richlewis42 / scikit-chem

skchem/features/chemaxon.py

#! /usr/bin/env python
#
# Copyright (C) 2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD

"""
## skchem.descriptors.atom

Module specifying atom based descriptor generators.
"""

import logging
import subprocess
import re
from abc import ABCMeta

import pandas as pd

The import pandas could not be resolved.

import numpy as np

The import numpy could not be resolved.

from ..utils import line_count, nanarray
from ..base import (
    CLIWrapper, Transformer, AtomTransformer, BatchTransformer, Featurizer
)

LOGGER = logging.getLogger(__file__)

# TODO: fix averagemicrospeciescharge

TODO and FIXME comments should generally be avoided.

# TODO: fix logd logp logs

TODO and FIXME comments should generally be avoided.

# TODO: oen (orbital electronegativity) - sigma + pi

TODO and FIXME comments should generally be avoided.

# TODO: water accessible surface area

TODO and FIXME comments should generally be avoided.

#  TODO: these don't produce csv

TODO and FIXME comments should generally be avoided.

# ['doublebondstereoisomers', 'conformers', 'stereoisomers',
# 'moleculardynamics', 'stereoanalysis', 'lowestenergyconformer', 'msdistr2',
# 'conformations', 'dominanttautomerdistribution', 'hnmr', 'moldyn', 'cnmr',
# 'frameworks', 'microspeciesdistribution', 'nmr', 'leconformer', 'msdistr',
# 'tetrahedralstereoisomers']
#

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


class ChemAxonBaseFeaturizer(CLIWrapper, Featurizer):

The method axes_names which was declared abstract in the super-class BaseTransformer
was not overridden.

The method transform which was declared abstract in the super-class BaseTransformer
was not overridden.

    """ Base class for ChemAxonFeaturizers (using cxcalc).

    Concrete subclasses inheriting from this should override
    `_all_feats`, `_optimal_features`.
    """

    __metaclass__ = ABCMeta

    install_hint = CHEMAXON_HINT

    _feat_columns = {'averagepol': ['a_avg'], 'name': ['preferred_iupac_name'],
                     'aromaticbondcount': ['aromatic_bond_count'],
                     'maximalprojectionradius': ['maximal_projection_radius'],
                     'tpolarizability': ['a_avg', 'a_xx', 'a_yy', 'a_zz'],
                     'distance': ['distance'],
                     'acceptor': ['acceptor_count', 'acceptor_site_count'],
                     'fusedringcount': ['fused_ring_count'],
                     'charge': ['total_charge'],
                     'donor': ['donor_count', 'donor_site_count'],
                     'ringcount': ['ring_count'],
                     'chainbond': ['chain_bond'],
                     'mmff94energy': ['mmff94_energy'],
                     'huckel': ['aromatic_e+/nu-_order',
                                'localization_energy_l_+/l-', 'pi_energy',
                                'electron_density', 'charge_density'],
                     'chainatom': ['chain_atom'],
                     'shortestpath': ['shortest_path'],
                     'resonantcount': ['resonant_count'],
                     'tpol': ['a_avg', 'a_xx', 'a_yy', 'a_zz'],
                     'moststabletautomer': ['most_stable_tautomer'],
                     'generictautomer': ['generictautomer'],
                     'hmoelectrophilicityorder': ['hmo_aromatic_e+_order'],
                     'ringsystemcountofsize': ['ring_system_count_of_size'],
                     'largestatomringsize': ['largest_ring_size_of_atom'],
                     'tetrahedralstereoisomercount': [
                         'tetrahedral_stereoisomer_count'],
                     'enumerations': ['enumerations'],
                     'ringatom': ['ring_atom'], 'connected': ['connected'],
                     'hmolocalizationenergy': [
                         'hmo_localization_energy_l+/l-'],
                     'averagemolecularpolarizability': ['a_avg'],
                     'donorsitecount': ['donor_site_count'],
                     'donorcount': ['donor_count'],
                     'asymmetricatom': ['asymmetric_atom'],
                     'pienergy': ['pi_energy'],
                     'bondcount': ['bond_count'],
                     'chiralcenters': ['chiral_centers'],
                     'hmohuckel': ['hmo_aromatic_e+/nu-_order',
                                   'hmo_localization_energy_l+/l-',
                                   'hmo_pi_energy',
                                   'hmo_electron_density',
                                   'hmo_charge_density'],
                     'huckeleigenvector': ['eigenvector'],
                     'ringcountofsize': ['ring_count_of_size'],
                     'heteroaliphaticringcount': [
                         'heteroaliphatic_ring_count'],
                     'markushenumerations': ['enumerations'],
                     'minimalprojectionradius': ['minimal_projection_radius'],
                     'dipole': ['dipole'],
                     'balabanindex': ['balaban_index'],
                     'aromaticnucleophilicityorder': ['aromatic_nu-_order'],
                     'tautomercount': ['tautomer_count'],
                     'cyclomaticnumber': ['cyclomatic_number'],
                     'psa': ['polar_surface_area'], 'isoelectricpoint': ['pi'],
                     'hmopienergy': ['hmo_pi_energy'],
                     'ayypol': ['a_yy'], 'fragmentcount': ['fragment_count'],
                     'acceptormultiplicity': ['acceptor_multiplicity'],
                     'topologyanalysistable': ['atom_count',
                                               'aliphatic_atom_count',
                                               'aromatic_atom_count',
                                               'bond_count',
                                               'aliphatic_bond_count',
                                               'aromatic_bond_count',
                                               'rotatable_bond_count',
                                               'ring_count',
                                               'aliphatic_ring_count',
                                               'aromatic_ring_count',
                                               'hetero_ring_count',
                                               'heteroaliphatic_ring_count',
                                               'heteroaromatic_ring_count',
                                               'ring_atom_count',
                                               'ring_bond_count',
                                               'chain_atom_count',
                                               'chain_bond_count',
                                               'smallest_ring_size',
                                               'largest_ring_size'],
                     'ioncharge': ['charge'],
                     'asymmetricatoms': ['asymmetric_atoms'],
                     'wateraccessiblesurfacearea': ['asa', 'asa+', 'asa-',
                                                    'asa_h', 'asa_p'],
                     'avgpol': ['a_avg'],
                     'carboaliphaticringcount': ['carboaliphatic_ring_count'],
                     'aliphaticringcount': ['aliphatic_ring_count'],
                     'donormultiplicity': ['donor_multiplicity'],
                     'minimalprojectionarea': ['minimal_projection_area'],
                     'nucleophiliclocalizationenergy': [
                         'localization_energy_l-'], 'dihedral': ['dihedral'],
                     'heteroringcount': ['hetero_ring_count'],
                     'azzpol': ['a_zz'],
                     'molecularsurfacearea': ['van_der_waals_surface_area_3d'],
                     'hmonucleophiliclocalizationenergy': [
                         'hmo_localization_energy_l-'],
                     'chargedistribution': ['charge_distribution'],
                     'pol': ['a_mol', 'a_atom'],
                     'hmoelectrondensity': ['hmo_electron_density'],
                     'carboaromaticringcount': ['carboaromatic_ring_count'],
                     'acceptorsitecount': ['acceptor_site_count'],
                     'markushenumerationcount': ['markush_library_size'],
                     'localizationenergy': ['localization_energy_l+/l-'],
                     'hararyindex': ['harary_index'],
                     'asa': ['asa', 'asa+', 'asa-', 'asa_h', 'asa_p'],
                     'acc': ['acc'], 'majortautomer': ['major_tautomer'],
                     'majormicrospecies': ['major-ms'],
                     'aliphaticatomcount': ['aliphatic_atom_count'],
                     'angle': ['angle'], 'huckeleigenvalue': ['eigenvalue'],
                     'axxpol': ['a_xx'],
                     'chiralcenter': ['chiral_center'],
                     'aliphaticbondcount': ['aliphatic_bond_count'],
                     'smallestatomringsize': ['smallest_ring_size_of_atom'],
                     'dreidingenergy': ['dreiding_energy'],
                     'maximalprojectionsize': [
                         'length_perpendicular_to_the_max_area'],
                     'largestringsystemsize': ['largest_ring_system_size'],
                     'accsitecount': ['acceptor_site_count'],
                     'refractivity': ['refractivity'],
                     'bondtype': ['bond_type'],
                     'chargedensity': ['charge_density'],
                     'resonants': ['resonants'],
                     'aromaticatomcount': ['aromatic_atom_count'],
                     'distancedegree': ['distance_degree'],
                     'hasvalidconformer': ['has_valid_conformer'],
                     'electrondensity': ['electron_density'],
                     'asymmetricatomcount': ['asymmetric_atom_count'],
                     'fsp3': ['fsp3'], 'don': ['don'],
                     'fusedaliphaticringcount': ['fused_aliphatic_ring_count'],
                     'pkat': ['pkat'],
                     'fusedaromaticringcount': ['fused_aromatic_ring_count'],
                     'majorms2': ['majorms2'],
                     'maximalprojectionarea': ['maximal_projection_area'],
                     'hbonddonoracceptor': ['acceptor_count', 'donor_count',
                                            'acceptor_site_count',
                                            'donor_site_count'],
                     'acceptorcount': ['acceptor_count'],
                     'molecularpolarizability': ['a_mol'],
                     'huckeltable': ['aromatic_e+/nu-_order',
                                     'localization_energy_l+/l-', 'pi_energy',
                                     'electron_density', 'charge_density'],
                     'rotatablebondcount': ['rotatable_bond_count'],
                     'minimalprojectionsize': [
                         'length_perpendicular_to_the_min_area'],
                     'polarizability': ['a_mol', 'a_atom'],
                     'acceptortable': ['acceptor_count',
                                       'acceptor_site_count'],
                     'aliphaticringcountofsize': [
                         'aliphatic_ring_count_of_size'], 'hlb': ['hlb'],
                     'eccentricity': ['eccentricity'],
                     'hmochargedensity': ['hmo_charge_density'],
                     'hmohuckeleigenvalue': ['hmo_eigenvalue'],
                     'totalchargedensity': ['total_charge_density'],
                     'hmonucleophilicityorder': ['hmo_aromatic_nu-_order'],
                     'aromaticringcountofsize': [
                         'aromatic_ring_count_of_size'],
                     'electrophilicityorder': ['aromatic_e+_order'],
                     'connectedgraph': ['connected_graph'],
                     'plattindex': ['platt_index'], 'logp': ['logp'],
                     'topanal': ['atom_count', 'aliphatic_atom_count',
                                 'aromatic_atom_count', 'bond_count',
                                 'aliphatic_bond_count', 'aromatic_bond_count',
                                 'rotatable_bond_count', 'ring_count',
                                 'aliphatic_ring_count', 'aromatic_ring_count',
                                 'hetero_ring_count',
                                 'heteroaliphatic_ring_count',
                                 'heteroaromatic_ring_count',
                                 'ring_atom_count',
                                 'ring_bond_count', 'chain_atom_count',
                                 'chain_bond_count', 'smallest_ring_size',
                                 'largest_ring_size'],
                     'logdcalculator': ['ph=0', 'ph=1', 'ph=2', 'ph=3', 'ph=4',
                                        'ph=5', 'ph=6', 'ph=7', 'ph=8', 'ph=9',
                                        'ph=10', 'ph=11', 'ph=12', 'ph=13',
                                        'ph=14', 'unnamed:_16'],
                     'logs': ['ph=0.0', 'ph=1.0', 'ph=2.0', 'ph=3.0', 'ph=4.0',
                              'ph=5.0', 'ph=6.0', 'ph=7.0', 'ph=8.0',
                              'ph=9.0', 'ph=10.0', 'ph=11.0', 'ph=12.0',
                              'ph=13.0', 'ph=14.0', 'unnamed:_16'],
                     'atompol': ['a_atom'], 'canonicalresonant': ['structure'],
                     'ringbond': ['ring_bond'],
                     'ringatomcount': ['ring_atom_count'],
                     'donortable': ['donor_count', 'donor_site_count'],
                     'randicindex': ['randic_index'],
                     'rotatablebond': ['rotatable_bond'],
                     'hyperwienerindex': ['hyper_wiener_index'],
                     'hmohuckeleigenvector': ['hmo_eigenvector'],
                     'carboringcount': ['carbo_ring_count'],
                     'logpcalculator': ['logp', 'unnamed:_2'],
                     'ringsystemcount': ['ring_system_count'],
                     'largestringsize': ['largest_ring_size'],
                     'stereodoublebondcount': ['stereo_double_bond_count'],
                     'pi': ['pi'],
                     'stericeffectindex': ['steric_effect_index'],
                     'volume': ['van_der_waals_volume'],
                     'averagemicrospeciescharge': ['charge'],
                     'pka': ['apka1', 'apka2', 'bpka1', 'bpka2', 'atoms'],
                     'hmohuckeltable': ['hmo_aromatic_e+/nu-_order',
                                        'hmo_localization_energy_l+/l-',
                                        'hmo_pi_energy',
                                        'hmo_electron_density',
                                        'hmo_charge_density'],
                     'ringcountofatom': ['ring_count_of_atom'],
                     'aromaticelectrophilicityorder': ['aromatic_e+_order'],
                     'hindrance': ['steric_hindrance'],
                     'chainatomcount': ['chain_atom_count'],
                     'pkacalculator': ['apka1', 'apka2', 'bpka1', 'bpka2',
                                       'atoms'],
                     'heteroaromaticringcount': ['heteroaromatic_ring_count'],
                     'sterichindrance': ['steric_hindrance'],
                     'hbda': ['acceptor_count', 'donor_count',
                              'acceptor_site_count', 'donor_site_count'],
                     'molpol': ['a_mol'],
                     'atomicpolarizability': ['a_atom'],
                     'msdon': ['ph=0.00', 'ph=1.00', 'ph=2.00', 'ph=3.00',
                               'ph=4.00', 'ph=5.00', 'ph=6.00', 'ph=7.00',
                               'ph=8.00', 'ph=9.00', 'ph=10.00', 'ph=11.00',
                               'ph=12.00', 'ph=13.00', 'ph=14.00'],
                     'enumerationcount': ['markush_library_size'],
                     'vdwsa': ['van_der_waals_surface_area_3d'],
                     'orbitalelectronegativity': [
                         'sigma_orbital_electronegativity',
                         'pi_orbital_electronegativity'],
                     'hmoelectrophiliclocalizationenergy': [
                         'hmo_localization_energy_l+'],
                     'smallestringsize': ['smallest_ring_size'],
                     'szegedindex': ['szeged_index'],
                     'nucleophilicityorder': ['aromatic_nu-_order'],
                     'canonicaltautomer': ['canonical_tautomer'],
                     'stereoisomercount': ['stereoisomer_count'],
                     'msa': ['van_der_waals_surface_area_3d'],
                     'donsitecount': ['donor_site_count'],
                     'randommarkushenumerations': [
                         'randommarkushenumerations'],
                     'wienerindex': ['wiener_index'],
                     'huckelorbitals': ['orbitals'],
                     'doublebondstereoisomercount': [
                         'double_bond_stereoisomer_count'],
                     'tautomers': ['tautomers'],
                     'polarsurfacearea': ['polar_surface_area'],
                     'chiralcentercount': ['chiral_center_count'],
                     'electrophiliclocalizationenergy': [
                         'localization_energy_l+'],
                     'aliphaticatom': ['aliphatic_atom'],
                     'ringbondcount': ['ring_bond_count'],
                     'wienerpolarity': ['wiener_polarity'],
                     'msacc': ['ph=0.00', 'ph=1.00', 'ph=2.00', 'ph=3.00',
                               'ph=4.00', 'ph=5.00', 'ph=6.00', 'ph=7.00',
                               'ph=8.00', 'ph=9.00', 'ph=10.00', 'ph=11.00',
                               'ph=12.00', 'ph=13.00', 'ph=14.00'],
                     'formalcharge': ['formal_charge'],
                     'smallestringsystemsize': ['smallest_ring_system_size'],
                     'majorms': ['major-ms'],
                     'tholepolarizability': ['a_avg', 'a_xx', 'a_yy', 'a_zz'],
                     'aromaticatom': ['aromatic_atom'],
                     'oen': ['sigma_orbital_electronegativity',
                             'pi_orbital_electronegativity'],
                     'chainbondcount': ['chain_bond_count'],
                     'logd': ['ph=0.00', 'ph=1.00', 'ph=2.00', 'ph=3.00',
                              'ph=4.00', 'ph=5.00', 'ph=6.00', 'ph=7.00',
                              'ph=8.00', 'ph=9.00', 'ph=10.00', 'ph=11.00',
                              'ph=12.00', 'ph=13.00', 'ph=14.00'],
                     'hmohuckelorbitals': ['hmo_orbitals'],
                     'aromaticringcount': ['aromatic_ring_count'],
                     'pichargedensity': ['pi_charge_density']}

    _optimal_feats = []  # override this

    def __init__(self, features='optimal', verbose=True):
        self._features = None
        super(ChemAxonBaseFeaturizer, self).__init__(verbose=verbose)
        self.features = features

    @property
    def features(self):

This method should have a docstring.

        return self._features

    @features.setter
    def features(self, features):

This method should have a docstring.

        if features in ('optimal', 'all'):
            self._features = self._optimal_feats
        elif isinstance(features, str):
            self.features = [features]
        elif isinstance(features, (list, tuple)):
            valid = np.array([feat in self._feat_columns.keys()
                              for feat in features])
            if not all(valid):
                msg = 'Descriptor "{}" not available.'.format(
                    np.array(features)[~valid])
                raise NotImplementedError(msg)
            else:
                self._features = list(features)
        else:
            raise NotImplementedError('Feature set {} not available.'.format(
                features))

    def _feature_index(self):
        return pd.Index(sum((self._feat_columns[feat]
                             for feat in self.features), []),
                        name='features')

    @staticmethod
    def validate_install():
        try:
            return 0 == subprocess.call(['cxcalc'],
                                        stderr=subprocess.DEVNULL,

The Module subprocess does not seem to have a member named DEVNULL.

                                        stdout=subprocess.DEVNULL)

The Module subprocess does not seem to have a member named DEVNULL.

        except FileNotFoundError:

Undefined variable 'FileNotFoundError'

            return False

    def monitor_progress(self, filename):
        res = line_count(filename)
        return res - 1 if res else 0

    def _cli_args(self, infile, outfile):
        return ['cxcalc', infile, '-o', outfile] + self.features

    def _parse_outfile(self, outfile):
        res = pd.read_table(outfile, engine='python').drop('id', axis=1)
        return res

    def _parse_errors(self, errs):
        LOGGER.debug('stderr: %s', errs)
        return []  # instances are not skipped ever, so don't return anything


class ChemAxonFeaturizer(ChemAxonBaseFeaturizer, BatchTransformer,

This class should have a docstring.

Too many ancestors (8/7)

                         Transformer):

    _optimal_feats = ['acceptorcount', 'accsitecount', 'aliphaticatomcount',
                      'aliphaticbondcount', 'aliphaticringcount',
                      'aromaticatomcount', 'aromaticbondcount',
                      'aromaticringcount', 'asymmetricatomcount',
                      'averagemolecularpolarizability', 'axxpol', 'ayypol',
                      'azzpol', 'balabanindex', 'bondcount',
                      'carboaliphaticringcount', 'carboaromaticringcount',
                      'carboringcount', 'chainatomcount',
                      'chainbondcount', 'chiralcentercount', 'connectedgraph',
                      'cyclomaticnumber', 'dipole',
                      'donorcount', 'donorsitecount',
                      'doublebondstereoisomercount', 'dreidingenergy',
                      'formalcharge',
                      'fragmentcount', 'fsp3', 'fusedaliphaticringcount',
                      'fusedaromaticringcount', 'fusedringcount',
                      'hararyindex', 'heteroaliphaticringcount',
                      'heteroaromaticringcount', 'heteroringcount', 'hlb',
                      'hmopienergy', 'hyperwienerindex', 'largestringsize',
                      'largestringsystemsize',
                      'markushenumerationcount', 'maximalprojectionarea',
                      'maximalprojectionradius',
                      'maximalprojectionsize', 'minimalprojectionarea',
                      'minimalprojectionradius',
                      'minimalprojectionsize', 'mmff94energy', 'molpol',
                      'pienergy', 'plattindex', 'psa', 'randicindex',
                      'refractivity', 'resonantcount', 'ringatomcount',
                      'ringbondcount', 'ringcount', 'ringsystemcount',
                      'rotatablebondcount', 'smallestringsize',
                      'smallestringsystemsize',
                      'stereodoublebondcount', 'stereoisomercount',
                      'szegedindex', 'tetrahedralstereoisomercount',
                      'vdwsa', 'volume', 'wateraccessiblesurfacearea',
                      'wienerindex', 'wienerpolarity']

    @property
    def name(self):

This method should have a docstring.

This method could be written as a function/class method.

        return 'cx_mol'

    @property
    def columns(self):
        return self._feature_index()

    def _parse_outfile(self, outfile):
        res = super(ChemAxonFeaturizer, self)._parse_outfile(outfile)

        def fix_failed(inp):

This function should have a docstring.

            if isinstance(inp, str) and 'FAILED' in inp:
                return np.nan
            else:
                return float(inp)

        return res.applymap(fix_failed)


class ChemAxonAtomFeaturizer(ChemAxonBaseFeaturizer, AtomTransformer,

This class should have a docstring.

Too many ancestors (8/7)

This abstract class does not seem to be used anywhere.

                             BatchTransformer):
    _optimal_feats = ['acceptormultiplicity', 'aliphaticatom', 'aromaticatom',
                      'aromaticelectrophilicityorder', 'asymmetricatom',
                      'atomicpolarizability', 'chainatom', 'chargedensity',
                      'chiralcenter', 'distancedegree', 'donormultiplicity',
                      'eccentricity', 'electrondensity',
                      'electrophiliclocalizationenergy', 'hindrance',
                      'hmochargedensity', 'hmoelectrondensity',
                      'hmoelectrophilicityorder',
                      'hmoelectrophiliclocalizationenergy',
                      'hmonucleophilicityorder',
                      'hmonucleophiliclocalizationenergy', 'ioncharge',
                      'largestatomringsize', 'nucleophilicityorder',
                      'nucleophiliclocalizationenergy', 'oen',
                      'pichargedensity', 'ringatom', 'ringcountofatom',
                      'stericeffectindex', 'totalchargedensity']

    _h_inc_feats = ['acc', 'atomicpolarizability', 'charge', 'distancedegree',
                    'don', 'eccentricity', 'hindrance', 'largestatomringsize',
                    'oen', 'ringcountofatom', 'smallestatomringsize',
                    'stericeffectindex']

    @property
    def name(self):

This method should have a docstring.

This method could be written as a function/class method.

        return 'cx_atom'

    @property
    def minor_axis(self):
        return self._feature_index()

    def _transform_atom(self, atom):
        raise NotImplementedError('Cannot calculate per atom with ChemAxon')

    def _parse_outfile(self, outfile):
        res = super(ChemAxonAtomFeaturizer, self)._parse_outfile(outfile)

        def parse_string(s):

The name s does not conform to the argument naming conventions ([a-z_][a-z0-9_]{2,30}$).

This function should have a docstring.

            if s == '':
                return np.nan
            elif s == 'false':
                return 0
            elif s == 'true':
                return 1
            else:
                try:
                    return float(s)
                except ValueError:
                    return np.nan

        def to_padded(s):

The name s does not conform to the argument naming conventions ([a-z_][a-z0-9_]{2,30}$).

This function should have a docstring.

            inner_res = np.repeat(np.nan, self.max_atoms)
            ans = np.array([parse_string(i) for i in str(s).split(';')])
            inner_res[:len(ans)] = ans
            return inner_res

        res = res.applymap(to_padded)
        return pd.Panel(res.values.tolist()).swapaxes(1, 2)


class ChemAxonNMRPredictor(ChemAxonBaseFeaturizer, BatchTransformer,

This class should have a docstring.

Too many ancestors (8/7)

This abstract class does not seem to be used anywhere.

                           AtomTransformer):

    _feat_columns = {'cnmr': ['cnmr'], 'hnmr': ['hnmr']}
    _optimal_feats = ['cnmr']

    @property
    def name(self):

This method should have a docstring.

This method could be written as a function/class method.

        return 'cx_nmr'

    def _transform_atom(self, atom):
        raise NotImplementedError('ChemAxon cannot predict for atoms.')

    def monitor_progress(self, filename):
        return sum(1 for l in open(filename, 'rb')
                   if l == b'##PEAKASSIGNMENTS=(XYMA)\r\n')

    @property
    def minor_axis(self):
        return pd.Index(self.features, name='shift')

    @property
    def features(self):
        return self._features

    @features.setter
    def features(self, val):

Arguments number differs from overridden 'features' method

        if val == 'c':
            self._features = ['cnmr']
        elif val == 'h':
            self._features = ['hnmr']
        else:
            raise NotImplementedError('Feature {} not implemented'.format(val))

    def _parse_outfile(self, outfile):
        n_mols = self.monitor_progress(outfile)
        res = nanarray((n_mols, self.max_atoms, 1))
        regex = re.compile(b'\((-?\d+.\d+),\d+,[A-Z],<([0-9\,]+)>\)\r\n')

A suspicious escape sequence \( was found. Did you maybe forget to add an r prefix?

A suspicious escape sequence \d was found. Did you maybe forget to add an r prefix?

A suspicious escape sequence \, was found. Did you maybe forget to add an r prefix?

A suspicious escape sequence \) was found. Did you maybe forget to add an r prefix?

        mol_idx = 0

        with open(outfile, 'rb') as f:

The name f does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

            # loop through the file - inner loop will also advance the pointer
            for l in f:

The name l does not conform to the variable naming conventions ([a-z_][a-z0-9_]{2,30}$).

                if l == b'##PEAKASSIGNMENTS=(XYMA)\r\n':
                    for row in f:
                        if row == b'##END=\r\n':
                            break
                        else:
                            LOGGER.debug('Row to parse: %s', row)
                            shift, idxs = regex.match(row).groups()
                            shift = float(shift)
                            idxs = [int(idx) for idx in idxs.split(b',')]
                            for atom_idx in idxs:
                                res[mol_idx, atom_idx] = shift
                    mol_idx += 1
        res = pd.Panel(res)
        return res

    def transform(self, inp):
        return super(ChemAxonNMRPredictor, self).transform(inp).T