series(self, data):
        X = np.repeat(np.nan,

                      len(self.feature_names) * self.max_atoms * len(data))\
                      .reshape((len(data), self.max_atoms, len(self.feature_names)))
        for i, mol in enumerate(data):
            X[i, :len(mol.atoms), :] = self._transform_mol(mol)
        res = pd.Panel(X, items=data.index)
        res.minor_axis = self.features.index
        res.major_axis.name = 'atom_idx'
        return res


    def __call__(self, *args, **kwargs):
        return self.transform(*args, **kwargs)

class DistanceCalculator(object):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
    def __init__(self, max_atoms=75):
        self.max_atoms = max_atoms

    def _transform_series(self, ser):
        bar = progressbar.ProgressBar()

        res = pd.Panel(np.array([self.transform(mol) for mol in bar(ser)]), items=ser.index)
        res.major_axis.name = res.minor_axis.name = 'atom_idx'
        return res

    def transform(self, obj):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""
        if isinstance(obj, core.Atom):
            return self._transform_atom(obj)

        elif isinstance(obj, core.Mol):
            return self._transform_mol(obj)

        elif isinstance(obj, pd.Series):
            return self._transform_series(obj)
        elif isinstance(obj, pd.DataFrame):
            return self._transform_series(obj.structure)
        elif isinstance(obj, (tuple, list)):
            return self._transform_series(obj)
        else:
            raise NotImplementedError

    def __call__(self, *args, **kwargs):
        return self.transform(*args, **kwargs)

class GraphDistanceCalculator(DistanceCalculator):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    def _transform_mol(self, mol):
        res = np.repeat(np.nan, self.max_atoms ** 2).reshape(self.max_atoms, self.max_atoms)
        res[:len(mol.atoms), :len(mol.atoms)] = Chem.GetDistanceMatrix(mol)
        return res

class SpaceDistanceCalculator(DistanceCalculator):
class SomeClass:
    def some_method(self):
        """Do x and return foo."""

    def __init__(self, max_atoms=75, warn_on_fail=True, error_on_fail=False, forcefield='uff'):
        self.forcefield = forcefields.get(forcefield)
        self.warn_on_fail = warn_on_fail
        self.error_on_fail = error_on_fail
        super(SpaceDistanceCalculator, self).__init__(max_atoms=max_atoms)

    def _transform_mol(self, mol):
        res = np.repeat(np.nan, self.max_atoms ** 2).reshape(self.max_atoms, self.max_atoms)
        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 res
            else:
                pass
        m_new = Chem.AddHs(mol, addCoords=True)

        self.forcefield.optimize(mol)
        res[:len(mol.atoms), :len(mol.atoms)] = Chem.Get3DDistanceMatrix(mol)
        return res


Push — master ( 4cde57...24f8d3 )

SpaceDistanceCalculator A

Complexity

Size/Duplication

Importance

2 Methods

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. 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. 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.descriptors.atom
8
9			Module specifying atom based descriptor generators.
10			"""
11
12			import pandas as pd
			0 ignored issues – show Configuration introduced 2016-01-19 23:07 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			import numpy as np
			0 ignored issues – show Configuration introduced 2016-06-03 13:34 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...
14			import progressbar
			0 ignored issues – show Configuration introduced 2016-07-10 23:48 UTC by Report Bug Copy Issue Report The import `progressbar` 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			from rdkit import Chem
			0 ignored issues – show Configuration introduced 2016-01-19 23:07 UTC by Report Bug Copy Issue Report The import `rdkit` 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...
17			from rdkit.Chem import Crippen
			0 ignored issues – show Configuration introduced 2016-01-19 23:07 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...
18			from rdkit.Chem import Lipinski
			0 ignored issues – show Configuration introduced 2016-01-19 23:07 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...
19			from rdkit.Chem import rdMolDescriptors, rdPartialCharges
			0 ignored issues – show Configuration introduced 2016-01-19 23:07 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...
20			from rdkit.Chem.rdchem import HybridizationType
			0 ignored issues – show Configuration introduced 2016-01-19 23:07 UTC by Report Bug Copy Issue Report The import `rdkit.Chem.rdchem` 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...
21			from rdkit.Chem.rdDistGeom import EmbedMolecule
			0 ignored issues – show Configuration introduced 2016-07-10 23:48 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...
22
23			import functools
24			import warnings
25
26			from .. import core
27			from ..data import PERIODIC_TABLE
28			from ..filters import OrganicFilter
29			from .. import forcefields
30
31			def element(a):

richlewis42 / scikit-chem

Push — master ( 4cde57...24f8d3 )

SpaceDistanceCalculator A

Complexity

Size/Duplication

Importance

2 Methods

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. 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. Missing Dependencies

2. Missing __init__.py files

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2. Missing init.py files

2. Missing init.py files