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

ChemAxonStandardizer.columns() A
last analyzed 2016-09-01 14:43 UTC

↳ Parent: ChemAxonStandardizer

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	1
CRAP Score	1.125

Importance

Changes

Metric	Value
c	0
b	0
f	0
dl	0
loc	3
ccs	1
cts	2
cp	0.5
rs	10
cc	1
crap	1.125

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

"""
## skchem.standardizers.chemaxon

Module wrapping ChemAxon Standardizer.  Must have standardizer installed and
license activated.
"""

import os
import sys
import re
import subprocess
import logging
import warnings

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

from .. import io
from ..utils import sdf_count
from ..base import CLIWrapper, Transformer, BatchTransformer
from ..filters.base import TransformFilter

LOGGER = logging.getLogger(__name__)

if sys.version_info[0] == 2:
    NoFoundError = OSError
    subprocess.DEVNULL = open(os.devnull, 'w')
else:
    NoFoundError = FileNotFoundError



class ChemAxonStandardizer(CLIWrapper, BatchTransformer, Transformer,

                           TransformFilter):

    """ ChemAxon Standardizer Wrapper.

    Args:
        config_path (str):
            The path of the config_file. If None, use the default one.

    Notes:
        ChemAxon Standardizer must be installed and accessible as `standardize`
        from the shell launching the program.

    Warnings:
        Must use a unique index (see #31).

    Examples:

        >>> import skchem
        >>> std = skchem.standardizers.ChemAxonStandardizer() # doctest:+SKIP
        >>> m = skchem.Mol.from_smiles('CC.CCC')
        >>> print(std.transform(m)) # doctest:+SKIP
        <Mol: CCC>

        >>> data = [m, skchem.Mol.from_smiles('C=CO'), skchem.Mol.from_smiles('C[O-]')]
        >>> std.transform(data) # doctest:+SKIP
        0     <Mol: CCC>
        1    <Mol: CC=O>
        2      <Mol: CO>
        Name: structure, dtype: object

        >>> will_fail = mol = '''932-97-8
        ...      RDKit          3D
        ...
        ...   9  9  0  0  0  0  0  0  0  0999 V2000
        ...    -0.9646    0.0000    0.0032 C   0  0  0  0  0  0  0  0  0  0  0  0
        ...    -0.2894   -1.2163    0.0020 C   0  0  0  0  0  0  0  0  0  0  0  0
        ...    -0.2894    1.2163    0.0025 C   0  0  0  0  0  0  0  0  0  0  0  0
        ...    -2.2146    0.0000   -0.0004 N   0  0  0  0  0  0  0  0  0  0  0  0
        ...     1.0710   -1.2610    0.0002 C   0  0  0  0  0  0  0  0  0  0  0  0
        ...     1.0710    1.2610    0.0007 C   0  0  0  0  0  0  0  0  0  0  0  0
        ...    -3.3386    0.0000   -0.0037 N   0  0  0  0  0  0  0  0  0  0  0  0
        ...     1.8248    0.0000   -0.0005 C   0  0  0  0  0  0  0  0  0  0  0  0
        ...     3.0435    0.0000   -0.0026 O   0  0  0  0  0  0  0  0  0  0  0  0
        ...   1  2  1  0
        ...   1  3  1  0
        ...   1  4  2  3
        ...   2  5  2  0
        ...   3  6  2  0
        ...   4  7  2  0
        ...   5  8  1  0
        ...   8  9  2  0
        ...   6  8  1  0
        ... M  CHG  2   4   1   7  -1
        ... M  END
        ... '''

        >>> will_fail = skchem.Mol.from_molblock(will_fail)
        >>> std.transform(will_fail) # doctest:+SKIP
        nan

        >>> data = [will_fail] + data

        >>> std.transform(data) # doctest:+SKIP
        0           None
        1     <Mol: CCC>
        2    <Mol: CC=O>
        3      <Mol: CO>
        Name: structure, dtype: object

        >>> std.transform_filter(data) # doctest:+SKIP
        1     <Mol: CCC>
        2    <Mol: CC=O>
        3      <Mol: CO>
        Name: structure, dtype: object

        >>> std.keep_failed = True # doctest:+SKIP
        >>> std.transform(data) # doctest:+SKIP
        0    <Mol: [N-]=[N+]=C1C=CC(=O)C=C1>
        1                         <Mol: CCC>
        2                        <Mol: CC=O>
        3                          <Mol: CO>
        Name: structure, dtype: object

    """
    install_hint = """ Install ChemAxon from https://www.chemaxon.com.  It requires a license,
    which can be freely obtained for academics. """

    DEFAULT_CONFIG = os.path.join(os.path.dirname(__file__),
                                  'default_config.xml')

    def __init__(self, config_path=None, keep_failed=False, **kwargs):

        super(ChemAxonStandardizer, self).__init__(**kwargs)

        if not config_path:
            config_path = self.DEFAULT_CONFIG
        self.config_path = config_path
        self.keep_failed = keep_failed

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

    def _transform_series(self, ser):

        # implement keep_failed functionality here
        res = super(ChemAxonStandardizer, self)._transform_series(ser)
        mask = pd.isnull(res)

        for m_in, m_out in zip(ser[~mask], res[~mask]):
            m_out.name = m_in.name

        if self.keep_failed:
            res[mask] = ser.iloc[mask]
        return res

    def _parse_outfile(self, outfile):
        """ Reads output file and returns a list"""
        return io.read_sdf(outfile, read_props=False)

    def _parse_errors(self, errs):
        """ Reads stderr and parses out failures as a list of indices. """
        LOGGER.debug('stderr: %s', errs if errs else None)
        errs = errs.strip().split('\n')
        errs = [re.findall('No. ([0-9]+):', err) for err in errs]
        return [int(err[0]) - 1 for err in errs if len(err)]

    def _cli_args(self, infile, outfile):
        """ The command line arguments to use for the subprocess. """

        return ['standardize', infile, '-c', self.config_path,
                '-f', 'sdf', '-o', outfile, '--ignore-error']

    @staticmethod
    def validate_install():
        """ Check if we can call cxcalc. """
        try:
            return subprocess.call(['standardize', '-h'],
                                   stdout=subprocess.DEVNULL,
                                   stderr=subprocess.DEVNULL) == 0
        except NoFoundError:
            return False

    def monitor_progress(self, filename):
        return sdf_count(filename)

    def filter(self, *args, **kwargs):
        warnings.warn('Filter returns the unstandardized Mols. Did you mean to'
                      'use `transform_filter`?')
        super(ChemAxonStandardizer, self).filter(*args, **kwargs)


ChemAxonStandardizer.columns() 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.standardizers.chemaxon
8
9		Module wrapping ChemAxon Standardizer. Must have standardizer installed and
10		license activated.
11		"""
12
13	1	import os
14	1	import sys
15	1	import re
16	1	import subprocess
17	1	import logging
18	1	import warnings
19
20	1	import pandas as pd
		0 ignored issues – show Configuration introduced 2016-06-07 13:27 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...
21
22	1	from .. import io
23	1	from ..utils import sdf_count
24	1	from ..base import CLIWrapper, Transformer, BatchTransformer
25	1	from ..filters.base import TransformFilter
26
27	1	LOGGER = logging.getLogger(__name__)
28
29	1	if sys.version_info[0] == 2:
30	1	NoFoundError = OSError
31	1	subprocess.DEVNULL = open(os.devnull, 'w')
32		else:
33		NoFoundError = FileNotFoundError
		0 ignored issues – show Coding Style Naming introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report The name `NoFoundError` does not conform to the constant naming conventions (`(([A-Z_][A-Z0-9_])\|(__.__))$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history... Comprehensibility Best Practice introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report Undefined variable 'FileNotFoundError' Loading history...
34
35
36	1	class ChemAxonStandardizer(CLIWrapper, BatchTransformer, Transformer,
		0 ignored issues – show best-practice introduced 2016-08-05 16:20 UTC by Report Bug Copy Issue Report Too many ancestors (8/7) Loading history...
37		TransformFilter):
38
39		""" ChemAxon Standardizer Wrapper.
40
41		Args:
42		config_path (str):
43		The path of the config_file. If None, use the default one.
44
45		Notes:
46		ChemAxon Standardizer must be installed and accessible as `standardize`
47		from the shell launching the program.
48
49		Warnings:
50		Must use a unique index (see #31).
51
52		Examples:
53
54		>>> import skchem
55		>>> std = skchem.standardizers.ChemAxonStandardizer() # doctest:+SKIP
56		>>> m = skchem.Mol.from_smiles('CC.CCC')
57		>>> print(std.transform(m)) # doctest:+SKIP
58		<Mol: CCC>
59
60		>>> data = [m, skchem.Mol.from_smiles('C=CO'), skchem.Mol.from_smiles('C[O-]')]
61		>>> std.transform(data) # doctest:+SKIP
62		0 <Mol: CCC>
63		1 <Mol: CC=O>
64		2 <Mol: CO>
65		Name: structure, dtype: object
66
67		>>> will_fail = mol = '''932-97-8
68		... RDKit 3D
69		...
70		... 9 9 0 0 0 0 0 0 0 0999 V2000
71		... -0.9646 0.0000 0.0032 C 0 0 0 0 0 0 0 0 0 0 0 0
72		... -0.2894 -1.2163 0.0020 C 0 0 0 0 0 0 0 0 0 0 0 0
73		... -0.2894 1.2163 0.0025 C 0 0 0 0 0 0 0 0 0 0 0 0
74		... -2.2146 0.0000 -0.0004 N 0 0 0 0 0 0 0 0 0 0 0 0
75		... 1.0710 -1.2610 0.0002 C 0 0 0 0 0 0 0 0 0 0 0 0
76		... 1.0710 1.2610 0.0007 C 0 0 0 0 0 0 0 0 0 0 0 0
77		... -3.3386 0.0000 -0.0037 N 0 0 0 0 0 0 0 0 0 0 0 0
78		... 1.8248 0.0000 -0.0005 C 0 0 0 0 0 0 0 0 0 0 0 0
79		... 3.0435 0.0000 -0.0026 O 0 0 0 0 0 0 0 0 0 0 0 0
80		... 1 2 1 0
81		... 1 3 1 0
82		... 1 4 2 3
83		... 2 5 2 0
84		... 3 6 2 0
85		... 4 7 2 0
86		... 5 8 1 0
87		... 8 9 2 0
88		... 6 8 1 0
89		... M CHG 2 4 1 7 -1
90		... M END
91		... '''
92
93		>>> will_fail = skchem.Mol.from_molblock(will_fail)
94		>>> std.transform(will_fail) # doctest:+SKIP
95		nan
96
97		>>> data = [will_fail] + data
98
99		>>> std.transform(data) # doctest:+SKIP
100		0 None
101		1 <Mol: CCC>
102		2 <Mol: CC=O>
103		3 <Mol: CO>
104		Name: structure, dtype: object
105
106		>>> std.transform_filter(data) # doctest:+SKIP
107		1 <Mol: CCC>
108		2 <Mol: CC=O>
109		3 <Mol: CO>
110		Name: structure, dtype: object
111
112		>>> std.keep_failed = True # doctest:+SKIP
113		>>> std.transform(data) # doctest:+SKIP
114		0 <Mol: [N-]=[N+]=C1C=CC(=O)C=C1>
115		1 <Mol: CCC>
116		2 <Mol: CC=O>
117		3 <Mol: CO>
118		Name: structure, dtype: object
119
120		"""
121	1	install_hint = """ Install ChemAxon from https://www.chemaxon.com. It requires a license,
122		which can be freely obtained for academics. """
123
124	1	DEFAULT_CONFIG = os.path.join(os.path.dirname(__file__),
125		'default_config.xml')
126
127	1	def __init__(self, config_path=None, keep_failed=False, **kwargs):
128
129		super(ChemAxonStandardizer, self).__init__(**kwargs)
130
131		if not config_path:
132		config_path = self.DEFAULT_CONFIG
133		self.config_path = config_path
134		self.keep_failed = keep_failed
135
136	1	@property
137		def columns(self):
138		return ['structure']
139
140	1	def _transform_series(self, ser):
141
142		# implement keep_failed functionality here
143		res = super(ChemAxonStandardizer, self)._transform_series(ser)
144		mask = pd.isnull(res)
145
146		for m_in, m_out in zip(ser[~mask], res[~mask]):
147		m_out.name = m_in.name
148
149		if self.keep_failed:
150		res[mask] = ser.iloc[mask]
151		return res
152
153	1	def _parse_outfile(self, outfile):
154		""" Reads output file and returns a list"""
155		return io.read_sdf(outfile, read_props=False)
156
157	1	def _parse_errors(self, errs):
158		""" Reads stderr and parses out failures as a list of indices. """
159		LOGGER.debug('stderr: %s', errs if errs else None)
160		errs = errs.strip().split('\n')
161		errs = [re.findall('No. ([0-9]+):', err) for err in errs]
162		return [int(err[0]) - 1 for err in errs if len(err)]
163
164	1	def _cli_args(self, infile, outfile):
165		""" The command line arguments to use for the subprocess. """
166
167		return ['standardize', infile, '-c', self.config_path,
168		'-f', 'sdf', '-o', outfile, '--ignore-error']
169
170	1	@staticmethod
171		def validate_install():
172		""" Check if we can call cxcalc. """
173		try:
174		return subprocess.call(['standardize', '-h'],
175		stdout=subprocess.DEVNULL,
176		stderr=subprocess.DEVNULL) == 0
177		except NoFoundError:
178		return False
179
180	1	def monitor_progress(self, filename):
181		return sdf_count(filename)
182
183	1	def filter(self, args, *kwargs):
184		warnings.warn('Filter returns the unstandardized Mols. Did you mean to'
185		'use `transform_filter`?')
186		super(ChemAxonStandardizer, self).filter(args, *kwargs)
187

richlewis42 / scikit-chem

ChemAxonStandardizer.columns() A last analyzed 2016-09-01 14:43 UTC

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2. Missing __init__.py files

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ChemAxonStandardizer.columns() A
last analyzed 2016-09-01 14:43 UTC

2. Missing init.py files