<commit_before>##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
#         Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: <NAME>
# Contributors: <NAME>, <NAME>
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################

_SOLVENT_TYPES = frozenset(['118', '119', '1AL', '1CU', '2FK', '2HP', '2OF', '3CO', '3MT',
        '3NI', '3OF', '4MO', '543', '6MO', 'ACT', 'AG', 'AL', 'ALF', 'ATH',
        'AU', 'AU3', 'AUC', 'AZI', 'Ag', 'BA', 'BAR', 'BCT', 'BEF', 'BF4',
        'BO4', 'BR', 'BS3', 'BSY', 'Be', 'CA', 'CA+2', 'Ca+2', 'CAC', 'CAD',
        'CAL', 'CD', 'CD1', 'CD3', 'CD5', 'CE', 'CES', 'CHT', 'CL', 'CL-',
        'CLA', 'Cl-', 'CO', 'CO3', 'CO5', 'CON', 'CR', 'CS', 'CSB', 'CU',
        'CU1', 'CU3', 'CUA', 'CUZ', 'CYN', 'Cl-', 'Cr', 'DME', 'DMI', 'DSC',
        'DTI', 'DY', 'E4N', 'EDR', 'EMC', 'ER3', 'EU', 'EU3', 'F', 'FE', 'FE2',
        'FPO', 'GA', 'GD3', 'GEP', 'HAI', 'HG', 'HGC', 'HOH', 'IN', 'IOD',
        'ION', 'IR', 'IR3', 'IRI', 'IUM', 'K', 'K+', 'KO4', 'LA', 'LCO', 'LCP',
        'LI', 'LIT', 'LU', 'MAC', 'MG', 'MH2', 'MH3', 'MLI', 'MMC', 'MN',
        'MN3', 'MN5', 'MN6', 'MO1', 'MO2', 'MO3', 'MO4', 'MO5', 'MO6', 'MOO',
        'MOS', 'MOW', 'MW1', 'MW2', 'MW3', 'NA', 'NA+2', 'NA2', 'NA5', 'NA6',
        'NAO', 'NAW', 'Na+2', 'NET', 'NH4', 'NI', 'NI1', 'NI2', 'NI3', 'NO2',
        'NO3', 'NRU', 'Na+', 'O4M', 'OAA', 'OC1', 'OC2', 'OC3', 'OC4', 'OC5',
        'OC6', 'OC7', 'OC8', 'OCL', 'OCM', 'OCN', 'OCO', 'OF1', 'OF2', 'OF3',
        'OH', 'OS', 'OS4', 'OXL', 'PB', 'PBM', 'PD', 'PER', 'PI', 'PO3', 'PO4',
        'POT', 'PR', 'PT', 'PT4', 'PTN', 'RB', 'RH3', 'RHD', 'RU', 'RUB', 'Ra',
        'SB', 'SCN', 'SE4', 'SEK', 'SM', 'SMO', 'SO3', 'SO4', 'SOD', 'SR',
        'Sm', 'Sn', 'T1A', 'TB', 'TBA', 'TCN', 'TEA', 'THE', 'TL', 'TMA',
        'TRA', 'UNX', 'V', 'V2+', 'VN3', 'VO4', 'W', 'WO5', 'Y1', 'YB', 'YB2',
        'YH', 'YT3', 'ZN', 'ZN2', 'ZN3', 'ZNA', 'ZNO', 'ZO3'])

_PROTEIN_RESIDUES = frozenset([
    'ACE', 'AIB', 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'FOR', 'GLN', 'GLU',
    'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'NH2', 'NME', 'ORN', 'PCA',
    'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'UNK', 'VAL'])


_WATER_RESIDUES = frozenset([
'H2O', 'HHO', 'OHH', 'HOH', 'OH2', 'SOL',
                             'WAT', 'TIP', 'TIP2', 'TIP3', 'TIP4'])<commit_msg>Fix tabs<commit_after>##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
#         Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: <NAME>
# Contributors: <NAME>, <NAME>
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################

_SOLVENT_TYPES = frozenset(['118', '119', '1AL', '1CU', '2FK', '2HP', '2OF', '3CO', '3MT',
        '3NI', '3OF', '4MO', '543', '6MO', 'ACT', 'AG', 'AL', 'ALF', 'ATH',
        'AU', 'AU3', 'AUC', 'AZI', 'Ag', 'BA', 'BAR', 'BCT', 'BEF', 'BF4',
        'BO4', 'BR', 'BS3', 'BSY', 'Be', 'CA', 'CA+2', 'Ca+2', 'CAC', 'CAD',
        'CAL', 'CD', 'CD1', 'CD3', 'CD5', 'CE', 'CES', 'CHT', 'CL', 'CL-',
        'CLA', 'Cl-', 'CO', 'CO3', 'CO5', 'CON', 'CR', 'CS', 'CSB', 'CU',
        'CU1', 'CU3', 'CUA', 'CUZ', 'CYN', 'Cl-', 'Cr', 'DME', 'DMI', 'DSC',
        'DTI', 'DY', 'E4N', 'EDR', 'EMC', 'ER3', 'EU', 'EU3', 'F', 'FE', 'FE2',
        'FPO', 'GA', 'GD3', 'GEP', 'HAI', 'HG', 'HGC', 'HOH', 'IN', 'IOD',
        'ION', 'IR', 'IR3', 'IRI', 'IUM', 'K', 'K+', 'KO4', 'LA', 'LCO', 'LCP',
        'LI', 'LIT', 'LU', 'MAC', 'MG', 'MH2', 'MH3', 'MLI', 'MMC', 'MN',
        'MN3', 'MN5', 'MN6', 'MO1', 'MO2', 'MO3', 'MO4', 'MO5', 'MO6', 'MOO',
        'MOS', 'MOW', 'MW1', 'MW2', 'MW3', 'NA', 'NA+2', 'NA2', 'NA5', 'NA6',
        'NAO', 'NAW', 'Na+2', 'NET', 'NH4', 'NI', 'NI1', 'NI2', 'NI3', 'NO2',
        'NO3', 'NRU', 'Na+', 'O4M', 'OAA', 'OC1', 'OC2', 'OC3', 'OC4', 'OC5',
        'OC6', 'OC7', 'OC8', 'OCL', 'OCM', 'OCN', 'OCO', 'OF1', 'OF2', 'OF3',
        'OH', 'OS', 'OS4', 'OXL', 'PB', 'PBM', 'PD', 'PER', 'PI', 'PO3', 'PO4',
        'POT', 'PR', 'PT', 'PT4', 'PTN', 'RB', 'RH3', 'RHD', 'RU', 'RUB', 'Ra',
        'SB', 'SCN', 'SE4', 'SEK', 'SM', 'SMO', 'SO3', 'SO4', 'SOD', 'SR',
        'Sm', 'Sn', 'T1A', 'TB', 'TBA', 'TCN', 'TEA', 'THE', 'TL', 'TMA',
        'TRA', 'UNX', 'V', 'V2+', 'VN3', 'VO4', 'W', 'WO5', 'Y1', 'YB', 'YB2',
        'YH', 'YT3', 'ZN', 'ZN2', 'ZN3', 'ZNA', 'ZNO', 'ZO3'])

_PROTEIN_RESIDUES = frozenset([
    'ACE', 'AIB', 'ALA', 'ARG', 'ASN', 'ASP', 'CYS', 'FOR', 'GLN', 'GLU',
    'GLY', 'HIS', 'ILE', 'LEU', 'LYS', 'MET', 'NH2', 'NME', 'ORN', 'PCA',
    'PHE', 'PRO', 'SER', 'THR', 'TRP', 'TYR', 'UNK', 'VAL'])


_WATER_RESIDUES = frozenset([
    'H2O', 'HHO', 'OHH', 'HOH', 'OH2', 'SOL',
    'WAT', 'TIP', 'TIP2', 'TIP3', 'TIP4'])
{'fraction_non_alphanumeric': 0.32787411689145796, 'fraction_numerical': 0.03596660244059088, 'mean_word_length': 3.83993783993784, 'pattern_counts': {'":': 0, '<': 11, '<?xml version=': 0, '>': 11, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5872851', 'n_tokens_mistral': 2747, 'n_tokens_neox': 2615, 'n_words': 782}