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bp-kelley / descriptastorus

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The values used to normalize the molecular descriptors. #31

Closed StefanIsSmart closed 1 week ago

StefanIsSmart commented 4 months ago

Great work! But I have a sample question. Why do we use these values for normalization? How to get these values?

dists={
    'VSA_EState1': ('betaprime', (0.12979362790686721, 2.0084510281921832, -1.7874327445880742e-34, 0.4022005514286884), 0.0, 0.0, 0.0, 0.0),
    'Chi4n': ('mielke', (3.4334547302721328, 4.644325894559659, -0.1540765028544061, 3.7724626101152783), 0.0, 60.15570624032009, 3.5583748823804937, 1.9340011133496022),
    'EState_VSA3': ('pearson3', (1.2130333692507862, 20.490424246483514, 14.913598628728794), 0.0, 707.4193712196022, 20.490458921014422, 15.02692979610578),
    'PEOE_VSA3': ('recipinvgauss', (2039990.2035692804, -1.514157558116536e-12, 5.862765691466683), 0.0, 278.49556054006456, 5.883620301814973, 7.114346140218968),
    'PEOE_VSA10': ('ncx2', (1.2634981555275662, 2.1503143438355354, -2.21123444897305e-31, 2.606409115395213), 0.0, 494.0556831191233, 9.763622525936078, 12.915305068064065),
    'Chi2v': ('fisk', (5.416294252795936, -0.46711733318914683, 7.911730855234288), 0.0, 152.03415385974233, 7.97051218652611, 4.006279197425447),
    'SMR_VSA8': ('betaprime', (0.12979362790686721, 2.0084510281921832, -1.7874327445880742e-34, 0.4022005514286884), 0.0, 0.0, 0.0, 0.0),
    'ExactMolWt': ('mielke', (6.030507225812184, 6.081069808326847, -3.1905715544779594, 393.79789827541134), 7.01545597009, 7902.703267132, 413.2180535712111, 196.11660291127603),
    'fr_imidazole': ('wald', (-0.017711130586117518, 0.05908774988990952), 0, 11, 0.10202714189993299, 0.35905461339251266),
    'fr_aldehyde': ('halflogistic', (-2.2802084549638172e-10, 0.003260151958473212), 0, 2, 0.0032602282159751184, 0.057529151986179125),
    'fr_Al_COO': ('beta', (0.6951891478660377, 401.3878921392054, -1.8490162599417683e-28, 14.902552079575546), 0, 9, 0.05697398817917254, 0.2720833952111172),
    'NumAliphaticHeterocycles': ('alpha', (5.571361455216543e-09, -0.07477286399593108, 0.10965986221560856), 0, 22, 0.7546628263978479, 0.9186038062617755),
    'fr_Ar_NH': ('wald', (-0.01991313112984635, 0.06651081784403591), 0, 13, 0.11327792945506185, 0.37297284960554855),
    'NumHAcceptors': ('logistic', (5.039523695264815, 1.2773064178194637), 0, 199, 5.285449981498705, 3.9293707904214674),
    'fr_lactam': ('halflogistic', (-1.9994772259051099e-10, 0.0019599976691355514), 0, 2, 0.0019601372096046724, 0.04490322117641692),
    'fr_NH2': ('wald', (-0.025886531735103906, 0.08666379088388962), 0, 17, 0.14403008210574741, 0.5080894197040707),
    'fr_Ndealkylation1': ('wald', (-0.014170257884871005, 0.047146436951077536), 0, 8, 0.08431590211314792, 0.3528598050157884),
    'SlogP_VSA7': ('recipinvgauss', (124626.03395996531, -5.039104162427062e-11, 0.4157942168226829), 0.0, 77.05538951387919, 1.1814079834441082, 2.9446812598365155),
    'fr_Ar_N': ('halfgennorm', (0.32377704425495, -8.49433587779278e-22, 0.010554705354503424), 0, 66, 1.3546848279379557, 1.7700301662397686),
    'NumSaturatedHeterocycles': ('halfgennorm', (0.39340463716320073, -3.084884622335595e-23, 0.007755844850523552), 0, 22, 0.545018151270589, 0.8423690871097294),
    'NumAliphaticRings': ('gennorm', (0.16214999420806342, 1.0000000000000002, 1.2644170558638866e-06), 0, 24, 0.9787585130959167, 1.0878564569993276),
    'SMR_VSA4': ('betaprime', (0.8177035716382387, 2.026000293708502, -2.7076233813444817e-29, 0.8955328046106019), 0.0, 169.22417394169068, 3.521664764716257, 6.367910012270387),
    'Chi0v': ('mielke', (5.8775750667785065, 5.969290153282742, -0.051645183224216795, 16.255522569236142), 1.0, 310.3665679014367, 17.129538294841, 7.923870846730872),
    'qed': ('johnsonsb', (-0.537683817552717, 0.9438392221113977, -0.05971660981816428, 1.0270014571751256), 0.001610010104943233, 0.9484019712261345, 0.5707778636205341, 0.21314724659491038),
    'fr_sulfonamd': ('betaprime', (0.6061868535729906, 2.47005272151398, -1.7109734983680305e-30, 0.024136054923030247), 0, 2, 0.09929695078655505, 0.3106727570704293),
    'fr_halogen': ('exponweib', (1.5936220372251417, 0.4773265592552294, -6.305557196427465e-30, 0.11136163589207024), 0, 22, 0.6656565959617173, 1.1538784657180654),
    'Chi4v': ('mielke', (3.641407704651825, 4.9160753250874905, -0.19612721404766648, 4.272311768092421), 0.0, 80.31016831275534, 3.997197941292901, 2.1822145921791463),
    'MolLogP': ('nct', (5.423133497140618, -0.2505422147848311, 3.787125066469563, 1.447521060093181), -27.121900000000043, 26.476990000000036, 3.357664737331615, 1.8518910248841818),
    'Chi2n': ('burr', (5.323167832131418, 0.9614449953883716, -0.5182229173193543, 7.403200388112394), 0.0, 140.4224584835206, 7.320378282785918, 3.6830713407241156),
    'fr_Al_OH': ('pareto', (8.075644989366163, -0.6961711017351564, 0.6961711017065046), 0, 37, 0.18985328973028112, 0.5806908433990465),
    'LabuteASA': ('mielke', (5.9033344150609555, 6.093254767597408, -1.1647561264561102, 165.59359494140412), 19.375022664857827, 3138.810989711936, 172.78618537968595, 78.72241596326842),
    'SMR_VSA5': ('johnsonsu', (-6.770383826447828, 1.5639816052567266, -8.885737844117894, 0.8747218279195421), 0.0, 1059.7000355910607, 31.92088861776502, 31.701702832660054),
    'fr_guanido': ('halflogistic', (-2.8948632876909134e-11, 0.012390710083318518), 0, 8, 0.012390867360715251, 0.1352692056473331),
    'SlogP_VSA6': ('dweibull', (1.2651196828193871, 44.8855208417171, 19.999416617652344), 0.0, 425.50532391912986, 46.86150277566015, 23.994033852363053),
    'NumRadicalElectrons': ('halfnorm', (-3.3556536839857015e-09, 0.047012245813331466), 0, 10, 0.0002900203014210995, 0.047011387972006546),
    'HeavyAtomCount': ('mielke', (5.542942710744559, 6.0129203920305345, -0.10475651052005365, 28.19145327714555), 1, 545, 29.187713139919794, 13.728021647131865),
    'fr_Ar_COO': ('pearson3', (2.284860216852766, 0.009533409939207087, 0.010891254550521512), 0, 4, 0.019321352494674628, 0.14278703946614923),
    'fr_ester': ('wald', (-0.021345006038942453, 0.07132669030690274), 0, 9, 0.12089846289240247, 0.3816605577678055),
    'NumSaturatedCarbocycles': ('invweibull', (0.6897602654592729, -1.687045423250026e-28, 0.04100428545396396), 0, 9, 0.16625163761463302, 0.5048961994063688),
    'MolMR': ('burr', (6.172170768729716, 0.8936060537538131, -0.6260689145704982, 109.36170666360255), 0.0, 1943.4740000000081, 111.75295175062253, 49.21222833407792),
    'fr_SH': ('halflogistic', (-5.627308315330754e-10, 0.002940168145955494), 0, 2, 0.0029402058144070084, 0.057719918625515),
    'fr_ketone_Topliss': ('invweibull', (0.7845359779027771, -5.104827196981351e-29, 0.013651958761797665), 0, 5, 0.052113647955356876, 0.24762602874204098),
    'MolWt': ('burr', (6.292103975443265, 0.9448356544126613, -2.576132139748636, 398.4147809834958), 6.941, 7906.685999999983, 413.6754726605188, 196.24518387547647),
    'Kappa1': ('fisk', (5.090249068250488, 1.5243046476343975, 17.457634086393984), 1.5974025974025972, 452.4780879471051, 20.511369181587643, 10.901150147628785),
    'fr_term_acetylene': ('tukeylambda', (1.56196184906287, 0.005212203460720155, 0.008141262955574484), 0, 2, 0.004260298220875461, 0.06634877000162641),
    'Chi0n': ('mielke', (4.913702328256858, 5.56535100301131, 0.892757720674525, 15.151908382349568), 1.0, 310.3665679014367, 16.565702068330904, 7.789694974456289),
    'SMR_VSA9': ('betaprime', (0.6371524412800221, 0.1653001011937434, -1.1096304834919027e-26, 0.008200829448013355), 0.0, 68.99414199940686, 6.711933474546377, 7.898303955057197),
    'fr_hdrzine': ('genexpon', (2.2033965201556205, 4.581950155773536e-11, 1.9344067808226306, -6.071473724440753e-12, 0.021418241524934097), 0, 3, 0.009720680447631334, 0.10023082470639716),
    'PEOE_VSA11': ('betaprime', (0.5343466300982029, 2.0391606100747115, -5.644268412961732e-28, 1.3724974434068684), 0.0, 130.7949739456163, 3.9163487225567097, 6.085123241223355),
    'PEOE_VSA2': ('genlogistic', (1025.7536859090253, -32.00326592275044, 5.426751909719114), 0.0, 436.5016359224807, 8.968372740727396, 10.688899230076526),
    'fr_C_O': ('dweibull', (0.799241338494272, 1.0000000000000002, 1.1376361682177123), 0, 79, 1.3462142349964497, 1.7126177063621493),
    'EState_VSA2': ('dgamma', (1.6208597357735999, 14.722163518402503, 5.927601342234055), 0.0, 348.2229478088118, 16.17693847024966, 14.300245340171864),
    'fr_aryl_methyl': ('pareto', (2.2590951540541755, -0.03484369022048178, 0.03484369021605811), 0, 10, 0.42467972758093064, 0.7334626175897146),
    'EState_VSA9': ('gompertz', (157762717330.9355, -8.297980815964564e-12, 1740272081706.4692), 0.0, 459.53012783207976, 9.405433826279932, 11.29251583636432),
    'SlogP_VSA1': ('betaprime', (24.555424043054373, 8.676784435768978, -8.426380550481028, 5.728625412480383), 0.0, 409.4953592555066, 9.984737467652149, 9.779830593415184),
    'PEOE_VSA9': ('betaprime', (3.445175492809242, 31.144739014821592, -4.51163967848681, 170.01655826137412), 0.0, 811.1436563731141, 14.95011048070105, 13.041254445054955),
    'SMR_VSA2': ('wald', (-0.048767578220460746, 0.16186950174913545), 0.0, 43.27426884633218, 0.29905148573740525, 1.360442550951591),
    'fr_quatN': ('halflogistic', (-1.8398640615463982e-10, 0.0022802512521409345), 0, 2, 0.002280159611172782, 0.05094097451844112),
    'fr_dihydropyridine': ('tukeylambda', (1.5508163529247363, 0.002932569691259215, 0.004547877033296321), 0, 1, 0.002350164511515806, 0.04842149562213685),
    'MinPartialCharge': ('johnsonsu', (-2.7149539980911284, 1.0038367476615098, -0.5139064061681397, 0.008495052829614172), -0.7539104058810929, 1.0, -0.4200780304196831, 0.07189165509088434),
    'fr_ketone': ('wald', (-0.01054998963908324, 0.035036217635414556), 0, 6, 0.06421449501465103, 0.27790680727297107),
    'MaxAbsEStateIndex': ('t', (1.3108542430395254, 12.75352190648762, 0.7106673064513349), 0.0, 18.093289294329608, 12.009719840202807, 2.3499823939671187),
    'MaxAbsPartialCharge': ('johnsonsu', (1.7917111012287341, 0.9884411996798824, 0.509455736564852, 0.019080208112214614), 0.044672166080629815, 3.0, 0.4246995864209025, 0.07158969964653725),
    'Chi1v': ('burr', (7.687954133980298, 1.4497345379886477, -5.291458017141911, 14.007066785153341), 0.0, 193.52184470749225, 10.233294455235377, 4.9372866377359905),
    'fr_benzodiazepine': ('tukeylambda', (1.5687789926087756, 0.0024158367934644202, 0.0037899140207594472), 0, 1, 0.0019601372096046724, 0.04423002455034584),
    'EState_VSA5': ('exponweib', (0.2671814730479748, 1.165636178704992, -1.382245994068274e-31, 22.76769085633479), 0.0, 352.5201628431787, 13.722297283129771, 14.369271762415691),
    'VSA_EState7': ('loggamma', (0.00016582407490511742, 4.690543031567471e-07, 5.38971779436177e-08), -0.23935820315780676, 0.0, -2.393749594049651e-06, 0.0007569398071209723),
    'fr_C_O_noCOO': ('gennorm', (0.3061307987512025, 1.0, 0.0046024831025323395), 0, 71, 1.2699788985228966, 1.6247465287374963),
    'Chi3v': ('mielke', (4.392997381604184, 5.27028468604366, -0.32791696488665867, 5.890409366481655), 0.0, 106.26777041156456, 5.646449010813653, 2.881905780196624),
    'PEOE_VSA5': ('gilbrat', (-0.04993824025443838, 0.13664006325267003), 0.0, 73.11939707590946, 2.0398397458425537, 4.669463461453408),
    'fr_epoxide': ('hypsecant', (9.775361773901804e-06, 0.004229322664644675), 0, 3, 0.0015001050073505146, 0.041205202260121296),
    'fr_prisulfonamd': ('betaprime', (0.12979362790686721, 2.0084510281921832, -1.7874327445880742e-34, 0.4022005514286884), 0, 0, 0.0, 0.0),
    'fr_phenol': ('invweibull', (0.8135991555193818, -4.806156168974463e-28, 0.016229148422267782), 0, 8, 0.05026351844629124, 0.2534132017880052),
    'fr_sulfide': ('gengamma', (1.5106281082392625, 0.5574261640341269, -4.4413855396989186e-30, 0.0038351572717300027), 0, 6, 0.08101567109697679, 0.2882927997299278),
    'fr_alkyl_halide': ('wald', (-0.04358050576953841, 0.1452321478197392), 0, 17, 0.25484783934875443, 0.9066667900753467),
    'NumAromaticHeterocycles': ('halfgennorm', (0.19057145504745865, -1.897689882032624e-17, 2.1261316374019246e-05), 0, 33, 0.9458862120348425, 1.0262824322901387),
    'fr_Ar_OH': ('wald', (-0.0100135027386673, 0.03324263418577556), 0, 8, 0.06124428710009701, 0.2766130074506664),
    'fr_thiazole': ('wald', (-0.007257531762340398, 0.024068128495977677), 0, 6, 0.04502315162061344, 0.217339283746722),
    'fr_imide': ('pearson3', (2.2221583002327714, 0.018063449381832734, 0.02006992198733707), 0, 6, 0.02752192653485744, 0.1778336591269578),
    'NumSaturatedRings': ('halfgennorm', (0.23246838885007082, -2.4267394888596534e-25, 0.00026458005932038795), 0, 22, 0.711269788885222, 0.9971159900281824),
    'fr_hdrzone': ('wald', (-0.003105521778228028, 0.010274411296672493), 0, 2, 0.019951396597761843, 0.14280545219170362),
    'fr_lactone': ('tukeylambda', (1.527151454037369, 0.013585748455595358, 0.020747495508148833), 0, 6, 0.011000770053903774, 0.11242720454031359),
    'FractionCSP3': ('gausshyper', (0.4771522405083861, 9.066071275571563, -7.620494949081857, 3.1818106084013347, -4.691817003086665e-28, 1.3215636376781599), 0.0, 1.0, 0.3432847243844843, 0.19586440800503926),
    'HallKierAlpha': ('logistic', (-2.756871651517898, 0.6249482292466357), -56.5600000000003, 3.0300000000000002, -2.8236952794487813, 1.362245033459619),
    'fr_para_hydroxylation': ('gilbrat', (-0.00874073035192809, 0.023988673379858362), 0, 7, 0.2581980738651706, 0.5588920168597382),
    'HeavyAtomMolWt': ('burr', (6.148243331396738, 0.9539656352826273, -2.0597306351675164, 373.86535994513247), 6.941, 7542.798000000015, 389.1014159096795, 184.23918925686846),
    'SlogP_VSA12': ('lomax', (1.3526140858007119, -3.8436281815982077e-13, 0.5306720480047502), 0.0, 199.36606648479187, 6.222469001946574, 9.773336061271038),
    'fr_allylic_oxid': ('wald', (-0.012125985576272109, 0.04021754130884261), 0, 12, 0.07526526856879981, 0.43369194377652315),
    'fr_alkyl_carbamate': ('wald', (-0.0028043421468934076, 0.009276348457582401), 0, 3, 0.018071264988549197, 0.13836470784532925),
    'fr_HOCCN': ('wald', (-0.0019826051357043533, 0.006555328648504729), 0, 2, 0.01286090026301841, 0.11373440248499654),
    'Chi1n': ('mielke', (4.960260518842145, 5.594233665274178, -0.0629921400622475, 9.415745103559818), 0.0, 179.81742433151658, 9.668289027429788, 4.636496265706159),
    'PEOE_VSA4': ('pareto', (1.764490302170505, -1.0130190528730951, 1.0130190526084408), 0.0, 74.63705581047195, 2.871044297114316, 5.252580084878072),
    'NOCount': ('dgamma', (0.9114891050741081, 5.999999999999998, 2.360844051557576), 0, 237, 6.576580360625244, 5.165410541429347),
    'EState_VSA4': ('foldnorm', (0.005911506485819916, -9.396020384268004e-10, 29.86848626045161), 0.0, 309.6802047001077, 23.73312663187225, 18.134786070135654),
    'VSA_EState6': ('betaprime', (0.12979362790686721, 2.0084510281921832, -1.7874327445880742e-34, 0.4022005514286884), 0.0, 0.0, 0.0, 0.0),
    'Chi3n': ('mielke', (3.8419002158163336, 5.021067627998188, -0.12843494993055915, 5.26846058565802), 0.0, 89.41912553532535, 5.1024891606395135, 2.6233324773423217),
    'fr_barbitur': ('genhalflogistic', (0.0020825723750872178, -0.0014169372235491489, 0.005286684885304822), 0, 2, 0.0014100987069094837, 0.03805408163051986),
    'fr_Al_OH_noTert': ('gompertz', (35118115.876645096, -1.5683266541399722e-10, 5712177.117752606), 0, 37, 0.16987189103237227, 0.5550559671673745),
    'fr_COO2': ('wald', (-0.012755896711276589, 0.04241946965978133), 0, 9, 0.07634534417409218, 0.3067871977652909),
    'fr_azo': ('genhalflogistic', (0.00040002675029834824, -2.796838513658869e-05, 0.0031033294350019196), 0, 2, 0.0006700469032832298, 0.027011148452530685),
    'FpDensityMorgan1': ('t', (7.1357369753127795, 1.0971430458813116, 0.17213544486837606), 0.07971014492753623, 2.111111111111111, 1.0947677251482226, 0.20201147073315795),
    'fr_aniline': ('halfgennorm', (0.1049174054668825, -0.0004210957634456598, 2.0561338188621596e-11), 0, 17, 0.6701569109837688, 0.8999932508248457),
    'SMR_VSA3': ('dgamma', (1.7525536696583415, 12.349493875194277, 4.09734805299208), 0.0, 394.2610115631847, 12.654567199384484, 11.238213406272283),
    'fr_tetrazole': ('wald', (-0.0018040357049599466, 0.005964316702018277), 0, 2, 0.011720820457432021, 0.1080900079828228),
    'VSA_EState10': ('gennorm', (0.325862160652744, -1.5857598255070421e-27, 0.009249443355545232), -22.789260764991006, 74.77274927572002, 1.3375950132085297, 3.8197200206817126),
    'fr_phenol_noOrthoHbond': ('invweibull', (0.8136034301945807, -5.137954972709019e-29, 0.01610798208070398), 0, 8, 0.049623473643155024, 0.2514798405151786),
    'PEOE_VSA8': ('dgamma', (1.49159666908677, 21.468624511796396, 8.385920333308711), 0.0, 311.7903524102208, 25.24827589064641, 16.37842558375825),
    'EState_VSA8': ('genexpon', (0.8492139229831794, 0.898456899940423, 1.8794539462657145, -7.998786049300654e-10, 28.40401980183114), 0.0, 364.8615531780818, 21.03371597445418, 18.393077792682497),
    'BalabanJ': ('nct', (4.182658638749994, 2.0965263482828114, 1.1271767054584343, 0.2616489125636474), 0.0, 7.289359191119452, 1.8039183288289355, 0.47846986656304485),
    'fr_C_S': ('tukeylambda', (1.373229786243365, 0.006142154117625993, 0.008434588986021351), 0, 2, 0.017351214585020952, 0.13360466287284203),
    'fr_ArN': ('tukeylambda', (1.4424188577152934, 0.03329139576768536, 0.04802013705497249), 0, 16, 0.05239366755672897, 0.33593599906289534),
    'NumAromaticRings': ('dgamma', (2.5851733541458035, 2.495448308226644, 0.3726216029742541), 0, 34, 2.480923664656526, 1.2619073213233434),
    'fr_Imine': ('wald', (-0.004133581140781835, 0.013682691065125839), 0, 4, 0.02636184532917304, 0.17166002580284992),
    'NumAliphaticCarbocycles': ('halfgennorm', (0.39096958306392793, -4.260236992450893e-24, 0.0012095685496975065), 0, 9, 0.22409568669806887, 0.5847294862795492),
    'fr_piperzine': ('invweibull', (0.7886440189451933, -2.4256731163377907e-29, 0.02564081626730841), 0, 5, 0.08231576210334723, 0.28309044391366156),
    'fr_nitroso': ('genhalflogistic', (2.1084981882574176e-07, -4.9280506479729835e-05, 0.0027110708397517554), 0, 2, 0.00014000980068604803, 0.012648778519674015),
    'FpDensityMorgan2': ('johnsonsu', (0.7111118816857295, 1.7569762969412164, 1.9820508520621796, 0.3566466873696017), 0.13043478260869565, 2.75, 1.807249299497176, 0.26404333001263824),
    'SlogP_VSA3': ('genhalflogistic', (0.00150187910000416, -2.3112405176891454e-10, 9.57718508471936), 0.0, 486.412075845355, 13.207558092806261, 14.07198140237455),
    'fr_urea': ('wald', (-0.011156011934882477, 0.03708223885227959), 0, 4, 0.06708469592871501, 0.2580011979049133),
    'VSA_EState9': ('t', (2.778511535506783, 54.00468044177123, 14.841602340950482), -61.35386460040703, 1513.3333333333328, 58.298150276013196, 32.97223516741629),
    'fr_nitro_arom': ('exponweib', (1.1347393331388103, 0.7642415443821742, -9.540668167412522e-31, 0.00766605879556546), 0, 4, 0.03152220655445881, 0.18587317845266496),
    'fr_amidine': ('gompertz', (1256395099718.369, -3.6322380930315925e-14, 17278550801.355766), 0, 4, 0.0163211424799736, 0.13976768727132605),
    'fr_nitro_arom_nonortho': ('wald', (-0.002927735757054801, 0.009685114750495933), 0, 3, 0.01884131889232246, 0.14002286241970868),
    'SlogP_VSA11': ('invweibull', (0.4147001922244138, -1.4325296088889312e-27, 0.4348351110420754), 0.0, 68.99414199940686, 3.2168374575889174, 5.0279560653331945),
    'RingCount': ('dgamma', (2.186557671264268, 3.4836909786085286, 0.49776105041563334), 0, 57, 3.4596821777524425, 1.5775840075847496),
    'fr_azide': ('hypsecant', (0.0011100250221481181, 0.002817992740312428), 0, 2, 0.0009900693048513396, 0.03238970929040505),
    'Ipc': ('ncf', (2.2307091334463722, 0.10899090116091759, 1.0000000000366653, -1.1981582241278056e+221, 0.5596425180505273), 0.0, 9.476131257211451e+221, 1.0245870093128289e+217, inf),
    'fr_benzene': ('dgamma', (3.3192814002631734, 1.5061477493525466, 0.23910537147076447), 0, 14, 1.5344274099186943, 0.9561701389956593),
    'fr_thiocyan': ('gengamma', (0.5076950581215369, 1.2254477892001665, -1.4543304035389683e-31, 0.00801926074913513), 0, 2, 0.0002900203014210995, 0.017605044440269665),
    'PEOE_VSA14': ('pareto', (1.7596722287597166, -2.239860392602096, 2.239860392451776), 0.0, 416.4980987917504, 3.013749589704376, 6.883189641607028),
    'PEOE_VSA7': ('dgamma', (1.4806417259357412, 39.98160154845938, 10.168406696469939), 0.0, 508.39601533563194, 41.78662552891026, 19.81428403790816),
    'VSA_EState5': ('genhalflogistic', (4.73389199695264e-09, -0.030429032584450635, 0.09155583517487542), 0.0, 68.19071853741498, 0.008147278492018148, 0.5030871156371451),
    'EState_VSA7': ('powerlaw', (0.2103250937511124, -1.031145487494383e-26, 231.78083977397324), 0.0, 225.3129516643085, 25.741886434607192, 21.953593999938157),
    'fr_N_O': ('exponnorm', (5045.039118637744, -2.4181865220268798e-05, 5.7188007391269775e-06), 0, 6, 0.028882021741521907, 0.23864172665999558),
    'VSA_EState4': ('betaprime', (0.12979362790686721, 2.0084510281921832, -1.7874327445880742e-34, 0.4022005514286884), 0.0, 0.0, 0.0, 0.0),
    'EState_VSA6': ('chi', (0.5386485681683548, -2.640567062882436e-29, 30.844792175705116), 0.0, 298.3055333422921, 18.147758868775043, 16.4171251936251),
    'PEOE_VSA6': ('exponpow', (0.9016211226446249, -5.748343789415991e-27, 53.824180129747546), 0.0, 415.6833365808712, 30.51404957069927, 23.580292452344),
    'fr_diazo': ('halfnorm', (-8.299739916759084e-10, 0.0031623214263548586), 0, 1, 1.000070004900343e-05, 0.0031623725326093326),
    'MaxEStateIndex': ('t', (1.3108542430395254, 12.753521906487567, 0.7106673064513349), 0.0, 18.093289294329608, 12.009719840202806, 2.3499823939671187),
    'fr_oxime': ('pearson3', (2.517850854435552, 0.009251874821651483, 0.011647420462412978), 0, 3, 0.015401078075465282, 0.1267436305065821),
    'SlogP_VSA10': ('betaprime', (0.4375490925573042, 1.8760340999346696, -1.050475196211794e-28, 1.367988164331459), 0.0, 99.49189265982736, 6.345391750680324, 7.373907457789322),
    'fr_nitrile': ('invweibull', (0.813385754265167, -2.609225753111669e-30, 0.010587145126146093), 0, 5, 0.04477313411938836, 0.2211084100854278),
    'fr_COO': ('wald', (-0.01274707189437067, 0.04238860957269042), 0, 9, 0.07629534067384718, 0.306587684326303),
    'VSA_EState8': ('cauchy', (0.4615208647039756, 1.4176964379023667), -4.311579244789392, 610.9052623831149, 9.971522100585924, 18.488170207714543),
    'SlogP_VSA2': ('lognorm', (0.5117956692971417, -7.272585382702083, 42.859086084122595), 0.0, 1181.0895715112954, 41.959432071647804, 34.15538345697471),
    'fr_priamide': ('exponweib', (1.0954611988211496, 0.7544974723445165, -8.879663989913682e-32, 0.012058631113746431), 0, 6, 0.03770263918474293, 0.21274815822293996),
    'SMR_VSA1': ('cauchy', (13.199049915613251, 5.44099244703784), 0.0, 611.7284512306612, 15.881198059745422, 15.324918915564249),
    'FpDensityMorgan3': ('johnsonsu', (1.054397168130864, 1.7348730697701296, 2.7630213444641853, 0.3798207348262541), 0.18115942028985507, 3.5454545454545454, 2.4726320476023513, 0.32057971250733736),
    'fr_bicyclic': ('beta', (0.5840060328350145, 474.4004348752039, -2.2007759769553093e-31, 286.9088171814874), 0, 31, 0.7892552478673507, 1.2222619740000107),
    'TPSA': ('johnsonsu', (-0.8579013079024209, 1.232465212393282, 51.250072658107214, 29.00917664083923), 0.0, 3183.790000000002, 83.57268198773914, 74.84752227939705),
    'NumHeteroatoms': ('genlogistic', (22.144409538152043, -1.4241236643022548, 2.462142139013319), 0, 259, 7.61976338343684, 5.484367394332425),
    'fr_pyridine': ('gilbrat', (-0.006105798295798184, 0.016715004503743934), 0, 5, 0.22085545988219174, 0.48191548762954484),
    'MinEStateIndex': ('cauchy', (-0.4065559618468691, 0.4370714902017909), -9.858201857916416, 1.4242592592592593, -1.1147863044659592, 1.550385821215674),
    'NumHDonors': ('johnsonsu', (-6.303785805420036, 1.2935688877340756, -0.44063513396543863, 0.023159008664878106), 0, 104, 1.6016621163481444, 2.2472252977995697),
    'NumValenceElectrons': ('t', (2.854251470602213, 144.3027466924646, 32.00913472185999), 0, 2996, 153.57779044533117, 75.10240753520117),
    'Chi0': ('fisk', (5.941141785557418, -0.07374276109511947, 19.65464437888598), 0.0, 405.82501416452726, 20.82806399367901, 9.928368342000695),
    'Kappa2': ('fisk', (4.668432120081604, 0.2539009602536103, 7.822349728630153), 0.2713156408808583, 225.9686552554005, 8.912276904621457, 5.461845335100644),
    'NHOHCount': ('invgamma', (3.8797587021158746, -1.1307664222598288, 8.227943634490117), 0, 117, 1.7429120038402688, 2.563177769965799),
    'SMR_VSA10': ('dweibull', (1.1539393051818632, 20.846729374180775, 11.835976638334323), 0.0, 491.00242136254764, 23.906689304667765, 16.4741302013246),
    'PEOE_VSA12': ('alpha', (0.5429249279739217, -1.1871493007688236, 2.145045390430375), 0.0, 419.4097607839573, 5.59007921551618, 9.564823801075985),
    'PEOE_VSA1': ('burr', (3.9268049096073985, 0.48995232102675695, -1.6407085406832138, 19.294424729301284), 0.0, 561.0838284951058, 14.999241834817811, 13.776374483985686),
    'fr_ether': ('fisk', (0.8051168725131534, -2.567380610408963e-22, 0.23753230483392967), 0, 60, 0.8167371716020121, 1.2247008120931449),
    'EState_VSA1': ('foldcauchy', (0.0067487067434300755, -2.744934012978528e-09, 4.288215504541297), 0.0, 1261.848165001823, 12.539067008486557, 28.935889287596773),
    'VSA_EState3': ('betaprime', (0.12979362790686721, 2.0084510281921832, -1.7874327445880742e-34, 0.4022005514286884), 0.0, 0.0, 0.0, 0.0),
    'SlogP_VSA9': ('betaprime', (0.12979362790686721, 2.0084510281921832, -1.7874327445880742e-34, 0.4022005514286884), 0.0, 0.0, 0.0, 0.0),
    'MaxPartialCharge': ('dgamma', (0.8966427125022032, 0.26138963441733876, 0.06744166351965852), -0.03856361615904991, 3.0, 0.27854710402529237, 0.08364524848258846),
    'BertzCT': ('beta', (18.188950676898635, 6538386706999.18, -671.968519633414, 592927086280210.0), 0.0, 30826.22636467273, 987.5790655792254, 632.1534060688446),
    'fr_isocyan': ('genhalflogistic', (2.176451524678801e-10, -8.586837508181029e-13, 0.003318792604734705), 0, 1, 0.00011000770053903773, 0.010487878662763976),
    'fr_phos_ester': ('genhalflogistic', (3.2594653253264924e-11, -0.0012483281868383108, 0.02952659923331233), 0, 22, 0.007020491434400408, 0.3369253069398357),
    'fr_Nhpyrrole': ('wald', (-0.01991313112984635, 0.06651081784403544), 0, 13, 0.11327792945506185, 0.3729728496055485),
    'RDKit2D_calculated': ('betaprime', (0.3413091898181908, 238.4251067091114, 0.9999999999999999, 0.8834384815227141), True, True, 1.0, 0.0),
    'fr_sulfone': ('pearson3', (2.196096781694557, 0.009513879681788937, 0.01044670027530296), 0, 3, 0.021361495304671328, 0.14807178403739918),
    'MinAbsPartialCharge': ('laplace', (0.26315857867884, 0.0561294628943012), 0.00017822665335796042, 1.0, 0.2739606546909672, 0.07533771658554175),
    'SMR_VSA6': ('recipinvgauss', (0.5082650634594839, -6.086954132180281, 8.524443845355009), 0.0, 817.1820035633156, 19.209113622421707, 17.41580422042883),
    'fr_thiophene': ('halfgennorm', (0.5766089104240131, -6.723634040192055e-19, 0.0018219011330323374), 0, 3, 0.050743552048643406, 0.22669113213778155),
    'EState_VSA11': ('genhalflogistic', (0.0010872264517366357, -4.398093849911524e-07, 0.31899977022818193), 0.0, 163.01426425844207, 0.11426916104059913, 1.8841357303463615),
    'fr_NH0': ('foldnorm', (0.05865369911318355, -2.4259159741023723e-09, 2.811848848966825), 0, 59, 2.174432210254718, 1.785860796591467),
    'SlogP_VSA5': ('genexpon', (0.002852587331303075, 0.23353705964951516, 0.2144337777778184, -2.3573191470339223, 4.447211770059805), 0.0, 649.935656436369, 30.740541351785637, 23.895007786195226),
    'EState_VSA10': ('genexpon', (2.705707701965304, 3.771883657629245, 5.375903761907104, -4.354556984551863e-07, 54.16500289129278), 0.0, 322.991248574887, 11.740129013811245, 11.161898269805397),
    'fr_NH1': ('exponnorm', (2892.636726669909, -0.0012981492832112645, 0.00037957863319105643), 0, 70, 1.1072875101257087, 1.5590446880501752),
    'SlogP_VSA4': ('halfgennorm', (0.13290288528045635, -2.16370553583873e-12, 4.03300081749346e-08), 0.0, 116.32363116174835, 6.358583799897668, 7.800100182361395),
    'fr_Ndealkylation2': ('wald', (-0.031069214119069204, 0.10443777001623708), 0, 12, 0.16626163831468202, 0.4316735416648144),
    'SMR_VSA7': ('dweibull', (1.215378550488066, 56.28465156519039, 23.02916244099079), 0.0, 551.7863436604832, 58.73997506473642, 28.427064508331743),
    'fr_nitro': ('wald', (-0.006030983799621385, 0.019984499845659677), 0, 4, 0.03786265038552699, 0.20368952922550065),
    'SlogP_VSA8': ('ncf', (0.010351345715274272, 2.238220060195106, 2.3979254167173853, -2.0305306869043397e-08, 0.00093545475888877), 0.0, 133.9023781814824, 6.766619840611257, 8.671848120645365),
    'VSA_EState2': ('genlogistic', (1.415613774458108, -4.0305012625995696e-05, 0.001088572076970272), -0.7726899469689867, 0.0802671757431348, -3.2739988469591856e-05, 0.004083178209614408),
    'NumAromaticCarbocycles': ('dgamma', (3.319688925350106, 1.5062285243564748, 0.23908502549666388), 0, 14, 1.5350374526216835, 0.956147979224174),
    'fr_furan': ('halfgennorm', (0.5939855958815875, -5.726016095250532e-19, 0.001778526530384881), 0, 2, 0.038802716190133306, 0.19747704781754222),
    'PEOE_VSA13': ('halfgennorm', (0.2726011593040699, -6.070628359122943e-24, 0.0023718323492315794), 0.0, 78.17764936502758, 3.30010114873348, 4.358778167233281),
    'fr_oxazole': ('wald', (-0.0018806042805029088, 0.006217750403694874), 0, 2, 0.012210854759833188, 0.11073284872542345),
    'Kappa3': ('foldnorm', (0.7381901404044835, 0.07499999952842873, 4.410636124980368), 0.07500000000000012, 1760.9964197530858, 4.873556896466643, 6.732045653350472),
    'fr_morpholine': ('exponweib', (1.5683748664994073, 0.5053553495208175, -2.1400950538163005e-30, 0.0033466480252323464), 0, 3, 0.046923284629924095, 0.21977656974074022),
    'fr_unbrch_alkane': ('genhalflogistic', (0.0001735874860695949, -2.406745376333286e-08, 0.2558409046054385), 0, 167, 0.2555878911523807, 1.8216755193439447),
    'fr_amide': ('recipinvgauss', (220103.5665089948, -1.4778017808899836e-11, 0.7451439305459917), 0, 71, 1.1422999609972697, 1.6398141260141192),
    'NumRotatableBonds': ('mielke', (2.902960148717509, 4.199193993037961, -0.9968227721720102, 8.267126836374882), 0, 304, 7.140309821687518, 6.233943765856294),
    'Chi1': ('mielke', (5.372526418714403, 6.068367649928466, -0.06790886881111757, 13.725737593680664), 0.0, 256.9697300670324, 14.033526281218712, 6.54332057037178),
    'fr_phos_acid': ('genhalflogistic', (3.2594653253264924e-11, -0.0012483281868383108, 0.02952659923331233), 0, 22, 0.007130499134939446, 0.3375013082055841),
    'fr_piperdine': ('halfgennorm', (0.4238794287379706, -1.2796542653568352e-22, 0.0018770831152461857), 0, 6, 0.14572020041402897, 0.39164760531240855),
    'fr_isothiocyan': ('genhalflogistic', (8.886662035991823e-09, -0.0008924947259535538, 0.002685293974604489), 0, 2, 0.0002300161011270789, 0.015810268619422887),
    'MinAbsEStateIndex': ('genpareto', (0.11654274500988507, -4.295406365103898e-11, 0.13245709790535898), 0.0, 2.5115740740740735, 0.15016751055787822, 0.17292082606243664),
    'fr_methoxy': ('gilbrat', (-0.01550907507397075, 0.042866902160229356), 0, 8, 0.31338193673557146, 0.6523713877037112)
}
StefanIsSmart commented 3 months ago

Any one could help me?

bp-kelley commented 3 months ago

These are the distributions fit to the raw data in the gz files here: https://github.com/bp-kelley/descriptastorus/tree/e5a2e98973a4cfd62402d53faae49f838d160656/data/d_descriptors

which are a random sample from chembl as of six years ago

KnathanM commented 3 months ago

Thank you for pointing us to that folder of raw data @bp-kelley. Two follow up questions: I see the raw data is an array of numbers. Was the list of molecules randomly sampled also saved in addition to their descriptor values? Do you know why certain distributions were chosen for each descriptor? For example, mielke for ExactMolWt, with clipping cutoffs 7.01545597009 and 7902.703267132.

bp-kelley commented 2 months ago

The distributions are fitted using this script:

https://github.com/bp-kelley/descriptastorus/blob/master/data/d_descriptors/make_histdists.py

There is another normalization method

RDKit2DHistogramNormalized

which only uses the raw values to make the CDF and doesn't fit distributions. This is quite a bit faster but hasn't been tested as heavily.

bp-kelley commented 2 months ago

I regret that I didn't save the chembl molecule used to make the descriptors, I'll see if I have them floating around anywhere.

bp-kelley commented 2 months ago

The molecules were randomly selected from ChEMBL btw..

bp-kelley commented 4 weeks ago

If looks like I didn't fully answer the question, spipy distributions can be fit to pdfs: https://stackoverflow.com/questions/6620471/fitting-empirical-distribution-to-theoretical-ones-with-scipy-python

bp-kelley commented 4 weeks ago

This was the technique used,

bp-kelley commented 1 week ago

For the next major version, I'll have the compounds used for the distribution and the code used to make them in the Data directory.