diff --git a/CIMtools/preprocessing/solvent.py b/CIMtools/preprocessing/solvent.py index 2f2aa1e..0efee77 100644 --- a/CIMtools/preprocessing/solvent.py +++ b/CIMtools/preprocessing/solvent.py @@ -1,6 +1,8 @@ # -*- coding: utf-8 -*- # # Copyright 2018-2020 Ramil Nugmanov +# Copyright 2021 Ilnura Kashafutdinova +# Copyright 2021 Assima Rakhimbekova # This file is part of CIMtools. # # CIMtools is free software; you can redistribute it and/or modify @@ -26,7 +28,7 @@ class SolventVectorizer(CIMtoolsTransformerMixin): def __init__(self, polarizability_form1=True, polarizability_form2=True, permettivity_form1=True, permettivity_form2=True, permettivity_form3=True, permettivity_form4=True, permettivity_polarizability=True, alpha_kamlet_taft=True, beta_kamlet_taft=True, pi_kamlet_taft=True, - spp_katalan=True, sb_katalan=True, sa_katalan=True): + spp_katalan=True, sb_katalan=True, sa_katalan=True, boiling_point=False, melting_point=False): self.polarizability_form1 = polarizability_form1 self.polarizability_form2 = polarizability_form2 self.permettivity_form1 = permettivity_form1 @@ -40,6 +42,8 @@ def __init__(self, polarizability_form1=True, polarizability_form2=True, permett self.spp_katalan = spp_katalan self.sb_katalan = sb_katalan self.sa_katalan = sa_katalan + self.boiling_point = boiling_point + self.melting_point = melting_point self.__prepare_header() def __getstate__(self): @@ -150,66 +154,66 @@ def transform(self, x): described_solvents = dict(( - ('1-phenylethan-1-one', (.31, .237, .845, .943, .458, .891, .109, .04, .49, .9, .9, .37, .04)), - ('1,2-dichloroethane', (.266, .21, .757, .903, .431, .824, .091, .0, .1, .81, .89, .13, .03)), - ('1,2-dimethoxyethane', (.23, .19, .67, .86, .4, .76, .08, .0, .41, .53, .79, .64, .0)), - ('propane-1,2,3-triol', (.28, .22, .94, .98, .48, .96, .11, 1.21, .51, .62, .95, .31, .65)), - ('1,3-dimethylbenzene', (.293, .226, .318, .583, .241, .412, .055, .0, .11, .47, .62, .16, .0)), - ('1,3,5‐trimethylbenzene', (.294, .227, .318, .583, .241, .412, .055, .0, .13, .41, .58, .19, .0)), - ('1,4-dioxane', (.253, .202, .287, .548, .223, .377, .045, .0, .37, .49, .7, .44, .0)), - ('2-methylbutan-2-ol', (.245, .197, .614, .827, .381, .705, .075, .28, .93, .4, .83, .94, .1)), - ('2-methylpropan-1-ol', (.24, .194, .84, .94, .456, .887, .088, .79, .84, .4, .83, .83, .31)), - ('2-methylpropan-2-ol', (.234, .19, .793, .92, .442, .852, .084, .42, .93, .41, .83, .93, .15)), - ('2,2,4-trimethylpentane', (.237, .191, .242, .49, .195, .324, .037, .0, .0, .04, .53, .04, .0)), - ('3-methylbutan-1-ol', (.245, .197, .825, .934, .452, .876, .089, .84, .86, .4, .81, .86, .32)), - ('acetic acid', (.226, .184, .632, .837, .387, .72, .071, 1.12, .45, .64, .78, .39, .69)), - ('acetonitrile', (.21, .174, .921, .972, .479, .946, .083, .19, .4, .66, .9, .29, .04)), - ('benzene', (.293, .227, .297, .559, .229, .388, .052, .0, .1, .55, .67, .12, .0)), - ('benzenecarbonitrile', (.31, .24, .89, .96, .47, .93, .11, .0, .37, .9, .96, .28, .05)), - ('bromobenzene', (.323, .244, .595, .815, .373, .688, .091, .0, .06, .79, .82, .19, .0)), - ('butan-1-ol', (.241, .194, .846, .943, .458, .892, .089, .84, .84, .47, .84, .81, .34)), - ('butan-2-ol', (.24, .193, .838, .94, .456, .886, .088, .69, .8, .4, .84, .89, .22)), - ('butan-2-one', (.23, .187, .851, .945, .46, .895, .086, .06, .48, .6, .88, .52, .0)), - ('chlorobenzene', (.304, .233, .606, .822, .377, .698, .088, .0, .07, .68, .82, .18, .0)), - ('cyclohexane', (.255, .203, .254, .505, .202, .338, .041, .0, .0, .0, .56, .07, .0)), - ('dichloromethane', (.254, .202, .726, .888, .42, .799, .085, .13, .1, .82, .88, .18, .04)), - ('ethane-1,2-diol', (.259, .205, .924, .973, .48, .948, .099, .9, .52, .92, .93, .53, .72)), - ('ethanol', (.22, .181, .887, .959, .47, .922, .085, .86, .75, .54, .85, .66, .4)), - ('ethoxybenzene', (.3, .23, .52, .76, .34, .62, .08, .0, .3, .69, .74, .3, .0)), - ('ethoxyethane', (.215, .177, .516, .762, .34, .615, .06, .0, .47, .24, .69, .56, .0)), - ('ethyl acetate', (.228, .19, .63, .83, .38, .72, .071, .0, .45, .55, .8, .54, .0)), - ('ethyl benzoate', (.297, .229, .625, .833, .385, .714, .088, .0, .41, .74, .84, .42, .0)), - ('formamide', (.267, .211, .973, .991, .493, .982, .104, .71, .48, .97, .83, .41, .55)), - ('deuterium oxide', (.203, .169, .963, .987, .49, .975, .083, 1.17, .47, 1.09, .96, .44, 1.06)), - ('heptan-1-ol', (.255, .203, .775, .912, .437, .838, .089, .79, .82, .4, .8, .91, .3)), - ('heptane', (.236, .19, .235, .479, .19, .315, .036, .0, .0, -.08, .53, .08, .0)), - ('hexamethylphosphoramide', (.277, .217, .906, .967, .475, .935, .103, .0, 1.05, .87, .93, .81, .0)), - ('hexan-1-ol', (.251, .201, .804, .925, .446, .86, .089, .8, .84, .4, .81, .88, .32)), - ('hexane', (.227, .185, .227, .468, .185, .306, .034, .0, .0, -.11, .52, .06, .0)), - ('methanedithione', (.355, .262, .348, .615, .258, .444, .068, .0, .07, .61, .59, .1, .0)), - ('methanesulfinylmethane', (.283, .22, .938, .978, .484, .958, .107, .0, .76, 1.0, 1.0, .65, .07)), - ('methanol', (.202, .168, .913, .969, .477, .941, .08, .98, .66, .6, .86, .55, .61)), - ('methoxybenzene', (.3, .23, .52, .77, .34, .62, .08, .0, .32, .73, .82, .3, .08)), - ('N,N-dimethylacetamide', (.26, .21, .92, .97, .48, .95, .1, .0, .76, .88, .97, .61, .03)), - ('N,N-dimethylformamide', (.257, .205, .923, .973, .48, .947, .098, .0, .69, .88, .95, .61, .03)), - ('nitrobenzene', (.319, .242, .918, .971, .479, .944, .116, .0, .3, .86, .97, .24, .06)), - ('nitromethane', (.231, .188, .921, .972, .479, .946, .09, .22, .06, .75, .91, .24, .08)), - ('octan-1-ol', (.257, .204, .757, .903, .431, .824, .088, .77, .81, .4, .79, .92, .3)), - ('oxolan-2-one', (.26, .207, .927, .974, .481, .95, .099, .0, .49, .85, .99, .4, .06)), - ('1,4-epoxybutane', (.245, .197, .687, .868, .407, .767, .08, .0, .55, .55, .84, .59, .0)), - ('1,4-dimethylbenzene', (.29, .226, .302, .565, .232, .394, .052, .0, .12, .43, .62, .16, .0)), - ('pentan-1-ol', (.247, .198, .811, .928, .448, .866, .089, .84, .86, .4, .82, .86, .32)), - ('phenylmethanol', (.313, .238, .796, .921, .443, .854, .106, .6, .52, .98, .89, .46, .41)), - ('piperidine', (.27, .213, .62, .83, .383, .71, .081, .0, 1.04, .3, .74, .93, .0)), - ('propan-1-ol', (.234, .189, .866, .951, .464, .907, .088, .84, .9, .52, .85, .78, .37)), - ('propan-2-ol', (.229, .186, .863, .95, .463, .904, .086, .76, .84, .48, .85, .83, .28)), - ('propan-2-one', (.218, .179, .867, .951, .464, .907, .083, .08, .48, .62, .88, .48, .0)), - ('propanenitrile', (.222, .182, .901, .965, .474, .932, .086, .0, .37, .64, .88, .37, .03)), - ('pyridine', (.298, .229, .799, .923, .444, .856, .102, .0, .64, .87, .92, .58, .03)), - ('tetrachloromethane', (.272, .214, .292, .554, .226, .383, .048, .0, .1, .21, .63, .04, .0)), - ('tetrahydrothiophene 1,1-dioxide', (.285, .222, .934, .977, .483, .955, .107, .0, .39, .9, 1.0, .37, .05)), - ('toluene', (.291, .226, .315, .58, .24, .408, .054, .0, .11, .49, .66, .13, .0)), - ('trichloromethane', (.265, .209, .565, .796, .361, .66, .076, .2, .1, .58, .79, .07, .05)), - ('water', (.205, .17, .963, .987, .49, .975, .084, 1.17, .47, 1.09, .96, .03, 1.06)))) + ('1-phenylethan-1-one', (.31, .237, .845, .943, .458, .891, .109, .04, .49, .9, .9, .37, .04, 202, 20)), + ('1,2-dichloroethane', (.266, .21, .757, .903, .431, .824, .091, .0, .1, .81, .89, .13, .03, 83.5, -35.5)), + ('1,2-dimethoxyethane', (.23, .19, .67, .86, .4, .76, .08, .0, .41, .53, .79, .64, .0, 85, -58)), + ('propane-1,2,3-triol', (.28, .22, .94, .98, .48, .96, .11, 1.21, .51, .62, .95, .31, .65, 290, 18.2)), + ('1,3-dimethylbenzene', (.293, .226, .318, .583, .241, .412, .055, .0, .11, .47, .62, .16, .0, 139.1, -47.8)), + ('1,3,5‐trimethylbenzene', (.294, .227, .318, .583, .241, .412, .055, .0, .13, .41, .58, .19, .0, 164.7, -44.7)), + ('1,4-dioxane', (.253, .202, .287, .548, .223, .377, .045, .0, .37, .49, .7, .44, .0, 101.5, 11.8)), + ('2-methylbutan-2-ol', (.245, .197, .614, .827, .381, .705, .075, .28, .93, .4, .83, .94, .1, 102.4, -9.1)), + ('2-methylpropan-1-ol', (.24, .194, .84, .94, .456, .887, .088, .79, .84, .4, .83, .83, .31, 107.8, -108)), + ('2-methylpropan-2-ol', (.234, .19, .793, .92, .442, .852, .084, .42, .93, .41, .83, .93, .15, 82.4, 25.4)), + ('2,2,4-trimethylpentane', (.237, .191, .242, .49, .195, .324, .037, .0, .0, .04, .53, .04, .0, 99.2, -107.3)), + ('3-methylbutan-1-ol', (.245, .197, .825, .934, .452, .876, .089, .84, .86, .4, .81, .86, .32, 131.1, -117.2)), + ('acetic acid', (.226, .184, .632, .837, .387, .72, .071, 1.12, .45, .64, .78, .39, .69, 117.9, 16.6)), + ('acetonitrile', (.21, .174, .921, .972, .479, .946, .083, .19, .4, .66, .9, .29, .04, 81.6, -43.8)), + ('benzene', (.293, .227, .297, .559, .229, .388, .052, .0, .1, .55, .67, .12, .0, 80, 5.5)), + ('benzenecarbonitrile', (.31, .24, .89, .96, .47, .93, .11, .0, .37, .9, .96, .28, .05, 191.1, -12.7)), + ('bromobenzene', (.323, .244, .595, .815, .373, .688, .091, .0, .06, .79, .82, .19, .0, 156, -30.6)), + ('butan-1-ol', (.241, .194, .846, .943, .458, .892, .089, .84, .84, .47, .84, .81, .34, 117.85, -89.8)), + ('butan-2-ol', (.24, .193, .838, .94, .456, .886, .088, .69, .8, .4, .84, .89, .22, 99.5, -114.7)), + ('butan-2-one', (.23, .187, .851, .945, .46, .895, .086, .06, .48, .6, .88, .52, .0, 79.5, -86.6)), + ('chlorobenzene', (.304, .233, .606, .822, .377, .698, .088, .0, .07, .68, .82, .18, .0, -131.7, -45.2)), + ('cyclohexane', (.255, .203, .254, .505, .202, .338, .041, .0, .0, .0, .56, .07, .0, 80.7, 6.6)), + ('dichloromethane', (.254, .202, .726, .888, .42, .799, .085, .13, .1, .82, .88, .18, .04, 40, -95.1)), + ('ethane-1,2-diol', (.259, .205, .924, .973, .48, .948, .099, .9, .52, .92, .93, .53, .72, 197.3, -13)), + ('ethanol', (.22, .181, .887, .959, .47, .922, .085, .86, .75, .54, .85, .66, .4, 78.2, -114.1)), + ('ethoxybenzene', (.3, .23, .52, .76, .34, .62, .08, .0, .3, .69, .74, .3, .0, 169.8, -29.5)), + ('ethoxyethane', (.215, .177, .516, .762, .34, .615, .06, .0, .47, .24, .69, .56, .0, 34.6, -116.3)), + ('ethyl acetate', (.228, .19, .63, .83, .38, .72, .071, .0, .45, .55, .8, .54, .0, 77.1, -83.6)), + ('ethyl benzoate', (.297, .229, .625, .833, .385, .714, .088, .0, .41, .74, .84, .42, .0, 212, -34)), + ('formamide', (.267, .211, .973, .991, .493, .982, .104, .71, .48, .97, .83, .41, .55, 220, 2.55)), + ('deuterium oxide', (.203, .169, .963, .987, .49, .975, .083, 1.17, .47, 1.09, .96, .44, 1.06, 101.42, 3.81)), + ('heptan-1-ol', (.255, .203, .775, .912, .437, .838, .089, .79, .82, .4, .8, .91, .3, 176.4, -34)), + ('heptane', (.236, .19, .235, .479, .19, .315, .036, .0, .0, -.08, .53, .08, .0, 98.5, -90.6)), + ('hexamethylphosphoramide', (.277, .217, .906, .967, .475, .935, .103, .0, 1.05, .87, .93, .81, .0, 232.5, 7.2)), + ('hexan-1-ol', (.251, .201, .804, .925, .446, .86, .089, .8, .84, .4, .81, .88, .32, 157.6, -44.6)), + ('hexane', (.227, .185, .227, .468, .185, .306, .034, .0, .0, -.11, .52, .06, .0, 68.7, -95.3)), + ('methanedithione', (.355, .262, .348, .615, .258, .444, .068, .0, .07, .61, .59, .1, .0, 46, -111.5)), + ('methanesulfinylmethane', (.283, .22, .938, .978, .484, .958, .107, .0, .76, 1.0, 1.0, .65, .07, 189, 18.5)), + ('methanol', (.202, .168, .913, .969, .477, .941, .08, .98, .66, .6, .86, .55, .61, 64.7, -97.6)), + ('methoxybenzene', (.3, .23, .52, .77, .34, .62, .08, .0, .32, .73, .82, .3, .08, 153.7, -37.5)), + ('N,N-dimethylacetamide', (.26, .21, .92, .97, .48, .95, .1, .0, .76, .88, .97, .61, .03, 165, -20)), + ('N,N-dimethylformamide', (.257, .205, .923, .973, .48, .947, .098, .0, .69, .88, .95, .61, .03, 153, -60.4)), + ('nitrobenzene', (.319, .242, .918, .971, .479, .944, .116, .0, .3, .86, .97, .24, .06, 210.8, 5.7)), + ('nitromethane', (.231, .188, .921, .972, .479, .946, .09, .22, .06, .75, .91, .24, .08, 101.1, -28.5)), + ('octan-1-ol', (.257, .204, .757, .903, .431, .824, .088, .77, .81, .4, .79, .92, .3, 195.1, -15.5)), + ('oxolan-2-one', (.26, .207, .927, .974, .481, .95, .099, .0, .49, .85, .99, .4, .06, 204, -43.3)), + ('1,4-epoxybutane', (.245, .197, .687, .868, .407, .767, .08, .0, .55, .55, .84, .59, .0, 65, -108.3)), + ('1,4-dimethylbenzene', (.29, .226, .302, .565, .232, .394, .052, .0, .12, .43, .62, .16, .0, 138.3, 13.2)), + ('pentan-1-ol', (.247, .198, .811, .928, .448, .866, .089, .84, .86, .4, .82, .86, .32, 137.9, -78.9)), + ('phenylmethanol', (.313, .238, .796, .921, .443, .854, .106, .6, .52, .98, .89, .46, .41, 205.3, -15.2)), + ('piperidine', (.27, .213, .62, .83, .383, .71, .081, .0, 1.04, .3, .74, .93, .0, 106, -7)), + ('propan-1-ol', (.234, .189, .866, .951, .464, .907, .088, .84, .9, .52, .85, .78, .37, 97.2, -126.1)), + ('propan-2-ol', (.229, .186, .863, .95, .463, .904, .086, .76, .84, .48, .85, .83, .28, 82.9, -89.5)), + ('propan-2-one', (.218, .179, .867, .951, .464, .907, .083, .08, .48, .62, .88, .48, .0, 55.75, -95.55)), + ('propanenitrile', (.222, .182, .901, .965, .474, .932, .086, .0, .37, .64, .88, .37, .03, 97.1, -92.8)), + ('pyridine', (.298, .229, .799, .923, .444, .856, .102, .0, .64, .87, .92, .58, .03, 115.2, -41.6)), + ('tetrachloromethane', (.272, .214, .292, .554, .226, .383, .048, .0, .1, .21, .63, .04, .0, 76.8, -23)), + ('tetrahydrothiophene 1,1-dioxide', (.285, .222, .934, .977, .483, .955, .107, .0, .39, .9, 1.0, .37, .05, 285, 27.6)), + ('toluene', (.291, .226, .315, .58, .24, .408, .054, .0, .11, .49, .66, .13, .0, 110.6, -94.9)), + ('trichloromethane', (.265, .209, .565, .796, .361, .66, .076, .2, .1, .58, .79, .07, .05, 61.1, -63.6)), + ('water', (.205, .17, .963, .987, .49, .975, .084, 1.17, .47, 1.09, .96, .03, 1.06, 100, 0)))) __all__ = ['SolventVectorizer'] diff --git a/Fragmentor/doc/Fragmentor2017_Manual.pdf b/Fragmentor/doc/Fragmentor2017_Manual.pdf deleted file mode 100644 index 8542259..0000000 Binary files a/Fragmentor/doc/Fragmentor2017_Manual.pdf and /dev/null differ diff --git a/doc/applicability_domain.rst b/doc/applicability_domain.rst deleted file mode 100644 index dd43c01..0000000 --- a/doc/applicability_domain.rst +++ /dev/null @@ -1,8 +0,0 @@ -CIMtools\.applicability_domain package -====================================== - -.. automodule:: CIMtools.applicability_domain - :members: - :undoc-members: - :show-inheritance: - :inherited-members: diff --git a/doc/tutorial/metric_constants.rst b/doc/tutorial/metric_constants.rst deleted file mode 100644 index b93643d..0000000 --- a/doc/tutorial/metric_constants.rst +++ /dev/null @@ -1,27 +0,0 @@ -Metric constants conversion -=========================== - -CIMtools\.metric_constants subpackage includes values of masses, volumes, etc for converting to SI values. - -Usage is very simple:: - - from CIMtools.metric_constants import * - - # convert pounds into kilograms - 2 * lb - - # reverse convert SI into pounds - 2 / lb - - # temperature conversion - 25 * C # now T in Kelvin - 298 / F # Kelvin (SI) into Fahrenheit - -According to order of math operation, power has higher priority. For prevent errors use ():: - - 2 * C ** 2 # wrong - (2 * C) ** 2 # first convert, after square - 2 * C * 3 # right - - -(C) Dr. Ramil Nugmanov