#!/usr/bin/env python

import json
import os

non_ligs = ['DMS', 'CL', 'MG', 'EDO', 'PEG', 'MLI', 'NI', 'SO4', 'WAT',  # `TP3` water is ambiguous and rare
                                              'LI', 'NA' , 'K', 'RB',  # group 1 cations
                                              'BE', 'MG', 'CA', 'SR',  # earth metal cations
                                               'F', 'CL', 'BR', 'I',  #halogens
                                               'MN', 'FE', 'CO',  'NI', 'CU', 'ZN',  # top period transition metals
                                                '3CO',  # cobalt (iii) ion
                                              'BUQ',  # 4-hydroxy-2-butanone
                                              'NAG',  # n-acetyl-d-glucosamine
                                              'NAD',  # nicotinamide-adenine-dinucleotide
                                              'CR',  # chromium ion
                                              'SF4',  # iron/sulfur cluster
                                              'EOH',  # ethanol
                                              'ZNO',  # zinc ion, 2 waters coordinated
                                              'NAO',  # sodium ion, 1 water coordinated
                                              'EOM',  # ethyloxymethoxyl
                                              'EHN',  # ethane
                                              'NAP',  # nadp nicotinamide-adenine-dinucleotide phosphate
                                              'CCN',  # acetonitrile
                                              'NAW',  # sodium ion, 3 waters coordinated
                                              'BR',  # bromide ion
                                              'EGL',  # ethylene glycol
                                              'NI2',  # nickel (ii) ion, 2 waters coordinated
                                              'GSH',  # glutathione
                                              'NI1',  # nickel ion, 1 water coordinated
                                              'O2',  # oxygen molecule
                                              'BA',  # barium ion
                                              'RU',  # ruthenium ion
                                              'SAH',  # s-adenosyl-l-homocysteine
                                              'GU7', # 2-amino-7-[2-(2-hydroxy-1-hydroxymethyl-ethylamino)-ethyl]-1,7-dihydro-purin-6-one
                                              'SAM',  # s-adenosylmethionine
                                              'TAS',  # trihydroxyarsenite(iii)
                                              'DCE',  # 1,2-dichloroethane
                                              '2BM',  # dibromomethane
                                              'TP7',  # coenzyme b
                                              'OF3',  # ferric ion, 1 water coordinated
                                              'OF1',  # ferrous ion, 1 water coordinated
                                              'RB',  # rubidium ion
                                              'IOH',  # 2-propanol, isopropanol
                                              'MW1',  # manganese ion, 1 water coordinated
                                              'IOD',  # iodide ion
                                              'C2O',  # cu-o-cu linkage
                                              'BNZ',  # benzene
                                              'TCN',  # tetracyanonickelate ion
                                              'ARS',  # arsenic
                                              'NH4',  # ammonium ion
                                              'GD',  # gadolinium atom
                                              'PER',  # peroxide ion
                                              'GA',  # gallium (iii) ion
                                              'TPP',  # thiamine diphosphate
                                              'CHX',  # cyclohexane
                                              'CME',  # s,s-(2-hydroxyethyl)thiocysteine
                                              'THB',  # tetrahydrobiopterin
                                              'IPA',  # isopropyl alcohol
                                              'CD1',  # cadmium ion, 1 water coordinated
                                              'OH',  # hydroxide ion
                                              'SO4',  # sulfate ion
                                              'DTT',  # 2,3-dihydroxy-1,4-dithiobutane
                                              'PQN',  # phylloquinone
                                              'CYN',  # cyanide ion
                                              'PQQ',  # pyrroloquinoline quinone
                                              'PYJ',  # phenylethane
                                              'PEO',  # hydrogen peroxide
                                              'NA6',  # sodium ion, 6 waters coordinated
                                              'MBR',  # tribromomethane
                                              'NA5',  # sodium ion, 5 waters coordinated
                                              'OS',  # osmium ion
                                              'MAN',  # alpha-d-mannose
                                              'CMO',  # carbon monoxide
                                              'OCL',  # cobalt ion, 1 water coordinated
                                              'DMF',  # dimethylformamide
                                              'OCN',  # cobalt ion, 2 waters coordinated
                                              'MO3',  # magnesium ion, 3 waters coordinated
                                              'NGN',  # nitrogen
                                              'ACT',  # acetate ion
                                              'U1',  # uranium atom
                                              'HDZ',  # nitrogen molecule
                                              'MO5',  # magnesium ion, 5 waters coordinated
                                              'MO4',  # magnesium ion, 4 waters coordinated
                                              'VO4',  # vanadate ion
                                              'DMS',  # dimethyl sulfoxide
                                              'FUC',  # alpha-l-fucose
                                              'PCL',  # platinum(ii) di-chloride
                                              'CB5',  # cobalt bis(1,2-dicarbollide)
                                              'EEE',  # ethyl acetate
                                              'HG',  # mercury (ii) ion
                                              'NO2',  # nitrite ion
                                              'CMP',  # adenosine-3',5'-cyclic-monophosphate
                                              'PR',  # praseodymium ion
                                              'BMA',  # beta-d-mannose
                                              'IUM',  # uranyl (vi) ion
                                              'PT',  # platinum (ii) ion
                                              'ZN2',  # zinc ion on 3-fold crystal axis
                                              'TTP',  # thymidine-5'-triphosphate
                                              'NO3',  # nitrate ion
                                              'YT3',  # yttrium (iii) ion
                                              'TYS',  # o-sulfo-l-tyrosine
                                              'PB',  # lead (ii) ion
                                              'M2M',  # 1-methoxy-2-(2-methoxyethoxy)ethane
                                              'ZO3',  # zinc ion, 3 waters coordinated
                                              'PD',  # palladium ion
                                              'AMP',  # adenosine monophosphate
                                              'PI',  # hydrogenphosphate ion
                                              'MH3',  # manganese ion, 1 hydroxyl coordinated
                                              'AF3',  # aluminum fluoride
                                              'ZN',  # zinc ion
                                              'MN3',  # manganese (iii) ion
                                              'OXY',  # oxygen molecule
                                              'NI',  # nickel (ii) ion
                                              'CSD',  # 3-sulfinoalanine
                                              'OX',  # bound oxygen
                                              'PS5',  # pentasulfide-sulfur
                                              'MN5',  # manganese ion, 5 waters coordinated
                                              'MN6',  # manganese ion, 6 waters coordinated
                                              'S',  # sulfur atom
                                              'W',  # tungsten ion
                                              'SB',  # antimony (iii) ion
                                              'FOL',  # folic acid
                                              'OXE',  # ortho-xylene
                                              'PT4',  # platinum (iv) ion
                                              'PBM',  # trimethyl lead ion
                                              'O',  # oxygen atom
                                              'MW2',  # manganese dihydrate ion
                                              'MG',  # magnesium ion
                                              '543',  # calcium ion, 6 waters plus ethanol coordinated
                                              'MSM',  # (methylsulfanyl)methane
                                              'C5P',  # cytidine-5'-monophosphate
                                              'ANL',  # aniline
                                              'MTO',  # bound water
                                              'NO',  # nitric oxide
                                              'TBU',  # tertiary-butyl alcohol
                                              'OPY',  # (3s)-4-oxo-4-piperidin-1-ylbutane-1,3-diamine
                                              'PC4',  # tetrachloroplatinate(ii)
                                              'GU3',  # methyl 3-o-methyl-2,6-di-o-sulfo-alpha-d-glucopyranoside
                                              'GU2',  # 2,3-di-o-methyl-alpha-l-idopyranuronic acid
                                              'GU1',  # 2,3-di-o-methyl-beta-d-glucopyranuronic acid
                                              'MOH',  # methanol
                                              'ANP',  # phosphoaminophosphonic acid-adenylate ester
                                              'GU6',  # 2,3,6-tri-o-sulfonato-alpha-d-glucopyranose
                                              'GU5',  # 2,3-di-o-methyl-6-o-sulfonato-alpha-d-glucopyranose
                                              'GU4',  # 2,3,4,6-tetra-o-sulfonato-alpha-d-glucopyranose
                                              'AU',  # gold ion
                                              'OC3',  # calcium ion, 3 waters coordinated
                                              'BTN',  # biotin
                                              'I42',  # hydroxy(dioxido)oxovanadium
                                              'OC4',  # calcium ion, 4 waters coordinated
                                              'OC7',  # calcium ion, 7 waters coordinated
                                              'OC6',  # calcium ion, 6 waters coordinated
                                              'TMP',  # thymidine-5'-phosphate
                                              'RE',  # rhenium
                                              'GD3',  # gadolinium ion
                                              'CTP',  # cytidine-5'-triphosphate
                                              'ACE',  # acetyl group
                                              '3OF',  # hydrated fe (iii) ion, 2 waters coordinated
                                              'ETZ',  # diethyl ether
                                              'MM4',  # molybdenum (iv) oxide
                                              'IN',  # indium (iii) ion
                                              'ACN',  # acetone
                                              'DOD',  # deuterated water
                                              'AST',  # arsenite
                                              'COA',  # coenzyme a
                                              'EU',  # europium ion
                                              'DOX',  # dioxane
                                              'COB',  # co-methylcobalamin
                                              'B12',  # cobalamin
                                              'REO',  # perrhenate
                                              'ATP',  # adenosine-5'-triphosphate
                                              'CD3',  # cadmium ion, 3 waters coordinated
                                              'U10',  # ubiquinone-10
                                              'ACY',  # acetic acid
                                              'PEG',  # di(hydroxyethyl)ether
                                              'YB',  # ytterbium (iii) ion
                                              'NDP',  # nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
                                              'NBZ',  # nitrobenzene
                                              'ETI',  # iodoethane
                                              'SER',  # serine
                                              'C2C',  # cu-cl-cu linkage
                                              'NA',  # sodium ion
                                              'FMT',  # formic acid
                                              'ASC',  # ascorbic acid
                                              'AU3',  # gold 3+ ion
                                              'FE2',  # fe (ii) ion
                                              'LNK',  # pentane
                                              'SEK',  # selenocyanate ion
                                              'MO1',  # magnesium ion, 1 water coordinated
                                              'EU3',  # europium (iii) ion
                                              '1BO',  # 1-butanol
                                              'AUC',  # gold (i) cyanide ion
                                              'CLO',  # chloro group
                                              'FE',  # fe (iii) ion
                                              'DUM',  # dummy atoms
                                              'ADP',  # adenosine-5'-diphosphate
                                              'OF2',  # 2 ferric ion, 1 bridging oxygen
                                              'BEF',  # beryllium trifluoride ion
                                              'FEL',  # hydrated fe
                                              'BF4',  # beryllium tetrafluoride ion
                                              'HEX',  # hexane
                                              'CUZ',  # (mu-4-sulfido)-tetra-nuclear copper ion
                                              'NDG',  # 2-(acetylamino)-2-deoxy-a-d-glucopyranose
                                              'XE',  # xenon
                                              'FMN',  # flavin mononucleotide
                                              'YAN',  # 1,2-dichlorobenzene
                                              'CUA',  # dinuclear copper ion
                                              'V',  # vanadium ion
                                              'CUO',  # cu2-o2 cluster
                                              'HEM',  # protoporphyrin ix containing fe
                                              'GMP',  # guanosine
                                              'CU',  # copper (ii) ion
                                              'MGF',  # trifluoromagnesate
                                              'GDP',  # guanosine-5'-diphosphate
                                              'CFT',  # trifluoromethane
                                              'SBT',  # 2-butanol
                                              'PLP',  # pyridoxal-5'-phosphate
                                              'SR',  # strontium ion
                                              'FU1',  # tetrahydrofuran
                                              'EDN',  # ethane-1,2-diamine
                                              'EDO',  # 1,2-ethanediol
                                              'H2S',  # hydrosulfuric acid
                                              'ND4',  # ammonium cation with d
                                              'BRO',  # bromo group
                                              'KR',  # krypton
                                              'CS',  # cesium ion
                                              'NME',  # methylamine
                                              'CDP',  # cytidine-5'-diphosphate
                                              'HGI',  # mercury (ii) iodide
                                              'SM',  # samarium (iii) ion
                                              'ALY',  # n(6)-acetyllysine
                                              'NMO',  # nitrogen monoxide
                                              'TDP',  # thiamin diphosphate
                                              'SE',  # selenium atom
                                              'HO',  # holmium atom
                                              '3CN',  # 3-aminopropane
                                              'AZI',  # azide ion
                                              'F42',  # coenzyme f420
                                              'FLO',  # fluoro group
                                              '6MO',  # molybdenum(vi) ion
                                              'EMC',  # ethyl mercury ion
                                              'Y1',  # yttrium ion
                                              'MO7', # bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (vi)
                                              'SE4',  # selenate ion
                                              'BF2',  # beryllium difluoride
                                              'CO',  # cobalt (ii) ion
                                              'NGD', # 3-(aminocarbonyl)-1-[(2r,3r,4s,5r)-5-({[(s)-{[(s)-{[(2r,3s,4r,5r)-5-(2-amino-6-oxo-1,6-dihydro-9h-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]pyridinium
                                              '2MO',  # molybdenum (iv)oxide
                                              '202',  # bromic acid
                                              'DIS',  # disordered solvent
                                              'MBN',  # toluene
                                              'LA',  # lanthanum (iii) ion
                                              'PGO',  # s-1,2-propanediol
                                              'CL',  # chloride ion
                                              'HP6',  # heptane
                                              'SO2',  # sulfur dioxide
                                              'LI',  # lithium ion
                                              'PPS',  # 3'-phosphate-adenosine-5'-phosphate sulfate
                                              'TPO',  # phosphothreonine
                                              'POL',  # n-propanol
                                              'GU0',  # 2,3,6-tri-o-sulfonato-alpha-l-galactopyranose
                                              'SGM',  # monothioglycerol
                                              'DTU',  # (2r,3s)-1,4-dimercaptobutane-2,3-diol
                                              'MOO',  # molybdate ion
                                              'TE',  # tellurium
                                              'TB',  # terbium(iii) ion
                                              'CA',  # calcium ion
                                              'FAD',  # flavin-adenine dinucleotide
                                              'CNV',  # propanenitrile
                                              'GOL',  # glycerol
                                              'SCN',  # thiocyanate ion
                                              'AG',  # silver ion
                                              'PO4',  # phosphate ion
                                              'IR',  # iridium ion
                                              'DIO',  # 1,4-diethylene dioxide
                                              'NH2',  # amino group
                                              '8CL',  # chlorobenzene
                                              '3NI',  # nickel (iii) ion
                                              'IRI',  # iridium hexammine ion
                                              'UTP',  # uridine 5'-triphosphate
                                              'AR',  # argon
                                              'N4M', # 5-formyltetrahydromethanopterin
                                              'CE',  # cerium (iii) ion
                                              'NH3',  # ammonia
                                              'MN',  # manganese (ii) ion
                                              'CNN',  # cyanamide
                                              'HGC',  # methyl mercury ion
                                              'GU8',  # 2,3,6-tri-o-methyl-beta-d-glucopyranose
                                              'GTP',  # guanosine-5'-triphosphate
                                              'UDP',  # uridine-5'-diphosphate
                                              'OC2',  # calcium ion, 2 waters coordinated
                                              'ART',  # arsenate
                                              'TFH',  # nitrogen of trifluoro-ethylhydrazine
                                              'MCH',  # trichloromethane
                                              '2NO',  # nitrogen dioxide
                                              '6WO',  # oxo-tungsten(vi)
                                              'CD5',  # cadmium ion, 5 waters coordinated
                                              'KCX',  # lysine nz-carboxylic acid
                                              'E1H',  # ethanimine
                                              'ARF',  # formamide
                                              'TL',  # thallium (i) ion
                                              'DXE',  # 1,2-dimethoxyethane
                                              'GU9',  # 2,3,6-tri-o-methyl-alpha-d-glucopyranose
                                              'IDO',  # iodo group
                                              'KO4',  # potassium ion, 4 waters coordinated
                                              'NRU',  # ruthenium (iii) hexaamine ion
                                              '4MO',  # molybdenum(iv) ion
                                              'HOH',
            ]
json.dump(non_ligs, open(os.path.join("non_ligs.json"), "w"))

d430ea7e811d531e1d603941bccdadc55e4f1088
<mask token>

<mask token>
json.dump(non_ligs, open(os.path.join('non_ligs.json'), 'w'))

<mask token>
non_ligs = ['DMS', 'CL', 'MG', 'EDO', 'PEG', 'MLI', 'NI', 'SO4', 'WAT',
    'LI', 'NA', 'K', 'RB', 'BE', 'MG', 'CA', 'SR', 'F', 'CL', 'BR', 'I',
    'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', '3CO', 'BUQ', 'NAG', 'NAD', 'CR',
    'SF4', 'EOH', 'ZNO', 'NAO', 'EOM', 'EHN', 'NAP', 'CCN', 'NAW', 'BR',
    'EGL', 'NI2', 'GSH', 'NI1', 'O2', 'BA', 'RU', 'SAH', 'GU7', 'SAM',
    'TAS', 'DCE', '2BM', 'TP7', 'OF3', 'OF1', 'RB', 'IOH', 'MW1', 'IOD',
    'C2O', 'BNZ', 'TCN', 'ARS', 'NH4', 'GD', 'PER', 'GA', 'TPP', 'CHX',
    'CME', 'THB', 'IPA', 'CD1', 'OH', 'SO4', 'DTT', 'PQN', 'CYN', 'PQQ',
    'PYJ', 'PEO', 'NA6', 'MBR', 'NA5', 'OS', 'MAN', 'CMO', 'OCL', 'DMF',
    'OCN', 'MO3', 'NGN', 'ACT', 'U1', 'HDZ', 'MO5', 'MO4', 'VO4', 'DMS',
    'FUC', 'PCL', 'CB5', 'EEE', 'HG', 'NO2', 'CMP', 'PR', 'BMA', 'IUM',
    'PT', 'ZN2', 'TTP', 'NO3', 'YT3', 'TYS', 'PB', 'M2M', 'ZO3', 'PD',
    'AMP', 'PI', 'MH3', 'AF3', 'ZN', 'MN3', 'OXY', 'NI', 'CSD', 'OX', 'PS5',
    'MN5', 'MN6', 'S', 'W', 'SB', 'FOL', 'OXE', 'PT4', 'PBM', 'O', 'MW2',
    'MG', '543', 'MSM', 'C5P', 'ANL', 'MTO', 'NO', 'TBU', 'OPY', 'PC4',
    'GU3', 'GU2', 'GU1', 'MOH', 'ANP', 'GU6', 'GU5', 'GU4', 'AU', 'OC3',
    'BTN', 'I42', 'OC4', 'OC7', 'OC6', 'TMP', 'RE', 'GD3', 'CTP', 'ACE',
    '3OF', 'ETZ', 'MM4', 'IN', 'ACN', 'DOD', 'AST', 'COA', 'EU', 'DOX',
    'COB', 'B12', 'REO', 'ATP', 'CD3', 'U10', 'ACY', 'PEG', 'YB', 'NDP',
    'NBZ', 'ETI', 'SER', 'C2C', 'NA', 'FMT', 'ASC', 'AU3', 'FE2', 'LNK',
    'SEK', 'MO1', 'EU3', '1BO', 'AUC', 'CLO', 'FE', 'DUM', 'ADP', 'OF2',
    'BEF', 'FEL', 'BF4', 'HEX', 'CUZ', 'NDG', 'XE', 'FMN', 'YAN', 'CUA',
    'V', 'CUO', 'HEM', 'GMP', 'CU', 'MGF', 'GDP', 'CFT', 'SBT', 'PLP', 'SR',
    'FU1', 'EDN', 'EDO', 'H2S', 'ND4', 'BRO', 'KR', 'CS', 'NME', 'CDP',
    'HGI', 'SM', 'ALY', 'NMO', 'TDP', 'SE', 'HO', '3CN', 'AZI', 'F42',
    'FLO', '6MO', 'EMC', 'Y1', 'MO7', 'SE4', 'BF2', 'CO', 'NGD', '2MO',
    '202', 'DIS', 'MBN', 'LA', 'PGO', 'CL', 'HP6', 'SO2', 'LI', 'PPS',
    'TPO', 'POL', 'GU0', 'SGM', 'DTU', 'MOO', 'TE', 'TB', 'CA', 'FAD',
    'CNV', 'GOL', 'SCN', 'AG', 'PO4', 'IR', 'DIO', 'NH2', '8CL', '3NI',
    'IRI', 'UTP', 'AR', 'N4M', 'CE', 'NH3', 'MN', 'CNN', 'HGC', 'GU8',
    'GTP', 'UDP', 'OC2', 'ART', 'TFH', 'MCH', '2NO', '6WO', 'CD5', 'KCX',
    'E1H', 'ARF', 'TL', 'DXE', 'GU9', 'IDO', 'KO4', 'NRU', '4MO', 'HOH']
json.dump(non_ligs, open(os.path.join('non_ligs.json'), 'w'))

import json
import os
non_ligs = ['DMS', 'CL', 'MG', 'EDO', 'PEG', 'MLI', 'NI', 'SO4', 'WAT',
    'LI', 'NA', 'K', 'RB', 'BE', 'MG', 'CA', 'SR', 'F', 'CL', 'BR', 'I',
    'MN', 'FE', 'CO', 'NI', 'CU', 'ZN', '3CO', 'BUQ', 'NAG', 'NAD', 'CR',
    'SF4', 'EOH', 'ZNO', 'NAO', 'EOM', 'EHN', 'NAP', 'CCN', 'NAW', 'BR',
    'EGL', 'NI2', 'GSH', 'NI1', 'O2', 'BA', 'RU', 'SAH', 'GU7', 'SAM',
    'TAS', 'DCE', '2BM', 'TP7', 'OF3', 'OF1', 'RB', 'IOH', 'MW1', 'IOD',
    'C2O', 'BNZ', 'TCN', 'ARS', 'NH4', 'GD', 'PER', 'GA', 'TPP', 'CHX',
    'CME', 'THB', 'IPA', 'CD1', 'OH', 'SO4', 'DTT', 'PQN', 'CYN', 'PQQ',
    'PYJ', 'PEO', 'NA6', 'MBR', 'NA5', 'OS', 'MAN', 'CMO', 'OCL', 'DMF',
    'OCN', 'MO3', 'NGN', 'ACT', 'U1', 'HDZ', 'MO5', 'MO4', 'VO4', 'DMS',
    'FUC', 'PCL', 'CB5', 'EEE', 'HG', 'NO2', 'CMP', 'PR', 'BMA', 'IUM',
    'PT', 'ZN2', 'TTP', 'NO3', 'YT3', 'TYS', 'PB', 'M2M', 'ZO3', 'PD',
    'AMP', 'PI', 'MH3', 'AF3', 'ZN', 'MN3', 'OXY', 'NI', 'CSD', 'OX', 'PS5',
    'MN5', 'MN6', 'S', 'W', 'SB', 'FOL', 'OXE', 'PT4', 'PBM', 'O', 'MW2',
    'MG', '543', 'MSM', 'C5P', 'ANL', 'MTO', 'NO', 'TBU', 'OPY', 'PC4',
    'GU3', 'GU2', 'GU1', 'MOH', 'ANP', 'GU6', 'GU5', 'GU4', 'AU', 'OC3',
    'BTN', 'I42', 'OC4', 'OC7', 'OC6', 'TMP', 'RE', 'GD3', 'CTP', 'ACE',
    '3OF', 'ETZ', 'MM4', 'IN', 'ACN', 'DOD', 'AST', 'COA', 'EU', 'DOX',
    'COB', 'B12', 'REO', 'ATP', 'CD3', 'U10', 'ACY', 'PEG', 'YB', 'NDP',
    'NBZ', 'ETI', 'SER', 'C2C', 'NA', 'FMT', 'ASC', 'AU3', 'FE2', 'LNK',
    'SEK', 'MO1', 'EU3', '1BO', 'AUC', 'CLO', 'FE', 'DUM', 'ADP', 'OF2',
    'BEF', 'FEL', 'BF4', 'HEX', 'CUZ', 'NDG', 'XE', 'FMN', 'YAN', 'CUA',
    'V', 'CUO', 'HEM', 'GMP', 'CU', 'MGF', 'GDP', 'CFT', 'SBT', 'PLP', 'SR',
    'FU1', 'EDN', 'EDO', 'H2S', 'ND4', 'BRO', 'KR', 'CS', 'NME', 'CDP',
    'HGI', 'SM', 'ALY', 'NMO', 'TDP', 'SE', 'HO', '3CN', 'AZI', 'F42',
    'FLO', '6MO', 'EMC', 'Y1', 'MO7', 'SE4', 'BF2', 'CO', 'NGD', '2MO',
    '202', 'DIS', 'MBN', 'LA', 'PGO', 'CL', 'HP6', 'SO2', 'LI', 'PPS',
    'TPO', 'POL', 'GU0', 'SGM', 'DTU', 'MOO', 'TE', 'TB', 'CA', 'FAD',
    'CNV', 'GOL', 'SCN', 'AG', 'PO4', 'IR', 'DIO', 'NH2', '8CL', '3NI',
    'IRI', 'UTP', 'AR', 'N4M', 'CE', 'NH3', 'MN', 'CNN', 'HGC', 'GU8',
    'GTP', 'UDP', 'OC2', 'ART', 'TFH', 'MCH', '2NO', '6WO', 'CD5', 'KCX',
    'E1H', 'ARF', 'TL', 'DXE', 'GU9', 'IDO', 'KO4', 'NRU', '4MO', 'HOH']
json.dump(non_ligs, open(os.path.join('non_ligs.json'), 'w'))

#!/usr/bin/env python

import json
import os

non_ligs = ['DMS', 'CL', 'MG', 'EDO', 'PEG', 'MLI', 'NI', 'SO4', 'WAT',  # `TP3` water is ambiguous and rare
                                              'LI', 'NA' , 'K', 'RB',  # group 1 cations
                                              'BE', 'MG', 'CA', 'SR',  # earth metal cations
                                               'F', 'CL', 'BR', 'I',  #halogens
                                               'MN', 'FE', 'CO',  'NI', 'CU', 'ZN',  # top period transition metals
                                                '3CO',  # cobalt (iii) ion
                                              'BUQ',  # 4-hydroxy-2-butanone
                                              'NAG',  # n-acetyl-d-glucosamine
                                              'NAD',  # nicotinamide-adenine-dinucleotide
                                              'CR',  # chromium ion
                                              'SF4',  # iron/sulfur cluster
                                              'EOH',  # ethanol
                                              'ZNO',  # zinc ion, 2 waters coordinated
                                              'NAO',  # sodium ion, 1 water coordinated
                                              'EOM',  # ethyloxymethoxyl
                                              'EHN',  # ethane
                                              'NAP',  # nadp nicotinamide-adenine-dinucleotide phosphate
                                              'CCN',  # acetonitrile
                                              'NAW',  # sodium ion, 3 waters coordinated
                                              'BR',  # bromide ion
                                              'EGL',  # ethylene glycol
                                              'NI2',  # nickel (ii) ion, 2 waters coordinated
                                              'GSH',  # glutathione
                                              'NI1',  # nickel ion, 1 water coordinated
                                              'O2',  # oxygen molecule
                                              'BA',  # barium ion
                                              'RU',  # ruthenium ion
                                              'SAH',  # s-adenosyl-l-homocysteine
                                              'GU7', # 2-amino-7-[2-(2-hydroxy-1-hydroxymethyl-ethylamino)-ethyl]-1,7-dihydro-purin-6-one
                                              'SAM',  # s-adenosylmethionine
                                              'TAS',  # trihydroxyarsenite(iii)
                                              'DCE',  # 1,2-dichloroethane
                                              '2BM',  # dibromomethane
                                              'TP7',  # coenzyme b
                                              'OF3',  # ferric ion, 1 water coordinated
                                              'OF1',  # ferrous ion, 1 water coordinated
                                              'RB',  # rubidium ion
                                              'IOH',  # 2-propanol, isopropanol
                                              'MW1',  # manganese ion, 1 water coordinated
                                              'IOD',  # iodide ion
                                              'C2O',  # cu-o-cu linkage
                                              'BNZ',  # benzene
                                              'TCN',  # tetracyanonickelate ion
                                              'ARS',  # arsenic
                                              'NH4',  # ammonium ion
                                              'GD',  # gadolinium atom
                                              'PER',  # peroxide ion
                                              'GA',  # gallium (iii) ion
                                              'TPP',  # thiamine diphosphate
                                              'CHX',  # cyclohexane
                                              'CME',  # s,s-(2-hydroxyethyl)thiocysteine
                                              'THB',  # tetrahydrobiopterin
                                              'IPA',  # isopropyl alcohol
                                              'CD1',  # cadmium ion, 1 water coordinated
                                              'OH',  # hydroxide ion
                                              'SO4',  # sulfate ion
                                              'DTT',  # 2,3-dihydroxy-1,4-dithiobutane
                                              'PQN',  # phylloquinone
                                              'CYN',  # cyanide ion
                                              'PQQ',  # pyrroloquinoline quinone
                                              'PYJ',  # phenylethane
                                              'PEO',  # hydrogen peroxide
                                              'NA6',  # sodium ion, 6 waters coordinated
                                              'MBR',  # tribromomethane
                                              'NA5',  # sodium ion, 5 waters coordinated
                                              'OS',  # osmium ion
                                              'MAN',  # alpha-d-mannose
                                              'CMO',  # carbon monoxide
                                              'OCL',  # cobalt ion, 1 water coordinated
                                              'DMF',  # dimethylformamide
                                              'OCN',  # cobalt ion, 2 waters coordinated
                                              'MO3',  # magnesium ion, 3 waters coordinated
                                              'NGN',  # nitrogen
                                              'ACT',  # acetate ion
                                              'U1',  # uranium atom
                                              'HDZ',  # nitrogen molecule
                                              'MO5',  # magnesium ion, 5 waters coordinated
                                              'MO4',  # magnesium ion, 4 waters coordinated
                                              'VO4',  # vanadate ion
                                              'DMS',  # dimethyl sulfoxide
                                              'FUC',  # alpha-l-fucose
                                              'PCL',  # platinum(ii) di-chloride
                                              'CB5',  # cobalt bis(1,2-dicarbollide)
                                              'EEE',  # ethyl acetate
                                              'HG',  # mercury (ii) ion
                                              'NO2',  # nitrite ion
                                              'CMP',  # adenosine-3',5'-cyclic-monophosphate
                                              'PR',  # praseodymium ion
                                              'BMA',  # beta-d-mannose
                                              'IUM',  # uranyl (vi) ion
                                              'PT',  # platinum (ii) ion
                                              'ZN2',  # zinc ion on 3-fold crystal axis
                                              'TTP',  # thymidine-5'-triphosphate
                                              'NO3',  # nitrate ion
                                              'YT3',  # yttrium (iii) ion
                                              'TYS',  # o-sulfo-l-tyrosine
                                              'PB',  # lead (ii) ion
                                              'M2M',  # 1-methoxy-2-(2-methoxyethoxy)ethane
                                              'ZO3',  # zinc ion, 3 waters coordinated
                                              'PD',  # palladium ion
                                              'AMP',  # adenosine monophosphate
                                              'PI',  # hydrogenphosphate ion
                                              'MH3',  # manganese ion, 1 hydroxyl coordinated
                                              'AF3',  # aluminum fluoride
                                              'ZN',  # zinc ion
                                              'MN3',  # manganese (iii) ion
                                              'OXY',  # oxygen molecule
                                              'NI',  # nickel (ii) ion
                                              'CSD',  # 3-sulfinoalanine
                                              'OX',  # bound oxygen
                                              'PS5',  # pentasulfide-sulfur
                                              'MN5',  # manganese ion, 5 waters coordinated
                                              'MN6',  # manganese ion, 6 waters coordinated
                                              'S',  # sulfur atom
                                              'W',  # tungsten ion
                                              'SB',  # antimony (iii) ion
                                              'FOL',  # folic acid
                                              'OXE',  # ortho-xylene
                                              'PT4',  # platinum (iv) ion
                                              'PBM',  # trimethyl lead ion
                                              'O',  # oxygen atom
                                              'MW2',  # manganese dihydrate ion
                                              'MG',  # magnesium ion
                                              '543',  # calcium ion, 6 waters plus ethanol coordinated
                                              'MSM',  # (methylsulfanyl)methane
                                              'C5P',  # cytidine-5'-monophosphate
                                              'ANL',  # aniline
                                              'MTO',  # bound water
                                              'NO',  # nitric oxide
                                              'TBU',  # tertiary-butyl alcohol
                                              'OPY',  # (3s)-4-oxo-4-piperidin-1-ylbutane-1,3-diamine
                                              'PC4',  # tetrachloroplatinate(ii)
                                              'GU3',  # methyl 3-o-methyl-2,6-di-o-sulfo-alpha-d-glucopyranoside
                                              'GU2',  # 2,3-di-o-methyl-alpha-l-idopyranuronic acid
                                              'GU1',  # 2,3-di-o-methyl-beta-d-glucopyranuronic acid
                                              'MOH',  # methanol
                                              'ANP',  # phosphoaminophosphonic acid-adenylate ester
                                              'GU6',  # 2,3,6-tri-o-sulfonato-alpha-d-glucopyranose
                                              'GU5',  # 2,3-di-o-methyl-6-o-sulfonato-alpha-d-glucopyranose
                                              'GU4',  # 2,3,4,6-tetra-o-sulfonato-alpha-d-glucopyranose
                                              'AU',  # gold ion
                                              'OC3',  # calcium ion, 3 waters coordinated
                                              'BTN',  # biotin
                                              'I42',  # hydroxy(dioxido)oxovanadium
                                              'OC4',  # calcium ion, 4 waters coordinated
                                              'OC7',  # calcium ion, 7 waters coordinated
                                              'OC6',  # calcium ion, 6 waters coordinated
                                              'TMP',  # thymidine-5'-phosphate
                                              'RE',  # rhenium
                                              'GD3',  # gadolinium ion
                                              'CTP',  # cytidine-5'-triphosphate
                                              'ACE',  # acetyl group
                                              '3OF',  # hydrated fe (iii) ion, 2 waters coordinated
                                              'ETZ',  # diethyl ether
                                              'MM4',  # molybdenum (iv) oxide
                                              'IN',  # indium (iii) ion
                                              'ACN',  # acetone
                                              'DOD',  # deuterated water
                                              'AST',  # arsenite
                                              'COA',  # coenzyme a
                                              'EU',  # europium ion
                                              'DOX',  # dioxane
                                              'COB',  # co-methylcobalamin
                                              'B12',  # cobalamin
                                              'REO',  # perrhenate
                                              'ATP',  # adenosine-5'-triphosphate
                                              'CD3',  # cadmium ion, 3 waters coordinated
                                              'U10',  # ubiquinone-10
                                              'ACY',  # acetic acid
                                              'PEG',  # di(hydroxyethyl)ether
                                              'YB',  # ytterbium (iii) ion
                                              'NDP',  # nadph dihydro-nicotinamide-adenine-dinucleotide phosphate
                                              'NBZ',  # nitrobenzene
                                              'ETI',  # iodoethane
                                              'SER',  # serine
                                              'C2C',  # cu-cl-cu linkage
                                              'NA',  # sodium ion
                                              'FMT',  # formic acid
                                              'ASC',  # ascorbic acid
                                              'AU3',  # gold 3+ ion
                                              'FE2',  # fe (ii) ion
                                              'LNK',  # pentane
                                              'SEK',  # selenocyanate ion
                                              'MO1',  # magnesium ion, 1 water coordinated
                                              'EU3',  # europium (iii) ion
                                              '1BO',  # 1-butanol
                                              'AUC',  # gold (i) cyanide ion
                                              'CLO',  # chloro group
                                              'FE',  # fe (iii) ion
                                              'DUM',  # dummy atoms
                                              'ADP',  # adenosine-5'-diphosphate
                                              'OF2',  # 2 ferric ion, 1 bridging oxygen
                                              'BEF',  # beryllium trifluoride ion
                                              'FEL',  # hydrated fe
                                              'BF4',  # beryllium tetrafluoride ion
                                              'HEX',  # hexane
                                              'CUZ',  # (mu-4-sulfido)-tetra-nuclear copper ion
                                              'NDG',  # 2-(acetylamino)-2-deoxy-a-d-glucopyranose
                                              'XE',  # xenon
                                              'FMN',  # flavin mononucleotide
                                              'YAN',  # 1,2-dichlorobenzene
                                              'CUA',  # dinuclear copper ion
                                              'V',  # vanadium ion
                                              'CUO',  # cu2-o2 cluster
                                              'HEM',  # protoporphyrin ix containing fe
                                              'GMP',  # guanosine
                                              'CU',  # copper (ii) ion
                                              'MGF',  # trifluoromagnesate
                                              'GDP',  # guanosine-5'-diphosphate
                                              'CFT',  # trifluoromethane
                                              'SBT',  # 2-butanol
                                              'PLP',  # pyridoxal-5'-phosphate
                                              'SR',  # strontium ion
                                              'FU1',  # tetrahydrofuran
                                              'EDN',  # ethane-1,2-diamine
                                              'EDO',  # 1,2-ethanediol
                                              'H2S',  # hydrosulfuric acid
                                              'ND4',  # ammonium cation with d
                                              'BRO',  # bromo group
                                              'KR',  # krypton
                                              'CS',  # cesium ion
                                              'NME',  # methylamine
                                              'CDP',  # cytidine-5'-diphosphate
                                              'HGI',  # mercury (ii) iodide
                                              'SM',  # samarium (iii) ion
                                              'ALY',  # n(6)-acetyllysine
                                              'NMO',  # nitrogen monoxide
                                              'TDP',  # thiamin diphosphate
                                              'SE',  # selenium atom
                                              'HO',  # holmium atom
                                              '3CN',  # 3-aminopropane
                                              'AZI',  # azide ion
                                              'F42',  # coenzyme f420
                                              'FLO',  # fluoro group
                                              '6MO',  # molybdenum(vi) ion
                                              'EMC',  # ethyl mercury ion
                                              'Y1',  # yttrium ion
                                              'MO7', # bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (vi)
                                              'SE4',  # selenate ion
                                              'BF2',  # beryllium difluoride
                                              'CO',  # cobalt (ii) ion
                                              'NGD', # 3-(aminocarbonyl)-1-[(2r,3r,4s,5r)-5-({[(s)-{[(s)-{[(2r,3s,4r,5r)-5-(2-amino-6-oxo-1,6-dihydro-9h-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-3,4-dihydroxytetrahydrofuran-2-yl]pyridinium
                                              '2MO',  # molybdenum (iv)oxide
                                              '202',  # bromic acid
                                              'DIS',  # disordered solvent
                                              'MBN',  # toluene
                                              'LA',  # lanthanum (iii) ion
                                              'PGO',  # s-1,2-propanediol
                                              'CL',  # chloride ion
                                              'HP6',  # heptane
                                              'SO2',  # sulfur dioxide
                                              'LI',  # lithium ion
                                              'PPS',  # 3'-phosphate-adenosine-5'-phosphate sulfate
                                              'TPO',  # phosphothreonine
                                              'POL',  # n-propanol
                                              'GU0',  # 2,3,6-tri-o-sulfonato-alpha-l-galactopyranose
                                              'SGM',  # monothioglycerol
                                              'DTU',  # (2r,3s)-1,4-dimercaptobutane-2,3-diol
                                              'MOO',  # molybdate ion
                                              'TE',  # tellurium
                                              'TB',  # terbium(iii) ion
                                              'CA',  # calcium ion
                                              'FAD',  # flavin-adenine dinucleotide
                                              'CNV',  # propanenitrile
                                              'GOL',  # glycerol
                                              'SCN',  # thiocyanate ion
                                              'AG',  # silver ion
                                              'PO4',  # phosphate ion
                                              'IR',  # iridium ion
                                              'DIO',  # 1,4-diethylene dioxide
                                              'NH2',  # amino group
                                              '8CL',  # chlorobenzene
                                              '3NI',  # nickel (iii) ion
                                              'IRI',  # iridium hexammine ion
                                              'UTP',  # uridine 5'-triphosphate
                                              'AR',  # argon
                                              'N4M', # 5-formyltetrahydromethanopterin
                                              'CE',  # cerium (iii) ion
                                              'NH3',  # ammonia
                                              'MN',  # manganese (ii) ion
                                              'CNN',  # cyanamide
                                              'HGC',  # methyl mercury ion
                                              'GU8',  # 2,3,6-tri-o-methyl-beta-d-glucopyranose
                                              'GTP',  # guanosine-5'-triphosphate
                                              'UDP',  # uridine-5'-diphosphate
                                              'OC2',  # calcium ion, 2 waters coordinated
                                              'ART',  # arsenate
                                              'TFH',  # nitrogen of trifluoro-ethylhydrazine
                                              'MCH',  # trichloromethane
                                              '2NO',  # nitrogen dioxide
                                              '6WO',  # oxo-tungsten(vi)
                                              'CD5',  # cadmium ion, 5 waters coordinated
                                              'KCX',  # lysine nz-carboxylic acid
                                              'E1H',  # ethanimine
                                              'ARF',  # formamide
                                              'TL',  # thallium (i) ion
                                              'DXE',  # 1,2-dimethoxyethane
                                              'GU9',  # 2,3,6-tri-o-methyl-alpha-d-glucopyranose
                                              'IDO',  # iodo group
                                              'KO4',  # potassium ion, 4 waters coordinated
                                              'NRU',  # ruthenium (iii) hexaamine ion
                                              '4MO',  # molybdenum(iv) ion
                                              'HOH',
            ]
json.dump(non_ligs, open(os.path.join("non_ligs.json"), "w"))
