n_bond_order() - Code Metrics - Inspection of "added constitutional descriptors" - richlewis42/scikit-chem - Measure and Improve Code Quality continuously with Scrutinizer

Completed

Push — master ( 360284...546a0f )

by Rich

created 2016-09-01 14:38 UTC

n_bond_order() A

↳ Parent: Project

Complexity

Conditions

Size

Total Lines

Duplication

Lines	0
Ratio	0 %

Code Coverage

Tests	2
CRAP Score	1.037

Importance

Changes	1
Bugs	0	Features	1

Metric	Value
cc	1
c	1
b	0
f	1
dl	0
loc	15
ccs	2
cts	3
cp	0.6667
crap	1.037
rs	9.4285

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

"""
# skchem.features.descriptors.constitutional

Constitutional features for scikit-chem.
"""

from collections import OrderedDict
from functools import partial

from rdkit.Chem import rdMolDescriptors, rdmolops, Descriptors
# .scrutinizer.yml
before_commands:
    - sudo pip install abc # Python2
    - sudo pip3 install abc # Python3

from .caching import cache, requires_h_filled, requires_h_depleted

from .fundamentals import bond_order_adjacency_matrix



def molecular_weight(mol):

    """ The molecular weight.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """
    return rdMolDescriptors.CalcExactMolWt(mol)


@requires_h_filled
def average_molecular_weight(mol):

    """ Average molecular weight of atoms.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return molecular_weight(mol) / len(mol.atoms)


def sum_van_der_waals_volume(mol):

    """ The sum of the Van der Waals volume.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.van_der_waals_volume.sum()


def sum_electronegativity(mol):

    """ The sum of the Sanderson electronegativities.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.sanderson_electronegativity.sum()


def sum_ionisation_energy(mol):

    """ The sum of the first ionisation energies.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.ionisation_energy.sum()


def sum_polarisability(mol):

    """ The sum of the polarisabilities.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.polarisability.sum()


def mean_van_der_waals_volume(mol):

    """ The mean of the Van der Waals volume.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.van_der_waals_volume.sum()


def mean_electronegativity(mol):

    """ The mean of the Sanderson electronegativity.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.sanderson_electronegativity.mean()


def mean_ionisation_energy(mol):

    """ The mean of the first ionisation energies.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.ionisation_energy.mean()


def mean_polarisability(mol):

    """ The mean of the polarizabilities.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return mol.atoms.polarisability.mean()


@requires_h_depleted
def graph_density(mol):

    """ The graph density of the h-depleted graph.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return 2 * len(mol.bonds) / (len(mol.atoms) * (len(mol.atoms) - 1))


def n_atoms(mol):

    """ The number of atoms.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return len(mol.atoms)


@requires_h_filled
def n_hyd(mol):

    """ The number of hydrogen atoms.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return sum(mol.atoms.atomic_number == 1)


@requires_h_depleted
def n_atom(mol, symbol='C'):

    """ The number of atoms of symbol *s*.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return sum(mol.atoms.symbol == symbol)


@requires_h_filled
def fract_atom(mol, symbol='C'):

    """ The fraction of atoms of symbol *s*.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return sum(mol.atoms.symbol == symbol) / len(mol.atoms)


def n_halo(mol):
    # TODO: memoize

    """ The number of halogens.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """
    return sum(n_atom(mol, s) for s in ('F', 'Cl', 'Br', 'I'))


@requires_h_filled
def fract_halo(mol):
    """ The fraction of halogens.

     Args:
         mol (skchem.Mol):
             The molecule for which to calculate the descriptor.

     Returns:
         float
     """

    return n_halo(mol) / len(mol.atoms)


def n_hetero(mol):

    """ The number of heteroatoms.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return rdMolDescriptors.CalcNumHeteroatoms(mol)


def n_heavy(mol):

    """ The number of heavy atoms.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return mol.GetNumHeavyAtoms()


def n_terminal(mol):

    """ The number of heavy atoms.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return mol.atoms.is_terminal.sum()


@requires_h_filled
def n_bonds(mol):

    """ The number of bonds.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return len(mol.bonds)


@requires_h_depleted
def n_bonds_non_h(mol):

    """ The number of bonds between atoms other than hydrogen.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return len(mol.bonds)


@requires_h_depleted
def n_bonds_multiple(mol):

    """ The number of multiple bonds.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return (mol.bonds.order > 1).sum()


@requires_h_depleted
def sum_of_conventional_bond_orders(mol):

    """ The sum of conventional bond orders (h-depleted).

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int
    """

    return mol.bonds.order.sum()


def n_rotatable_bonds(mol):

    """ The number of rotatable bonds.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        int

    """
    return rdMolDescriptors.CalcNumRotatableBonds(mol)


@requires_h_depleted
def fract_rotatable_bonds(mol):
    # TODO: memoize

    """ The fraction of rotatable bonds.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """
    return n_rotatable_bonds(mol) / n_bonds(mol)


@requires_h_depleted
def n_bond_order(mol, order=1):

    """ The number of bonds of order *i*.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

        order (int):
            The order of bonds.
    Returns:
        int
    """
    return (mol.bonds.order == order).sum()


def fract_c_hybrid(mol, h_state='SP3'):

    """ The fraction of carbons that are in a certain hybridization state.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

        h_state (str):
            The hybridization state for which to measure the fraction.
    Returns:
        float
    """

    carbs = mol.atoms.atomic_number == 6
    return (mol.atoms.hybridization_state == h_state)[carbs].sum() / carbs.sum()


def n_disconnected(mol):

    """ The number of disconnected fragments in the mol.

        Args:
            mol (skchem.Mol):
                The molecule for which to calculate the descriptor.

        Returns:
            int
        """

    return len(rdmolops.GetMolFrags(mol))


def total_charge(mol):

    """ The total charge of the molecule.

        Args:
            mol (skchem.Mol):
                The molecule for which to calculate the descriptor.

        Returns:
            float
        """

    return mol.atoms.formal_charge.sum()


def n_hba(mol):

    """ The number of h bond acceptors.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """
    return rdMolDescriptors.CalcNumHBA(mol)


def n_hba(mol):


    """ The number of h bond donors.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """
    return rdMolDescriptors.CalcNumHBD(mol)


def n_radical_electrons(mol):

    """ The number of radical electrons.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """
    return Descriptors.NumRadicalElectrons(mol)


def n_valence_electrons(mol):

    """ The number of valence electrons.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return Descriptors.NumValenceElectrons(mol)


def heavy_atom_mol_wt(x):


    """ The molecular weight of only heavy atoms.

    Args:
        mol (skchem.Mol):
            The molecule for which to calculate the descriptor.

    Returns:
        float
    """

    return rdMolDescriptors.CalcExactMolWt(x, True)


def n_hbd_lipinski(x):


    """ The number of hydrogen bond donors according to Lipinski."""

    return rdMolDescriptors.CalcNumLipinskiHBD(x)


def n_hba_lipinski(x):


    """ The number of hydrogen bond acceptors according to Lipinski."""

    return rdMolDescriptors.CalcNumLipinskiHBA(x)


@requires_h_depleted
def n_paths(mol, length=1):

    """ The number of paths of length *l*. """

    return len(rdmolops.FindAllPathsOfLengthN(mol, length))


DESCRIPTORS = OrderedDict((
    ('mol_wt', molecular_weight),
    ('avg_mol_wt', average_molecular_weight),
    ('sum_vdw_vol', sum_van_der_waals_volume),
    ('sum_eneg', sum_electronegativity),
    ('sum_pol', sum_polarisability),
    ('sum_ion_energy', sum_ionisation_energy),
    ('mean_vdw_vol', mean_van_der_waals_volume),
    ('mean_eneg', mean_electronegativity),
    ('mean_pol', mean_polarisability),
    ('mean_ion_energy', mean_ionisation_energy),
    ('graph_density', graph_density),
    ('n_atoms', n_atoms),
    ('n_term', n_terminal),
    ('n_bonds', n_bonds),
    ('n_bonds_non_h', n_bonds_non_h),
    ('n_bonds_mult', n_bonds_multiple),
    ('sum_bond_order', sum_of_conventional_bond_orders),
    ('n_rot_bonds', n_rotatable_bonds),
    ('fract_rot_bonds', fract_rotatable_bonds),
    ('n_hyd', n_hyd),
    ('n_halo', n_halo),
    ('n_heavy', n_heavy),
    ('n_hetero', n_hetero),
    ('n_hba', n_hba),
    ('n_atoms', n_atoms),
    ('fract_halo', fract_halo),
    ('n_disconn', n_disconnected),
    ('total_charge', total_charge),
    ('n_rad', n_radical_electrons),
    ('n_val', n_valence_electrons),
    ('heavy_mol_wt', heavy_atom_mol_wt),
    ('n_hbd_lip', n_hbd_lipinski),
    ('n_hba_lib', n_hba_lipinski)
))

SYMBOLS = ('C', 'N', 'O', 'P', 'S', 'F', 'Cl', 'Br', 'I', 'B')
HYBRIDS = ('SP3', 'SP2', 'SP')

DESCRIPTORS.update(('fract_c_{}'.format(hybrid), partial(fract_c_hybrid,
                                                         h_state=hybrid))
                   for hybrid in HYBRIDS)

DESCRIPTORS.update((('n_{}'.format(symbol), partial(n_atom, symbol=symbol))
                    for symbol in SYMBOLS))

DESCRIPTORS.update((('n_{}'.format(symbol), partial(fract_atom, symbol=symbol))
                    for symbol in ('H', 'C', 'N', 'O')))

DESCRIPTORS.update((('n_bond_{}'.format(order), partial(n_bond_order,
                                                       order=order))

                    for order in (1, 1.5, 2, 3)))

DESCRIPTORS.update((('n_paths_{}'.format(length), partial(n_paths, length=length))
                    for length in range(1, 7)))


Push — master ( 360284...546a0f )

n_bond_order() A

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.features.descriptors.constitutional
8
9		Constitutional features for scikit-chem.
10		"""
11
12	1	from collections import OrderedDict
13	1	from functools import partial
14
15	1	from rdkit.Chem import rdMolDescriptors, rdmolops, Descriptors
		0 ignored issues – show Configuration introduced 2016-09-01 14:43 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...
16
17	1	from .caching import cache, requires_h_filled, requires_h_depleted
		0 ignored issues – show Unused Code introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report Unused cache imported from caching Loading history...
18	1	from .fundamentals import bond_order_adjacency_matrix
		0 ignored issues – show Unused Code introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report Unused bond_order_adjacency_matrix imported from fundamentals Loading history...
19
20
21	1	def molecular_weight(mol):
22
23		""" The molecular weight.
24
25		Args:
26		mol (skchem.Mol):
27		The molecule for which to calculate the descriptor.
28
29		Returns:
30		float
31		"""
32		return rdMolDescriptors.CalcExactMolWt(mol)
33
34
35	1	@requires_h_filled
36		def average_molecular_weight(mol):
37
38		""" Average molecular weight of atoms.
39
40		Args:
41		mol (skchem.Mol):
42		The molecule for which to calculate the descriptor.
43
44		Returns:
45		float
46		"""
47
48		return molecular_weight(mol) / len(mol.atoms)
49
50
51	1	def sum_van_der_waals_volume(mol):
52
53		""" The sum of the Van der Waals volume.
54
55		Args:
56		mol (skchem.Mol):
57		The molecule for which to calculate the descriptor.
58
59		Returns:
60		float
61		"""
62
63		return mol.atoms.van_der_waals_volume.sum()
64
65
66	1	def sum_electronegativity(mol):
67
68		""" The sum of the Sanderson electronegativities.
69
70		Args:
71		mol (skchem.Mol):
72		The molecule for which to calculate the descriptor.
73
74		Returns:
75		float
76		"""
77
78		return mol.atoms.sanderson_electronegativity.sum()
79
80
81	1	def sum_ionisation_energy(mol):
82
83		""" The sum of the first ionisation energies.
84
85		Args:
86		mol (skchem.Mol):
87		The molecule for which to calculate the descriptor.
88
89		Returns:
90		float
91		"""
92
93		return mol.atoms.ionisation_energy.sum()
94
95
96	1	def sum_polarisability(mol):
97
98		""" The sum of the polarisabilities.
99
100		Args:
101		mol (skchem.Mol):
102		The molecule for which to calculate the descriptor.
103
104		Returns:
105		float
106		"""
107
108		return mol.atoms.polarisability.sum()
109
110
111	1	def mean_van_der_waals_volume(mol):
112
113		""" The mean of the Van der Waals volume.
114
115		Args:
116		mol (skchem.Mol):
117		The molecule for which to calculate the descriptor.
118
119		Returns:
120		float
121		"""
122
123		return mol.atoms.van_der_waals_volume.sum()
124
125
126	1	def mean_electronegativity(mol):
127
128		""" The mean of the Sanderson electronegativity.
129
130		Args:
131		mol (skchem.Mol):
132		The molecule for which to calculate the descriptor.
133
134		Returns:
135		float
136		"""
137
138		return mol.atoms.sanderson_electronegativity.mean()
139
140
141	1	def mean_ionisation_energy(mol):
142
143		""" The mean of the first ionisation energies.
144
145		Args:
146		mol (skchem.Mol):
147		The molecule for which to calculate the descriptor.
148
149		Returns:
150		float
151		"""
152
153		return mol.atoms.ionisation_energy.mean()
154
155
156	1	def mean_polarisability(mol):
157
158		""" The mean of the polarizabilities.
159
160		Args:
161		mol (skchem.Mol):
162		The molecule for which to calculate the descriptor.
163
164		Returns:
165		float
166		"""
167
168		return mol.atoms.polarisability.mean()
169
170
171	1	@requires_h_depleted
172		def graph_density(mol):
173
174		""" The graph density of the h-depleted graph.
175
176		Args:
177		mol (skchem.Mol):
178		The molecule for which to calculate the descriptor.
179
180		Returns:
181		float
182		"""
183
184		return 2 * len(mol.bonds) / (len(mol.atoms) * (len(mol.atoms) - 1))
185
186
187	1	def n_atoms(mol):
188
189		""" The number of atoms.
190
191		Args:
192		mol (skchem.Mol):
193		The molecule for which to calculate the descriptor.
194
195		Returns:
196		int
197		"""
198
199		return len(mol.atoms)
200
201
202	1	@requires_h_filled
203		def n_hyd(mol):
204
205		""" The number of hydrogen atoms.
206
207		Args:
208		mol (skchem.Mol):
209		The molecule for which to calculate the descriptor.
210
211		Returns:
212		int
213		"""
214
215		return sum(mol.atoms.atomic_number == 1)
216
217
218	1	@requires_h_depleted
219	1	def n_atom(mol, symbol='C'):
220
221		""" The number of atoms of symbol s.
222
223		Args:
224		mol (skchem.Mol):
225		The molecule for which to calculate the descriptor.
226
227		Returns:
228		int
229		"""
230
231		return sum(mol.atoms.symbol == symbol)
232
233
234	1	@requires_h_filled
235	1	def fract_atom(mol, symbol='C'):
236
237		""" The fraction of atoms of symbol s.
238
239		Args:
240		mol (skchem.Mol):
241		The molecule for which to calculate the descriptor.
242
243		Returns:
244		float
245		"""
246
247		return sum(mol.atoms.symbol == symbol) / len(mol.atoms)
248
249
250	1	def n_halo(mol):
251		# TODO: memoize
		0 ignored issues – show Coding Style introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report `TODO` and `FIXME` comments should generally be avoided. Loading history...
252		""" The number of halogens.
253
254		Args:
255		mol (skchem.Mol):
256		The molecule for which to calculate the descriptor.
257
258		Returns:
259		int
260		"""
261		return sum(n_atom(mol, s) for s in ('F', 'Cl', 'Br', 'I'))
262
263
264	1	@requires_h_filled
265		def fract_halo(mol):
266		""" The fraction of halogens.
267
268		Args:
269		mol (skchem.Mol):
270		The molecule for which to calculate the descriptor.
271
272		Returns:
273		float
274		"""
275
276		return n_halo(mol) / len(mol.atoms)
277
278
279	1	def n_hetero(mol):
280
281		""" The number of heteroatoms.
282
283		Args:
284		mol (skchem.Mol):
285		The molecule for which to calculate the descriptor.
286
287		Returns:
288		int
289		"""
290
291		return rdMolDescriptors.CalcNumHeteroatoms(mol)
292
293
294	1	def n_heavy(mol):
295
296		""" The number of heavy atoms.
297
298		Args:
299		mol (skchem.Mol):
300		The molecule for which to calculate the descriptor.
301
302		Returns:
303		int
304		"""
305
306		return mol.GetNumHeavyAtoms()
307
308
309	1	def n_terminal(mol):
310
311		""" The number of heavy atoms.
312
313		Args:
314		mol (skchem.Mol):
315		The molecule for which to calculate the descriptor.
316
317		Returns:
318		int
319		"""
320
321		return mol.atoms.is_terminal.sum()
322
323
324	1	@requires_h_filled
325		def n_bonds(mol):
326
327		""" The number of bonds.
328
329		Args:
330		mol (skchem.Mol):
331		The molecule for which to calculate the descriptor.
332
333		Returns:
334		int
335		"""
336
337		return len(mol.bonds)
338
339
340	1	@requires_h_depleted
341		def n_bonds_non_h(mol):
342
343		""" The number of bonds between atoms other than hydrogen.
344
345		Args:
346		mol (skchem.Mol):
347		The molecule for which to calculate the descriptor.
348
349		Returns:
350		int
351		"""
352
353		return len(mol.bonds)
354
355
356	1	@requires_h_depleted
357		def n_bonds_multiple(mol):
358
359		""" The number of multiple bonds.
360
361		Args:
362		mol (skchem.Mol):
363		The molecule for which to calculate the descriptor.
364
365		Returns:
366		int
367		"""
368
369		return (mol.bonds.order > 1).sum()
370
371
372	1	@requires_h_depleted
373		def sum_of_conventional_bond_orders(mol):
374
375		""" The sum of conventional bond orders (h-depleted).
376
377		Args:
378		mol (skchem.Mol):
379		The molecule for which to calculate the descriptor.
380
381		Returns:
382		int
383		"""
384
385		return mol.bonds.order.sum()
386
387
388	1	def n_rotatable_bonds(mol):
389
390		""" The number of rotatable bonds.
391
392		Args:
393		mol (skchem.Mol):
394		The molecule for which to calculate the descriptor.
395
396		Returns:
397		int
398
399		"""
400		return rdMolDescriptors.CalcNumRotatableBonds(mol)
401
402
403	1	@requires_h_depleted
404		def fract_rotatable_bonds(mol):
405		# TODO: memoize
		0 ignored issues – show Coding Style introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report `TODO` and `FIXME` comments should generally be avoided. Loading history...
406		""" The fraction of rotatable bonds.
407
408		Args:
409		mol (skchem.Mol):
410		The molecule for which to calculate the descriptor.
411
412		Returns:
413		float
414		"""
415		return n_rotatable_bonds(mol) / n_bonds(mol)
416
417
418	1	@requires_h_depleted
419	1	def n_bond_order(mol, order=1):
420
421		""" The number of bonds of order i.
422
423		Args:
424		mol (skchem.Mol):
425		The molecule for which to calculate the descriptor.
426
427		order (int):
428		The order of bonds.
429		Returns:
430		int
431		"""
432		return (mol.bonds.order == order).sum()
433
434
435	1	def fract_c_hybrid(mol, h_state='SP3'):
436
437		""" The fraction of carbons that are in a certain hybridization state.
438
439		Args:
440		mol (skchem.Mol):
441		The molecule for which to calculate the descriptor.
442
443		h_state (str):
444		The hybridization state for which to measure the fraction.
445		Returns:
446		float
447		"""
448
449		carbs = mol.atoms.atomic_number == 6
450		return (mol.atoms.hybridization_state == h_state)[carbs].sum() / carbs.sum()
451
452
453	1	def n_disconnected(mol):
454
455		""" The number of disconnected fragments in the mol.
456
457		Args:
458		mol (skchem.Mol):
459		The molecule for which to calculate the descriptor.
460
461		Returns:
462		int
463		"""
464
465		return len(rdmolops.GetMolFrags(mol))
466
467
468	1	def total_charge(mol):
469
470		""" The total charge of the molecule.
471
472		Args:
473		mol (skchem.Mol):
474		The molecule for which to calculate the descriptor.
475
476		Returns:
477		float
478		"""
479
480		return mol.atoms.formal_charge.sum()
481
482
483	1	def n_hba(mol):
484
485		""" The number of h bond acceptors.
486
487		Args:
488		mol (skchem.Mol):
489		The molecule for which to calculate the descriptor.
490
491		Returns:
492		float
493		"""
494		return rdMolDescriptors.CalcNumHBA(mol)
495
496
497	1	def n_hba(mol):
		0 ignored issues – show Bug introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report This function was already defined on line 483. Loading history...
498
499		""" The number of h bond donors.
500
501		Args:
502		mol (skchem.Mol):
503		The molecule for which to calculate the descriptor.
504
505		Returns:
506		float
507		"""
508		return rdMolDescriptors.CalcNumHBD(mol)
509
510
511	1	def n_radical_electrons(mol):
512
513		""" The number of radical electrons.
514
515		Args:
516		mol (skchem.Mol):
517		The molecule for which to calculate the descriptor.
518
519		Returns:
520		float
521		"""
522		return Descriptors.NumRadicalElectrons(mol)
523
524
525	1	def n_valence_electrons(mol):
526
527		""" The number of valence electrons.
528
529		Args:
530		mol (skchem.Mol):
531		The molecule for which to calculate the descriptor.
532
533		Returns:
534		float
535		"""
536
537		return Descriptors.NumValenceElectrons(mol)
538
539
540	1	def heavy_atom_mol_wt(x):
		0 ignored issues – show Coding Style Naming introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report The name `x` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
541
542		""" The molecular weight of only heavy atoms.
543
544		Args:
545		mol (skchem.Mol):
546		The molecule for which to calculate the descriptor.
547
548		Returns:
549		float
550		"""
551
552		return rdMolDescriptors.CalcExactMolWt(x, True)
553
554
555	1	def n_hbd_lipinski(x):
		0 ignored issues – show Coding Style Naming introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report The name `x` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
556
557		""" The number of hydrogen bond donors according to Lipinski."""
558
559		return rdMolDescriptors.CalcNumLipinskiHBD(x)
560
561
562	1	def n_hba_lipinski(x):
		0 ignored issues – show Coding Style Naming introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report The name `x` does not conform to the argument naming conventions (`[a-z_][a-z0-9_]{2,30}$`). 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...
563
564		""" The number of hydrogen bond acceptors according to Lipinski."""
565
566		return rdMolDescriptors.CalcNumLipinskiHBA(x)
567
568
569	1	@requires_h_depleted
570	1	def n_paths(mol, length=1):
571
572		""" The number of paths of length l. """
573
574		return len(rdmolops.FindAllPathsOfLengthN(mol, length))
575
576
577	1	DESCRIPTORS = OrderedDict((
578		('mol_wt', molecular_weight),
579		('avg_mol_wt', average_molecular_weight),
580		('sum_vdw_vol', sum_van_der_waals_volume),
581		('sum_eneg', sum_electronegativity),
582		('sum_pol', sum_polarisability),
583		('sum_ion_energy', sum_ionisation_energy),
584		('mean_vdw_vol', mean_van_der_waals_volume),
585		('mean_eneg', mean_electronegativity),
586		('mean_pol', mean_polarisability),
587		('mean_ion_energy', mean_ionisation_energy),
588		('graph_density', graph_density),
589		('n_atoms', n_atoms),
590		('n_term', n_terminal),
591		('n_bonds', n_bonds),
592		('n_bonds_non_h', n_bonds_non_h),
593		('n_bonds_mult', n_bonds_multiple),
594		('sum_bond_order', sum_of_conventional_bond_orders),
595		('n_rot_bonds', n_rotatable_bonds),
596		('fract_rot_bonds', fract_rotatable_bonds),
597		('n_hyd', n_hyd),
598		('n_halo', n_halo),
599		('n_heavy', n_heavy),
600		('n_hetero', n_hetero),
601		('n_hba', n_hba),
602		('n_atoms', n_atoms),
603		('fract_halo', fract_halo),
604		('n_disconn', n_disconnected),
605		('total_charge', total_charge),
606		('n_rad', n_radical_electrons),
607		('n_val', n_valence_electrons),
608		('heavy_mol_wt', heavy_atom_mol_wt),
609		('n_hbd_lip', n_hbd_lipinski),
610		('n_hba_lib', n_hba_lipinski)
611		))
612
613	1	SYMBOLS = ('C', 'N', 'O', 'P', 'S', 'F', 'Cl', 'Br', 'I', 'B')
614	1	HYBRIDS = ('SP3', 'SP2', 'SP')
615
616	1	DESCRIPTORS.update(('fract_c_{}'.format(hybrid), partial(fract_c_hybrid,
617		h_state=hybrid))
618		for hybrid in HYBRIDS)
619
620	1	DESCRIPTORS.update((('n_{}'.format(symbol), partial(n_atom, symbol=symbol))
621		for symbol in SYMBOLS))
622
623	1	DESCRIPTORS.update((('n_{}'.format(symbol), partial(fract_atom, symbol=symbol))
624		for symbol in ('H', 'C', 'N', 'O')))
625
626	1	DESCRIPTORS.update((('n_bond_{}'.format(order), partial(n_bond_order,
627		order=order))
		0 ignored issues – show Coding Style introduced 2016-09-01 14:43 UTC by Report Bug Copy Issue Report Wrong continued indentation. order=order)) ^\| Loading history...
628		for order in (1, 1.5, 2, 3)))
629
630	1	DESCRIPTORS.update((('n_paths_{}'.format(length), partial(n_paths, length=length))
631		for length in range(1, 7)))
632

richlewis42 / scikit-chem

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