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The Chemistry Development Kit
https://cdk.github.io/
GNU Lesser General Public License v2.1
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getInchi() #570

Closed likusta closed 5 years ago

likusta commented 5 years ago

Hello!

I have problem with transfer to inchi. The molecule normally reads from the file, but the transfer to the inchi return null.

CODE

IAtomContainer molecule; String filename = "C:\Users\-\Desktop\example3.MOL"; InputStream in = new FileInputStream(filename); MDLV2000Reader mdlv2000Reader = new MDLV2000Reader(in); molecule = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class); molecule =(IAtomContainer) mdlv2000Reader.read(molecule); System.out.println("MOLECULE IAtomContainer"+molecule); System.out.println(InChIGeneratorFactory.getInstance().getInChIGenerator(molecule).getInchi());mdlv2000Reader.close();

CONSOLE

MOLECULE IAtomContainerAtomContainer(707806938, #A:74, AtomRef{Atom(476402209, S:C, H:1, SP:1, 2D:[(0.6718, -4.563)], AtomType(476402209, FC:0, EV:4, Isotope(476402209, Element(476402209, S:C, AN:6))))}, AtomRef{Atom(1490180672, S:C, H:1, SP:1, 2D:[(0.6718, -3.738)], AtomType(1490180672, FC:0, EV:4, Isotope(1490180672, Element(1490180672, S:C, AN:6))))}, AtomRef{Atom(705265961, S:C, H:2, SP:0, 2D:[(-0.1128, -3.4831)], AtomType(705265961, FC:0, EV:4, Isotope(705265961, Element(705265961, S:C, AN:6))))}, AtomRef{Atom(428746855, S:C, H:0, SP:0, 2D:[(-0.5978, -4.1505)], AtomType(428746855, FC:0, EV:4, Isotope(428746855, Element(428746855, S:C, AN:6))))}, AtomRef{Atom(317983781, S:C, H:0, SP:0, 2D:[(-0.1128, -4.818)], AtomType(317983781, FC:0, EV:4, Isotope(317983781, Element(317983781, S:C, AN:6))))}, AtomRef{Atom(987405879, S:C, H:0, SP:0, 2D:[(-1.4182, -4.2367)], AtomType(987405879, FC:0, EV:4, Isotope(987405879, Element(987405879, S:C, AN:6))))}, AtomRef{Atom(1555845260, S:C, H:1, SP:0, 2D:[(-1.7538, -4.9904)], AtomType(1555845260, FC:0, EV:4, Isotope(1555845260, Element(1555845260, S:C, AN:6))))}, AtomRef{Atom(874088044, S:C, H:1, SP:0, 2D:[(-1.2689, -5.6579)], AtomType(874088044, FC:0, EV:4, Isotope(874088044, Element(874088044, S:C, AN:6))))}, AtomRef{Atom(104739310, S:C, H:1, SP:0, 2D:[(-0.4484, -5.5716)], AtomType(104739310, FC:0, EV:4, Isotope(104739310, Element(104739310, S:C, AN:6))))}, AtomRef{Atom(1761291320, S:C, H:0, SP:0, 2D:[(-2.0016, -3.6534)], AtomType(1761291320, FC:0, EV:4, Isotope(1761291320, Element(1761291320, S:C, AN:6))))}, AtomRef{Atom(1451043227, S:O, H:0, SP:0, 2D:[(1.3863, -4.9755)], AtomType(1451043227, FC:0, EV:2, Isotope(1451043227, Element(1451043227, S:O, AN:8))))}, AtomRef{Atom(783286238, S:C, H:0, SP:0, 2D:[(2.1007, -4.563)], AtomType(783286238, FC:0, EV:4, Isotope(783286238, Element(783286238, S:C, AN:6))))}, AtomRef{Atom(1500056228, S:C, H:0, SP:0, 2D:[(2.8152, -4.9755)], AtomType(1500056228, FC:0, EV:4, Isotope(1500056228, Element(1500056228, S:C, AN:6))))}, AtomRef{Atom(1749186397, S:C, H:0, SP:0, 2D:[(3.5297, -4.563)], AtomType(1749186397, FC:0, EV:4, Isotope(1749186397, Element(1749186397, S:C, AN:6))))}, AtomRef{Atom(1464642111, S:C, H:0, SP:0, 2D:[(3.5297, -3.738)], AtomType(1464642111, FC:0, EV:4, Isotope(1464642111, Element(1464642111, S:C, AN:6))))}, AtomRef{Atom(105704967, S:C, H:0, SP:0, 2D:[(2.8152, -3.3255)], AtomType(105704967, FC:0, EV:4, Isotope(105704967, Element(105704967, S:C, AN:6))))}, AtomRef{Atom(392292416, S:C, H:0, SP:0, 2D:[(2.1007, -3.738)], AtomType(392292416, FC:0, EV:4, Isotope(392292416, Element(392292416, S:C, AN:6))))}, AtomRef{PseudoAtom(1818402158, R2a, Atom(1818402158, S:R, H:0, SP:0, 2D:[(2.8152, -5.8005)], AtomType(1818402158, FC:0, EV:1, Isotope(1818402158, Element(1818402158, S:R, AN:0)))))}, AtomRef{PseudoAtom(1590550415, R2c, Atom(1590550415, S:R, H:0, SP:0, 2D:[(4.2441, -4.9755)], AtomType(1590550415, FC:0, EV:1, Isotope(1590550415, Element(1590550415, S:R, AN:0)))))}, AtomRef{Atom(1058025095, S:C, H:2, SP:0, 2D:[(4.2441, -3.3255)], AtomType(1058025095, FC:0, EV:4, Isotope(1058025095, Element(1058025095, S:C, AN:6))))}, AtomRef{PseudoAtom(665576141, R3., Atom(665576141, S:R, H:0, SP:0, 2D:[(4.9586, -3.738)], AtomType(665576141, FC:0, EV:1, Isotope(665576141, Element(665576141, S:R, AN:0)))))}, AtomRef{PseudoAtom(1599771323, R4, Atom(1599771323, S:R, H:0, SP:0, 2D:[(2.8152, -2.5005)], AtomType(1599771323, FC:0, EV:1, Isotope(1599771323, Element(1599771323, S:R, AN:0)))))}, AtomRef{PseudoAtom(1876631416, R2b, Atom(1876631416, S:R, H:0, SP:0, 2D:[(1.3863, -3.3255)], AtomType(1876631416, FC:0, EV:1, Isotope(1876631416, Element(1876631416, S:R, AN:0)))))}, AtomRef{Atom(1359044626, S:C, H:0, SP:0, 2D:[(-1.7881, -2.8565)], AtomType(1359044626, FC:0, EV:4, Isotope(1359044626, Element(1359044626, S:C, AN:6))))}, AtomRef{Atom(692342133, S:C, H:0, SP:0, 2D:[(-2.3714, -2.2731)], AtomType(692342133, FC:0, EV:4, Isotope(692342133, Element(692342133, S:C, AN:6))))}, AtomRef{Atom(578866604, S:C, H:0, SP:0, 2D:[(-3.1683, -2.4867)], AtomType(578866604, FC:0, EV:4, Isotope(578866604, Element(578866604, S:C, AN:6))))}, AtomRef{Atom(353842779, S:C, H:0, SP:0, 2D:[(-3.3818, -3.2835)], AtomType(353842779, FC:0, EV:4, Isotope(353842779, Element(353842779, S:C, AN:6))))}, AtomRef{Atom(1338823963, S:C, H:0, SP:0, 2D:[(-2.7985, -3.8669)], AtomType(1338823963, FC:0, EV:4, Isotope(1338823963, Element(1338823963, S:C, AN:6))))}, AtomRef{PseudoAtom(1156060786, R1b, Atom(1156060786, S:R, H:0, SP:0, 2D:[(-0.9912, -2.643)], AtomType(1156060786, FC:0, EV:1, Isotope(1156060786, Element(1156060786, S:R, AN:0)))))}, AtomRef{PseudoAtom(1612799726, R1c, Atom(1612799726, S:R, H:0, SP:0, 2D:[(-2.1579, -1.4762)], AtomType(1612799726, FC:0, EV:1, Isotope(1612799726, Element(1612799726, S:R, AN:0)))))}, AtomRef{PseudoAtom(1286084959, R1d, Atom(1286084959, S:R, H:0, SP:0, 2D:[(-3.7517, -1.9033)], AtomType(1286084959, FC:0, EV:1, Isotope(1286084959, Element(1286084959, S:R, AN:0)))))}, AtomRef{PseudoAtom(1709537756, L, Atom(1709537756, S:R, H:0, SP:0, 2D:[(-4.1787, -3.4971)], AtomType(1709537756, FC:0, EV:2, Isotope(1709537756, Element(1709537756, S:R, AN:0)))))}, AtomRef{PseudoAtom(1639622804, R1a, Atom(1639622804, S:R, H:0, SP:0, 2D:[(-3.012, -4.6638)], AtomType(1639622804, FC:0, EV:1, Isotope(1639622804, Element(1639622804, S:R, AN:0)))))}, AtomRef{PseudoAtom(184966243, Z, Atom(184966243, S:R, H:0, SP:0, 2D:[(-5.0037, -3.4971)], AtomType(184966243, FC:0, EV:1, Isotope(184966243, Element(184966243, S:R, AN:0)))))}, AtomRef{Atom(124313277, S:F, H:0, SP:0, 2D:[(0.6718, -2.913)], AtomType(124313277, FC:0, EV:1, Isotope(124313277, Element(124313277, S:F, AN:9))))}, AtomRef{Atom(1225616405, S:C, H:3, SP:0, 2D:[(-0.9138, -5.2784)], AtomType(1225616405, FC:0, EV:4, Isotope(1225616405, Element(1225616405, S:C, AN:6))))}, AtomRef{PseudoAtom(2101842856, (R\S5\n)\sn, Atom(2101842856, S:R, H:0, SP:0, 2D:[(-0.9138, -6.1034)], AtomType(2101842856, FC:0, EV:1, Isotope(2101842856, Element(2101842856, S:R, AN:0)))))}, AtomRef{Atom(460332449, S:C, H:1, SP:1, 2D:[(0.7169, 3.0167)], AtomType(460332449, FC:0, EV:4, Isotope(460332449, Element(460332449, S:C, AN:6))))}, AtomRef{Atom(1919892312, S:C, H:1, SP:2, 2D:[(0.7169, 3.8417)], AtomType(1919892312, FC:0, EV:4, Isotope(1919892312, Element(1919892312, S:C, AN:6))))}, AtomRef{Atom(1151020327, S:C, H:2, SP:0, 2D:[(-0.0677, 4.0966)], AtomType(1151020327, FC:0, EV:4, Isotope(1151020327, Element(1151020327, S:C, AN:6))))}, AtomRef{Atom(88579647, S:C, H:0, SP:0, 2D:[(-0.5526, 3.4292)], AtomType(88579647, FC:0, EV:4, Isotope(88579647, Element(88579647, S:C, AN:6))))}, AtomRef{Atom(654845766, S:C, H:0, SP:0, 2D:[(-0.0677, 2.7617)], AtomType(654845766, FC:0, EV:4, Isotope(654845766, Element(654845766, S:C, AN:6))))}, AtomRef{Atom(1712536284, S:C, H:0, SP:0, 2D:[(-1.3731, 3.3429)], AtomType(1712536284, FC:0, EV:4, Isotope(1712536284, Element(1712536284, S:C, AN:6))))}, AtomRef{Atom(2080166188, S:C, H:1, SP:0, 2D:[(-1.7087, 2.5893)], AtomType(2080166188, FC:0, EV:4, Isotope(2080166188, Element(2080166188, S:C, AN:6))))}, AtomRef{Atom(1123225098, S:C, H:1, SP:0, 2D:[(-1.2237, 1.9218)], AtomType(1123225098, FC:0, EV:4, Isotope(1123225098, Element(1123225098, S:C, AN:6))))}, AtomRef{Atom(606548741, S:C, H:1, SP:0, 2D:[(-0.4033, 2.0081)], AtomType(606548741, FC:0, EV:4, Isotope(606548741, Element(606548741, S:C, AN:6))))}, AtomRef{Atom(1528637575, S:C, H:0, SP:0, 2D:[(-1.9565, 3.9263)], AtomType(1528637575, FC:0, EV:4, Isotope(1528637575, Element(1528637575, S:C, AN:6))))}, AtomRef{Atom(1190524793, S:O, H:0, SP:0, 2D:[(1.4314, 2.6042)], AtomType(1190524793, FC:0, EV:2, Isotope(1190524793, Element(1190524793, S:O, AN:8))))}, AtomRef{Atom(472654579, S:C, H:0, SP:0, 2D:[(2.1459, 3.0167)], AtomType(472654579, FC:0, EV:4, Isotope(472654579, Element(472654579, S:C, AN:6))))}, AtomRef{Atom(26117480, S:C, H:0, SP:0, 2D:[(2.8603, 2.6042)], AtomType(26117480, FC:0, EV:4, Isotope(26117480, Element(26117480, S:C, AN:6))))}, AtomRef{Atom(870698190, S:C, H:0, SP:0, 2D:[(3.5748, 3.0167)], AtomType(870698190, FC:0, EV:4, Isotope(870698190, Element(870698190, S:C, AN:6))))}, AtomRef{Atom(1514322932, S:C, H:0, SP:0, 2D:[(3.5748, 3.8417)], AtomType(1514322932, FC:0, EV:4, Isotope(1514322932, Element(1514322932, S:C, AN:6))))}, AtomRef{Atom(654582261, S:C, H:0, SP:0, 2D:[(2.8603, 4.2542)], AtomType(654582261, FC:0, EV:4, Isotope(654582261, Element(654582261, S:C, AN:6))))}, AtomRef{Atom(1389647288, S:C, H:0, SP:0, 2D:[(2.1459, 3.8417)], AtomType(1389647288, FC:0, EV:4, Isotope(1389647288, Element(1389647288, S:C, AN:6))))}, AtomRef{PseudoAtom(1330278544, R2a, Atom(1330278544, S:R, H:0, SP:0, 2D:[(2.8603, 1.7792)], AtomType(1330278544, FC:0, EV:1, Isotope(1330278544, Element(1330278544, S:R, AN:0)))))}, AtomRef{PseudoAtom(1634198, R2c, Atom(1634198, S:R, H:0, SP:0, 2D:[(4.2893, 2.6042)], AtomType(1634198, FC:0, EV:1, Isotope(1634198, Element(1634198, S:R, AN:0)))))}, AtomRef{Atom(110456297, S:C, H:2, SP:0, 2D:[(4.2893, 4.2542)], AtomType(110456297, FC:0, EV:4, Isotope(110456297, Element(110456297, S:C, AN:6))))}, AtomRef{PseudoAtom(1989972246, R3, Atom(1989972246, S:R, H:0, SP:0, 2D:[(5.0037, 3.8417)], AtomType(1989972246, FC:0, EV:1, Isotope(1989972246, Element(1989972246, S:R, AN:0)))))}, AtomRef{PseudoAtom(1791930789, R4, Atom(1791930789, S:R, H:0, SP:0, 2D:[(2.8603, 5.0792)], AtomType(1791930789, FC:0, EV:1, Isotope(1791930789, Element(1791930789, S:R, AN:0)))))}, AtomRef{PseudoAtom(762152757, R2b, Atom(762152757, S:R, H:0, SP:0, 2D:[(1.4314, 4.2542)], AtomType(762152757, FC:0, EV:1, Isotope(762152757, Element(762152757, S:R, AN:0)))))}, AtomRef{Atom(12209492, S:C, H:0, SP:0, 2D:[(-1.743, 4.7232)], AtomType(12209492, FC:0, EV:4, Isotope(12209492, Element(12209492, S:C, AN:6))))}, AtomRef{Atom(314337396, S:C, H:0, SP:0, 2D:[(-2.3263, 5.3066)], AtomType(314337396, FC:0, EV:4, Isotope(314337396, Element(314337396, S:C, AN:6))))}, AtomRef{Atom(232824863, S:C, H:0, SP:0, 2D:[(-3.1232, 5.093)], AtomType(232824863, FC:0, EV:4, Isotope(232824863, Element(232824863, S:C, AN:6))))}, AtomRef{Atom(1282788025, S:C, H:0, SP:0, 2D:[(-3.3367, 4.2961)], AtomType(1282788025, FC:0, EV:4, Isotope(1282788025, Element(1282788025, S:C, AN:6))))}, AtomRef{Atom(519569038, S:C, H:0, SP:0, 2D:[(-2.7534, 3.7128)], AtomType(519569038, FC:0, EV:4, Isotope(519569038, Element(519569038, S:C, AN:6))))}, AtomRef{PseudoAtom(1870252780, R1b, Atom(1870252780, S:R, H:0, SP:0, 2D:[(-0.9461, 4.9367)], AtomType(1870252780, FC:0, EV:1, Isotope(1870252780, Element(1870252780, S:R, AN:0)))))}, AtomRef{PseudoAtom(1729199940, R1c, Atom(1729199940, S:R, H:0, SP:0, 2D:[(-2.1128, 6.1034)], AtomType(1729199940, FC:0, EV:1, Isotope(1729199940, Element(1729199940, S:R, AN:0)))))}, AtomRef{PseudoAtom(97730845, R1d, Atom(97730845, S:R, H:0, SP:0, 2D:[(-3.7066, 5.6764)], AtomType(97730845, FC:0, EV:1, Isotope(97730845, Element(97730845, S:R, AN:0)))))}, AtomRef{PseudoAtom(611437735, L, Atom(611437735, S:R, H:0, SP:0, 2D:[(-4.1336, 4.0826)], AtomType(611437735, FC:0, EV:2, Isotope(611437735, Element(611437735, S:R, AN:0)))))}, AtomRef{PseudoAtom(100555887, R1a, Atom(100555887, S:R, H:0, SP:0, 2D:[(-2.9669, 2.9159)], AtomType(100555887, FC:0, EV:1, Isotope(100555887, Element(100555887, S:R, AN:0)))))}, AtomRef{PseudoAtom(1769597131, Z, Atom(1769597131, S:R, H:0, SP:0, 2D:[(-4.9586, 4.0826)], AtomType(1769597131, FC:0, EV:1, Isotope(1769597131, Element(1769597131, S:R, AN:0)))))}, AtomRef{Atom(1983747920, S:F, H:0, SP:0, 2D:[(0.7169, 4.6667)], AtomType(1983747920, FC:0, EV:1, Isotope(1983747920, Element(1983747920, S:F, AN:9))))}, AtomRef{Atom(1543727556, S:C, H:3, SP:0, 2D:[(-0.8686, 2.3012)], AtomType(1543727556, FC:0, EV:4, Isotope(1543727556, Element(1543727556, S:C, AN:6))))}, AtomRef{PseudoAtom(736709391, (R\S5\n)\sn, Atom(736709391, S:R, H:0, SP:0, 2D:[(-0.8686, 1.4762)], AtomType(736709391, FC:0, EV:1, Isotope(736709391, Element(736709391, S:R, AN:0)))))}, #B:78, BondRef{Bond(225493257, #O:SINGLE, #S:NONE, #A:2, Atom(476402209, S:C, H:1, SP:1, 2D:[(0.6718, -4.563)], AtomType(476402209, FC:0, EV:4, Isotope(476402209, Element(476402209, S:C, AN:6)))), Atom(1490180672, S:C, H:1, SP:1, 2D:[(0.6718, -3.738)], AtomType(1490180672, FC:0, EV:4, Isotope(1490180672, Element(1490180672, S:C, AN:6)))), ElectronContainer(225493257EC:2))}, BondRef{Bond(401424608, #O:SINGLE, #S:NONE, #A:2, Atom(1490180672, S:C, H:1, SP:1, 2D:[(0.6718, -3.738)], AtomType(1490180672, FC:0, EV:4, Isotope(1490180672, Element(1490180672, S:C, AN:6)))), Atom(705265961, S:C, H:2, SP:0, 2D:[(-0.1128, -3.4831)], AtomType(705265961, FC:0, EV:4, Isotope(705265961, Element(705265961, S:C, AN:6)))), ElectronContainer(401424608EC:2))}, BondRef{Bond(1348949648, #O:SINGLE, #S:NONE, #A:2, Atom(705265961, S:C, H:2, SP:0, 2D:[(-0.1128, -3.4831)], AtomType(705265961, FC:0, EV:4, Isotope(705265961, Element(705265961, S:C, AN:6)))), Atom(428746855, S:C, H:0, SP:0, 2D:[(-0.5978, -4.1505)], AtomType(428746855, FC:0, EV:4, Isotope(428746855, Element(428746855, S:C, AN:6)))), ElectronContainer(1348949648EC:2))}, BondRef{Bond(834133664, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(428746855, S:C, H:0, SP:0, 2D:[(-0.5978, -4.1505)], AtomType(428746855, FC:0, EV:4, Isotope(428746855, Element(428746855, S:C, AN:6)))), Atom(317983781, S:C, H:0, SP:0, 2D:[(-0.1128, -4.818)], AtomType(317983781, FC:0, EV:4, Isotope(317983781, Element(317983781, S:C, AN:6)))), ElectronContainer(834133664EC:4))}, BondRef{Bond(985934102, #O:SINGLE, #S:NONE, #A:2, Atom(317983781, S:C, H:0, SP:0, 2D:[(-0.1128, -4.818)], AtomType(317983781, FC:0, EV:4, Isotope(317983781, Element(317983781, S:C, AN:6)))), Atom(476402209, S:C, H:1, SP:1, 2D:[(0.6718, -4.563)], AtomType(476402209, FC:0, EV:4, Isotope(476402209, Element(476402209, S:C, AN:6)))), ElectronContainer(985934102EC:2))}, BondRef{Bond(1205044462, #O:SINGLE, #S:NONE, #A:2, Atom(428746855, S:C, H:0, SP:0, 2D:[(-0.5978, -4.1505)], AtomType(428746855, FC:0, EV:4, Isotope(428746855, Element(428746855, S:C, AN:6)))), Atom(987405879, S:C, H:0, SP:0, 2D:[(-1.4182, -4.2367)], AtomType(987405879, FC:0, EV:4, Isotope(987405879, Element(987405879, S:C, AN:6)))), ElectronContainer(1205044462EC:2))}, BondRef{Bond(761960786, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(987405879, S:C, H:0, SP:0, 2D:[(-1.4182, -4.2367)], AtomType(987405879, FC:0, EV:4, Isotope(987405879, Element(987405879, S:C, AN:6)))), Atom(1555845260, S:C, H:1, SP:0, 2D:[(-1.7538, -4.9904)], AtomType(1555845260, FC:0, EV:4, Isotope(1555845260, Element(1555845260, S:C, AN:6)))), ElectronContainer(761960786EC:4))}, BondRef{Bond(581374081, #O:SINGLE, #S:NONE, #A:2, Atom(1555845260, S:C, H:1, SP:0, 2D:[(-1.7538, -4.9904)], AtomType(1555845260, FC:0, EV:4, Isotope(1555845260, Element(1555845260, S:C, AN:6)))), Atom(874088044, S:C, H:1, SP:0, 2D:[(-1.2689, -5.6579)], AtomType(874088044, FC:0, EV:4, Isotope(874088044, Element(874088044, S:C, AN:6)))), ElectronContainer(581374081EC:2))}, BondRef{Bond(959447386, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(874088044, S:C, H:1, SP:0, 2D:[(-1.2689, -5.6579)], AtomType(874088044, FC:0, EV:4, Isotope(874088044, Element(874088044, S:C, AN:6)))), Atom(104739310, S:C, H:1, SP:0, 2D:[(-0.4484, -5.5716)], AtomType(104739310, FC:0, EV:4, Isotope(104739310, Element(104739310, S:C, AN:6)))), ElectronContainer(959447386EC:4))}, BondRef{Bond(1654589030, #O:SINGLE, #S:NONE, #A:2, Atom(104739310, S:C, H:1, SP:0, 2D:[(-0.4484, -5.5716)], AtomType(104739310, FC:0, EV:4, Isotope(104739310, Element(104739310, S:C, AN:6)))), Atom(317983781, S:C, H:0, SP:0, 2D:[(-0.1128, -4.818)], AtomType(317983781, FC:0, EV:4, Isotope(317983781, Element(317983781, S:C, AN:6)))), ElectronContainer(1654589030EC:2))}, BondRef{Bond(466002798, #O:SINGLE, #S:NONE, #A:2, Atom(987405879, S:C, H:0, SP:0, 2D:[(-1.4182, -4.2367)], AtomType(987405879, FC:0, EV:4, Isotope(987405879, Element(987405879, S:C, AN:6)))), Atom(1761291320, S:C, H:0, SP:0, 2D:[(-2.0016, -3.6534)], AtomType(1761291320, FC:0, EV:4, Isotope(1761291320, Element(1761291320, S:C, AN:6)))), ElectronContainer(466002798EC:2))}, BondRef{Bond(33524623, #O:SINGLE, #S:DOWN, #A:2, Atom(476402209, S:C, H:1, SP:1, 2D:[(0.6718, -4.563)], AtomType(476402209, FC:0, EV:4, Isotope(476402209, Element(476402209, S:C, AN:6)))), Atom(1451043227, S:O, H:0, SP:0, 2D:[(1.3863, -4.9755)], AtomType(1451043227, FC:0, EV:2, Isotope(1451043227, Element(1451043227, S:O, AN:8)))), ElectronContainer(33524623EC:2))}, BondRef{Bond(947679291, #O:SINGLE, #S:NONE, #A:2, Atom(1451043227, S:O, H:0, SP:0, 2D:[(1.3863, -4.9755)], AtomType(1451043227, FC:0, EV:2, Isotope(1451043227, Element(1451043227, S:O, AN:8)))), Atom(783286238, S:C, H:0, SP:0, 2D:[(2.1007, -4.563)], AtomType(783286238, FC:0, EV:4, Isotope(783286238, Element(783286238, S:C, AN:6)))), ElectronContainer(947679291EC:2))}, BondRef{Bond(575335780, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(783286238, S:C, H:0, SP:0, 2D:[(2.1007, -4.563)], AtomType(783286238, FC:0, EV:4, Isotope(783286238, Element(783286238, S:C, AN:6)))), Atom(1500056228, S:C, H:0, SP:0, 2D:[(2.8152, -4.9755)], AtomType(1500056228, FC:0, EV:4, Isotope(1500056228, Element(1500056228, S:C, AN:6)))), ElectronContainer(575335780EC:4))}, BondRef{Bond(205125520, #O:SINGLE, #S:NONE, #A:2, Atom(1500056228, S:C, H:0, SP:0, 2D:[(2.8152, -4.9755)], AtomType(1500056228, FC:0, EV:4, Isotope(1500056228, Element(1500056228, S:C, AN:6)))), Atom(1749186397, S:C, H:0, SP:0, 2D:[(3.5297, -4.563)], AtomType(1749186397, FC:0, EV:4, Isotope(1749186397, Element(1749186397, S:C, AN:6)))), ElectronContainer(205125520EC:2))}, BondRef{Bond(1911006827, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(1749186397, S:C, H:0, SP:0, 2D:[(3.5297, -4.563)], AtomType(1749186397, FC:0, EV:4, Isotope(1749186397, Element(1749186397, S:C, AN:6)))), Atom(1464642111, S:C, H:0, SP:0, 2D:[(3.5297, -3.738)], AtomType(1464642111, FC:0, EV:4, Isotope(1464642111, Element(1464642111, S:C, AN:6)))), ElectronContainer(1911006827EC:4))}, BondRef{Bond(717356484, #O:SINGLE, #S:NONE, #A:2, Atom(1464642111, S:C, H:0, SP:0, 2D:[(3.5297, -3.738)], AtomType(1464642111, FC:0, EV:4, Isotope(1464642111, Element(1464642111, S:C, AN:6)))), Atom(105704967, S:C, H:0, SP:0, 2D:[(2.8152, -3.3255)], AtomType(105704967, FC:0, EV:4, Isotope(105704967, Element(105704967, S:C, AN:6)))), ElectronContainer(717356484EC:2))}, BondRef{Bond(1595212853, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(105704967, S:C, H:0, SP:0, 2D:[(2.8152, -3.3255)], AtomType(105704967, FC:0, EV:4, Isotope(105704967, Element(105704967, S:C, AN:6)))), Atom(392292416, S:C, H:0, SP:0, 2D:[(2.1007, -3.738)], AtomType(392292416, FC:0, EV:4, Isotope(392292416, Element(392292416, S:C, AN:6)))), ElectronContainer(1595212853EC:4))}, BondRef{Bond(475266352, #O:SINGLE, #S:NONE, #A:2, Atom(392292416, S:C, H:0, SP:0, 2D:[(2.1007, -3.738)], AtomType(392292416, FC:0, EV:4, Isotope(392292416, Element(392292416, S:C, AN:6)))), Atom(783286238, S:C, H:0, SP:0, 2D:[(2.1007, -4.563)], AtomType(783286238, FC:0, EV:4, Isotope(783286238, Element(783286238, S:C, AN:6)))), ElectronContainer(475266352EC:2))}, BondRef{Bond(1355531311, #O:SINGLE, #S:NONE, #A:2, Atom(1500056228, S:C, H:0, SP:0, 2D:[(2.8152, -4.9755)], AtomType(1500056228, FC:0, EV:4, Isotope(1500056228, Element(1500056228, S:C, AN:6)))), PseudoAtom(1818402158, R2a, Atom(1818402158, S:R, H:0, SP:0, 2D:[(2.8152, -5.8005)], AtomType(1818402158, FC:0, EV:1, Isotope(1818402158, Element(1818402158, S:R, AN:0))))), ElectronContainer(1355531311EC:2))}, BondRef{Bond(1967205423, #O:SINGLE, #S:NONE, #A:2, Atom(1749186397, S:C, H:0, SP:0, 2D:[(3.5297, -4.563)], AtomType(1749186397, FC:0, EV:4, Isotope(1749186397, Element(1749186397, S:C, AN:6)))), PseudoAtom(1590550415, R2c, Atom(1590550415, S:R, H:0, SP:0, 2D:[(4.2441, -4.9755)], AtomType(1590550415, FC:0, EV:1, Isotope(1590550415, Element(1590550415, S:R, AN:0))))), ElectronContainer(1967205423EC:2))}, BondRef{Bond(42121758, #O:SINGLE, #S:NONE, #A:2, Atom(1464642111, S:C, H:0, SP:0, 2D:[(3.5297, -3.738)], AtomType(1464642111, FC:0, EV:4, Isotope(1464642111, Element(1464642111, S:C, AN:6)))), Atom(1058025095, S:C, H:2, SP:0, 2D:[(4.2441, -3.3255)], AtomType(1058025095, FC:0, EV:4, Isotope(1058025095, Element(1058025095, S:C, AN:6)))), ElectronContainer(42121758EC:2))}, BondRef{Bond(20671747, #O:SINGLE, #S:NONE, #A:2, Atom(1058025095, S:C, H:2, SP:0, 2D:[(4.2441, -3.3255)], AtomType(1058025095, FC:0, EV:4, Isotope(1058025095, Element(1058025095, S:C, AN:6)))), PseudoAtom(665576141, R3., Atom(665576141, S:R, H:0, SP:0, 2D:[(4.9586, -3.738)], AtomType(665576141, FC:0, EV:1, Isotope(665576141, Element(665576141, S:R, AN:0))))), ElectronContainer(20671747EC:2))}, BondRef{Bond(257895351, #O:SINGLE, #S:NONE, #A:2, Atom(105704967, S:C, H:0, SP:0, 2D:[(2.8152, -3.3255)], AtomType(105704967, FC:0, EV:4, Isotope(105704967, Element(105704967, S:C, AN:6)))), PseudoAtom(1599771323, R4, Atom(1599771323, S:R, H:0, SP:0, 2D:[(2.8152, -2.5005)], AtomType(1599771323, FC:0, EV:1, Isotope(1599771323, Element(1599771323, S:R, AN:0))))), ElectronContainer(257895351EC:2))}, BondRef{Bond(1929600551, #O:SINGLE, #S:NONE, #A:2, Atom(392292416, S:C, H:0, SP:0, 2D:[(2.1007, -3.738)], AtomType(392292416, FC:0, EV:4, Isotope(392292416, Element(392292416, S:C, AN:6)))), PseudoAtom(1876631416, R2b, Atom(1876631416, S:R, H:0, SP:0, 2D:[(1.3863, -3.3255)], AtomType(1876631416, FC:0, EV:1, Isotope(1876631416, Element(1876631416, S:R, AN:0))))), ElectronContainer(1929600551EC:2))}, BondRef{Bond(1690716179, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(1761291320, S:C, H:0, SP:0, 2D:[(-2.0016, -3.6534)], AtomType(1761291320, FC:0, EV:4, Isotope(1761291320, Element(1761291320, S:C, AN:6)))), Atom(1359044626, S:C, H:0, SP:0, 2D:[(-1.7881, -2.8565)], AtomType(1359044626, FC:0, EV:4, Isotope(1359044626, Element(1359044626, S:C, AN:6)))), ElectronContainer(1690716179EC:4))}, BondRef{Bond(1053782781, #O:SINGLE, #S:NONE, #A:2, Atom(1359044626, S:C, H:0, SP:0, 2D:[(-1.7881, -2.8565)], AtomType(1359044626, FC:0, EV:4, Isotope(1359044626, Element(1359044626, S:C, AN:6)))), Atom(692342133, S:C, H:0, SP:0, 2D:[(-2.3714, -2.2731)], AtomType(692342133, FC:0, EV:4, Isotope(692342133, Element(692342133, S:C, AN:6)))), ElectronContainer(1053782781EC:2))}, BondRef{Bond(1211888640, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(692342133, S:C, H:0, SP:0, 2D:[(-2.3714, -2.2731)], AtomType(692342133, FC:0, EV:4, Isotope(692342133, Element(692342133, S:C, AN:6)))), Atom(578866604, S:C, H:0, SP:0, 2D:[(-3.1683, -2.4867)], AtomType(578866604, FC:0, EV:4, Isotope(578866604, Element(578866604, S:C, AN:6)))), ElectronContainer(1211888640EC:4))}, BondRef{Bond(564160838, #O:SINGLE, #S:NONE, #A:2, Atom(578866604, S:C, H:0, SP:0, 2D:[(-3.1683, -2.4867)], AtomType(578866604, FC:0, EV:4, Isotope(578866604, Element(578866604, S:C, AN:6)))), Atom(353842779, S:C, H:0, SP:0, 2D:[(-3.3818, -3.2835)], AtomType(353842779, FC:0, EV:4, Isotope(353842779, Element(353842779, S:C, AN:6)))), ElectronContainer(564160838EC:2))}, BondRef{Bond(2012232625, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(353842779, S:C, H:0, SP:0, 2D:[(-3.3818, -3.2835)], AtomType(353842779, FC:0, EV:4, Isotope(353842779, Element(353842779, S:C, AN:6)))), Atom(1338823963, S:C, H:0, SP:0, 2D:[(-2.7985, -3.8669)], AtomType(1338823963, FC:0, EV:4, Isotope(1338823963, Element(1338823963, S:C, AN:6)))), ElectronContainer(2012232625EC:4))}, BondRef{Bond(846063400, #O:SINGLE, #S:NONE, #A:2, Atom(1338823963, S:C, H:0, SP:0, 2D:[(-2.7985, -3.8669)], AtomType(1338823963, FC:0, EV:4, Isotope(1338823963, Element(1338823963, S:C, AN:6)))), Atom(1761291320, S:C, H:0, SP:0, 2D:[(-2.0016, -3.6534)], AtomType(1761291320, FC:0, EV:4, Isotope(1761291320, Element(1761291320, S:C, AN:6)))), ElectronContainer(846063400EC:2))}, BondRef{Bond(627150481, #O:SINGLE, #S:NONE, #A:2, Atom(1359044626, S:C, H:0, SP:0, 2D:[(-1.7881, -2.8565)], AtomType(1359044626, FC:0, EV:4, Isotope(1359044626, Element(1359044626, S:C, AN:6)))), PseudoAtom(1156060786, R1b, Atom(1156060786, S:R, H:0, SP:0, 2D:[(-0.9912, -2.643)], AtomType(1156060786, FC:0, EV:1, Isotope(1156060786, Element(1156060786, S:R, AN:0))))), ElectronContainer(627150481EC:2))}, BondRef{Bond(128526626, #O:SINGLE, #S:NONE, #A:2, Atom(692342133, S:C, H:0, SP:0, 2D:[(-2.3714, -2.2731)], AtomType(692342133, FC:0, EV:4, Isotope(692342133, Element(692342133, S:C, AN:6)))), PseudoAtom(1612799726, R1c, Atom(1612799726, S:R, H:0, SP:0, 2D:[(-2.1579, -1.4762)], AtomType(1612799726, FC:0, EV:1, Isotope(1612799726, Element(1612799726, S:R, AN:0))))), ElectronContainer(128526626EC:2))}, BondRef{Bond(1911728085, #O:SINGLE, #S:NONE, #A:2, Atom(578866604, S:C, H:0, SP:0, 2D:[(-3.1683, -2.4867)], AtomType(578866604, FC:0, EV:4, Isotope(578866604, Element(578866604, S:C, AN:6)))), PseudoAtom(1286084959, R1d, Atom(1286084959, S:R, H:0, SP:0, 2D:[(-3.7517, -1.9033)], AtomType(1286084959, FC:0, EV:1, Isotope(1286084959, Element(1286084959, S:R, AN:0))))), ElectronContainer(1911728085EC:2))}, BondRef{Bond(754666084, #O:SINGLE, #S:NONE, #A:2, Atom(353842779, S:C, H:0, SP:0, 2D:[(-3.3818, -3.2835)], AtomType(353842779, FC:0, EV:4, Isotope(353842779, Element(353842779, S:C, AN:6)))), PseudoAtom(1709537756, L, Atom(1709537756, S:R, H:0, SP:0, 2D:[(-4.1787, -3.4971)], AtomType(1709537756, FC:0, EV:2, Isotope(1709537756, Element(1709537756, S:R, AN:0))))), ElectronContainer(754666084EC:2))}, BondRef{Bond(88558700, #O:SINGLE, #S:NONE, #A:2, Atom(1338823963, S:C, H:0, SP:0, 2D:[(-2.7985, -3.8669)], AtomType(1338823963, FC:0, EV:4, Isotope(1338823963, Element(1338823963, S:C, AN:6)))), PseudoAtom(1639622804, R1a, Atom(1639622804, S:R, H:0, SP:0, 2D:[(-3.012, -4.6638)], AtomType(1639622804, FC:0, EV:1, Isotope(1639622804, Element(1639622804, S:R, AN:0))))), ElectronContainer(88558700EC:2))}, BondRef{Bond(1265210847, #O:SINGLE, #S:NONE, #A:2, PseudoAtom(1709537756, L, Atom(1709537756, S:R, H:0, SP:0, 2D:[(-4.1787, -3.4971)], AtomType(1709537756, FC:0, EV:2, Isotope(1709537756, Element(1709537756, S:R, AN:0))))), PseudoAtom(184966243, Z, Atom(184966243, S:R, H:0, SP:0, 2D:[(-5.0037, -3.4971)], AtomType(184966243, FC:0, EV:1, Isotope(184966243, Element(184966243, S:R, AN:0))))), ElectronContainer(1265210847EC:2))}, BondRef{Bond(801197928, #O:SINGLE, #S:UP, #A:2, Atom(1490180672, S:C, H:1, SP:1, 2D:[(0.6718, -3.738)], AtomType(1490180672, FC:0, EV:4, Isotope(1490180672, Element(1490180672, S:C, AN:6)))), Atom(124313277, S:F, H:0, SP:0, 2D:[(0.6718, -2.913)], AtomType(124313277, FC:0, EV:1, Isotope(124313277, Element(124313277, S:F, AN:9)))), ElectronContainer(801197928EC:2))}, BondRef{Bond(1495242910, #O:SINGLE, #S:NONE, #A:2, Atom(1225616405, S:C, H:3, SP:0, 2D:[(-0.9138, -5.2784)], AtomType(1225616405, FC:0, EV:4, Isotope(1225616405, Element(1225616405, S:C, AN:6)))), PseudoAtom(2101842856, (R\S5\n)\sn, Atom(2101842856, S:R, H:0, SP:0, 2D:[(-0.9138, -6.1034)], AtomType(2101842856, FC:0, EV:1, Isotope(2101842856, Element(2101842856, S:R, AN:0))))), ElectronContainer(1495242910EC:2))}, BondRef{Bond(1711574013, #O:SINGLE, #S:NONE, #A:2, Atom(460332449, S:C, H:1, SP:1, 2D:[(0.7169, 3.0167)], AtomType(460332449, FC:0, EV:4, Isotope(460332449, Element(460332449, S:C, AN:6)))), Atom(1919892312, S:C, H:1, SP:2, 2D:[(0.7169, 3.8417)], AtomType(1919892312, FC:0, EV:4, Isotope(1919892312, Element(1919892312, S:C, AN:6)))), ElectronContainer(1711574013EC:2))}, BondRef{Bond(1631862159, #O:SINGLE, #S:NONE, #A:2, Atom(1919892312, S:C, H:1, SP:2, 2D:[(0.7169, 3.8417)], AtomType(1919892312, FC:0, EV:4, Isotope(1919892312, Element(1919892312, S:C, AN:6)))), Atom(1151020327, S:C, H:2, SP:0, 2D:[(-0.0677, 4.0966)], AtomType(1151020327, FC:0, EV:4, Isotope(1151020327, Element(1151020327, S:C, AN:6)))), ElectronContainer(1631862159EC:2))}, BondRef{Bond(1146848448, #O:SINGLE, #S:NONE, #A:2, Atom(1151020327, S:C, H:2, SP:0, 2D:[(-0.0677, 4.0966)], AtomType(1151020327, FC:0, EV:4, Isotope(1151020327, Element(1151020327, S:C, AN:6)))), Atom(88579647, S:C, H:0, SP:0, 2D:[(-0.5526, 3.4292)], AtomType(88579647, FC:0, EV:4, Isotope(88579647, Element(88579647, S:C, AN:6)))), ElectronContainer(1146848448EC:2))}, BondRef{Bond(1638215613, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(88579647, S:C, H:0, SP:0, 2D:[(-0.5526, 3.4292)], AtomType(88579647, FC:0, EV:4, Isotope(88579647, Element(88579647, S:C, AN:6)))), Atom(654845766, S:C, H:0, SP:0, 2D:[(-0.0677, 2.7617)], AtomType(654845766, FC:0, EV:4, Isotope(654845766, Element(654845766, S:C, AN:6)))), ElectronContainer(1638215613EC:4))}, BondRef{Bond(591137559, #O:SINGLE, #S:NONE, #A:2, Atom(654845766, S:C, H:0, SP:0, 2D:[(-0.0677, 2.7617)], AtomType(654845766, FC:0, EV:4, Isotope(654845766, Element(654845766, S:C, AN:6)))), Atom(460332449, S:C, H:1, SP:1, 2D:[(0.7169, 3.0167)], AtomType(460332449, FC:0, EV:4, Isotope(460332449, Element(460332449, S:C, AN:6)))), ElectronContainer(591137559EC:2))}, BondRef{Bond(1674896058, #O:SINGLE, #S:NONE, #A:2, Atom(88579647, S:C, H:0, SP:0, 2D:[(-0.5526, 3.4292)], AtomType(88579647, FC:0, EV:4, Isotope(88579647, Element(88579647, S:C, AN:6)))), Atom(1712536284, S:C, H:0, SP:0, 2D:[(-1.3731, 3.3429)], AtomType(1712536284, FC:0, EV:4, Isotope(1712536284, Element(1712536284, S:C, AN:6)))), ElectronContainer(1674896058EC:2))}, BondRef{Bond(2075203460, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(1712536284, S:C, H:0, SP:0, 2D:[(-1.3731, 3.3429)], AtomType(1712536284, FC:0, EV:4, Isotope(1712536284, Element(1712536284, S:C, AN:6)))), Atom(2080166188, S:C, H:1, SP:0, 2D:[(-1.7087, 2.5893)], AtomType(2080166188, FC:0, EV:4, Isotope(2080166188, Element(2080166188, S:C, AN:6)))), ElectronContainer(2075203460EC:4))}, BondRef{Bond(866191240, #O:SINGLE, #S:NONE, #A:2, Atom(2080166188, S:C, H:1, SP:0, 2D:[(-1.7087, 2.5893)], AtomType(2080166188, FC:0, EV:4, Isotope(2080166188, Element(2080166188, S:C, AN:6)))), Atom(1123225098, S:C, H:1, SP:0, 2D:[(-1.2237, 1.9218)], AtomType(1123225098, FC:0, EV:4, Isotope(1123225098, Element(1123225098, S:C, AN:6)))), ElectronContainer(866191240EC:2))}, BondRef{Bond(1879492184, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(1123225098, S:C, H:1, SP:0, 2D:[(-1.2237, 1.9218)], AtomType(1123225098, FC:0, EV:4, Isotope(1123225098, Element(1123225098, S:C, AN:6)))), Atom(606548741, S:C, H:1, SP:0, 2D:[(-0.4033, 2.0081)], AtomType(606548741, FC:0, EV:4, Isotope(606548741, Element(606548741, S:C, AN:6)))), ElectronContainer(1879492184EC:4))}, BondRef{Bond(872627152, #O:SINGLE, #S:NONE, #A:2, Atom(606548741, S:C, H:1, SP:0, 2D:[(-0.4033, 2.0081)], AtomType(606548741, FC:0, EV:4, Isotope(606548741, Element(606548741, S:C, AN:6)))), Atom(654845766, S:C, H:0, SP:0, 2D:[(-0.0677, 2.7617)], AtomType(654845766, FC:0, EV:4, Isotope(654845766, Element(654845766, S:C, AN:6)))), ElectronContainer(872627152EC:2))}, BondRef{Bond(1207769059, #O:SINGLE, #S:NONE, #A:2, Atom(1712536284, S:C, H:0, SP:0, 2D:[(-1.3731, 3.3429)], AtomType(1712536284, FC:0, EV:4, Isotope(1712536284, Element(1712536284, S:C, AN:6)))), Atom(1528637575, S:C, H:0, SP:0, 2D:[(-1.9565, 3.9263)], AtomType(1528637575, FC:0, EV:4, Isotope(1528637575, Element(1528637575, S:C, AN:6)))), ElectronContainer(1207769059EC:2))}, BondRef{Bond(2094777811, #O:SINGLE, #S:DOWN, #A:2, Atom(460332449, S:C, H:1, SP:1, 2D:[(0.7169, 3.0167)], AtomType(460332449, FC:0, EV:4, Isotope(460332449, Element(460332449, S:C, AN:6)))), Atom(1190524793, S:O, H:0, SP:0, 2D:[(1.4314, 2.6042)], AtomType(1190524793, FC:0, EV:2, Isotope(1190524793, Element(1190524793, S:O, AN:8)))), ElectronContainer(2094777811EC:2))}, BondRef{Bond(984213526, #O:SINGLE, #S:NONE, #A:2, Atom(1190524793, S:O, H:0, SP:0, 2D:[(1.4314, 2.6042)], AtomType(1190524793, FC:0, EV:2, Isotope(1190524793, Element(1190524793, S:O, AN:8)))), Atom(472654579, S:C, H:0, SP:0, 2D:[(2.1459, 3.0167)], AtomType(472654579, FC:0, EV:4, Isotope(472654579, Element(472654579, S:C, AN:6)))), ElectronContainer(984213526EC:2))}, BondRef{Bond(400136488, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(472654579, S:C, H:0, SP:0, 2D:[(2.1459, 3.0167)], AtomType(472654579, FC:0, EV:4, Isotope(472654579, Element(472654579, S:C, AN:6)))), Atom(26117480, S:C, H:0, SP:0, 2D:[(2.8603, 2.6042)], AtomType(26117480, FC:0, EV:4, Isotope(26117480, Element(26117480, S:C, AN:6)))), ElectronContainer(400136488EC:4))}, BondRef{Bond(942986815, #O:SINGLE, #S:NONE, #A:2, Atom(26117480, S:C, H:0, SP:0, 2D:[(2.8603, 2.6042)], AtomType(26117480, FC:0, EV:4, Isotope(26117480, Element(26117480, S:C, AN:6)))), Atom(870698190, S:C, H:0, SP:0, 2D:[(3.5748, 3.0167)], AtomType(870698190, FC:0, EV:4, Isotope(870698190, Element(870698190, S:C, AN:6)))), ElectronContainer(942986815EC:2))}, BondRef{Bond(451111351, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(870698190, S:C, H:0, SP:0, 2D:[(3.5748, 3.0167)], AtomType(870698190, FC:0, EV:4, Isotope(870698190, Element(870698190, S:C, AN:6)))), Atom(1514322932, S:C, H:0, SP:0, 2D:[(3.5748, 3.8417)], AtomType(1514322932, FC:0, EV:4, Isotope(1514322932, Element(1514322932, S:C, AN:6)))), ElectronContainer(451111351EC:4))}, BondRef{Bond(1879034789, #O:SINGLE, #S:NONE, #A:2, Atom(1514322932, S:C, H:0, SP:0, 2D:[(3.5748, 3.8417)], AtomType(1514322932, FC:0, EV:4, Isotope(1514322932, Element(1514322932, S:C, AN:6)))), Atom(654582261, S:C, H:0, SP:0, 2D:[(2.8603, 4.2542)], AtomType(654582261, FC:0, EV:4, Isotope(654582261, Element(654582261, S:C, AN:6)))), ElectronContainer(1879034789EC:2))}, BondRef{Bond(875827115, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(654582261, S:C, H:0, SP:0, 2D:[(2.8603, 4.2542)], AtomType(654582261, FC:0, EV:4, Isotope(654582261, Element(654582261, S:C, AN:6)))), Atom(1389647288, S:C, H:0, SP:0, 2D:[(2.1459, 3.8417)], AtomType(1389647288, FC:0, EV:4, Isotope(1389647288, Element(1389647288, S:C, AN:6)))), ElectronContainer(875827115EC:4))}, BondRef{Bond(716157500, #O:SINGLE, #S:NONE, #A:2, Atom(1389647288, S:C, H:0, SP:0, 2D:[(2.1459, 3.8417)], AtomType(1389647288, FC:0, EV:4, Isotope(1389647288, Element(1389647288, S:C, AN:6)))), Atom(472654579, S:C, H:0, SP:0, 2D:[(2.1459, 3.0167)], AtomType(472654579, FC:0, EV:4, Isotope(472654579, Element(472654579, S:C, AN:6)))), ElectronContainer(716157500EC:2))}, BondRef{Bond(729864207, #O:SINGLE, #S:NONE, #A:2, Atom(26117480, S:C, H:0, SP:0, 2D:[(2.8603, 2.6042)], AtomType(26117480, FC:0, EV:4, Isotope(26117480, Element(26117480, S:C, AN:6)))), PseudoAtom(1330278544, R2a, Atom(1330278544, S:R, H:0, SP:0, 2D:[(2.8603, 1.7792)], AtomType(1330278544, FC:0, EV:1, Isotope(1330278544, Element(1330278544, S:R, AN:0))))), ElectronContainer(729864207EC:2))}, BondRef{Bond(984849465, #O:SINGLE, #S:NONE, #A:2, Atom(870698190, S:C, H:0, SP:0, 2D:[(3.5748, 3.0167)], AtomType(870698190, FC:0, EV:4, Isotope(870698190, Element(870698190, S:C, AN:6)))), PseudoAtom(1634198, R2c, Atom(1634198, S:R, H:0, SP:0, 2D:[(4.2893, 2.6042)], AtomType(1634198, FC:0, EV:1, Isotope(1634198, Element(1634198, S:R, AN:0))))), ElectronContainer(984849465EC:2))}, BondRef{Bond(787387795, #O:SINGLE, #S:NONE, #A:2, Atom(1514322932, S:C, H:0, SP:0, 2D:[(3.5748, 3.8417)], AtomType(1514322932, FC:0, EV:4, Isotope(1514322932, Element(1514322932, S:C, AN:6)))), Atom(110456297, S:C, H:2, SP:0, 2D:[(4.2893, 4.2542)], AtomType(110456297, FC:0, EV:4, Isotope(110456297, Element(110456297, S:C, AN:6)))), ElectronContainer(787387795EC:2))}, BondRef{Bond(2030562336, #O:SINGLE, #S:NONE, #A:2, Atom(110456297, S:C, H:2, SP:0, 2D:[(4.2893, 4.2542)], AtomType(110456297, FC:0, EV:4, Isotope(110456297, Element(110456297, S:C, AN:6)))), PseudoAtom(1989972246, R3, Atom(1989972246, S:R, H:0, SP:0, 2D:[(5.0037, 3.8417)], AtomType(1989972246, FC:0, EV:1, Isotope(1989972246, Element(1989972246, S:R, AN:0))))), ElectronContainer(2030562336EC:2))}, BondRef{Bond(1416233903, #O:SINGLE, #S:NONE, #A:2, Atom(654582261, S:C, H:0, SP:0, 2D:[(2.8603, 4.2542)], AtomType(654582261, FC:0, EV:4, Isotope(654582261, Element(654582261, S:C, AN:6)))), PseudoAtom(1791930789, R4, Atom(1791930789, S:R, H:0, SP:0, 2D:[(2.8603, 5.0792)], AtomType(1791930789, FC:0, EV:1, Isotope(1791930789, Element(1791930789, S:R, AN:0))))), ElectronContainer(1416233903EC:2))}, BondRef{Bond(1914572623, #O:SINGLE, #S:NONE, #A:2, Atom(1389647288, S:C, H:0, SP:0, 2D:[(2.1459, 3.8417)], AtomType(1389647288, FC:0, EV:4, Isotope(1389647288, Element(1389647288, S:C, AN:6)))), PseudoAtom(762152757, R2b, Atom(762152757, S:R, H:0, SP:0, 2D:[(1.4314, 4.2542)], AtomType(762152757, FC:0, EV:1, Isotope(762152757, Element(762152757, S:R, AN:0))))), ElectronContainer(1914572623EC:2))}, BondRef{Bond(679890578, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(1528637575, S:C, H:0, SP:0, 2D:[(-1.9565, 3.9263)], AtomType(1528637575, FC:0, EV:4, Isotope(1528637575, Element(1528637575, S:C, AN:6)))), Atom(12209492, S:C, H:0, SP:0, 2D:[(-1.743, 4.7232)], AtomType(12209492, FC:0, EV:4, Isotope(12209492, Element(12209492, S:C, AN:6)))), ElectronContainer(679890578EC:4))}, BondRef{Bond(1856426318, #O:SINGLE, #S:NONE, #A:2, Atom(12209492, S:C, H:0, SP:0, 2D:[(-1.743, 4.7232)], AtomType(12209492, FC:0, EV:4, Isotope(12209492, Element(12209492, S:C, AN:6)))), Atom(314337396, S:C, H:0, SP:0, 2D:[(-2.3263, 5.3066)], AtomType(314337396, FC:0, EV:4, Isotope(314337396, Element(314337396, S:C, AN:6)))), ElectronContainer(1856426318EC:2))}, BondRef{Bond(1792393294, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(314337396, S:C, H:0, SP:0, 2D:[(-2.3263, 5.3066)], AtomType(314337396, FC:0, EV:4, Isotope(314337396, Element(314337396, S:C, AN:6)))), Atom(232824863, S:C, H:0, SP:0, 2D:[(-3.1232, 5.093)], AtomType(232824863, FC:0, EV:4, Isotope(232824863, Element(232824863, S:C, AN:6)))), ElectronContainer(1792393294EC:4))}, BondRef{Bond(1748225580, #O:SINGLE, #S:NONE, #A:2, Atom(232824863, S:C, H:0, SP:0, 2D:[(-3.1232, 5.093)], AtomType(232824863, FC:0, EV:4, Isotope(232824863, Element(232824863, S:C, AN:6)))), Atom(1282788025, S:C, H:0, SP:0, 2D:[(-3.3367, 4.2961)], AtomType(1282788025, FC:0, EV:4, Isotope(1282788025, Element(1282788025, S:C, AN:6)))), ElectronContainer(1748225580EC:2))}, BondRef{Bond(1918627686, #O:DOUBLE, #S:E_Z_BY_COORDINATES, #A:2, Atom(1282788025, S:C, H:0, SP:0, 2D:[(-3.3367, 4.2961)], AtomType(1282788025, FC:0, EV:4, Isotope(1282788025, Element(1282788025, S:C, AN:6)))), Atom(519569038, S:C, H:0, SP:0, 2D:[(-2.7534, 3.7128)], AtomType(519569038, FC:0, EV:4, Isotope(519569038, Element(519569038, S:C, AN:6)))), ElectronContainer(1918627686EC:4))}, BondRef{Bond(716143810, #O:SINGLE, #S:NONE, #A:2, Atom(519569038, S:C, H:0, SP:0, 2D:[(-2.7534, 3.7128)], AtomType(519569038, FC:0, EV:4, Isotope(519569038, Element(519569038, S:C, AN:6)))), Atom(1528637575, S:C, H:0, SP:0, 2D:[(-1.9565, 3.9263)], AtomType(1528637575, FC:0, EV:4, Isotope(1528637575, Element(1528637575, S:C, AN:6)))), ElectronContainer(716143810EC:2))}, BondRef{Bond(1849433705, #O:SINGLE, #S:NONE, #A:2, Atom(12209492, S:C, H:0, SP:0, 2D:[(-1.743, 4.7232)], AtomType(12209492, FC:0, EV:4, Isotope(12209492, Element(12209492, S:C, AN:6)))), PseudoAtom(1870252780, R1b, Atom(1870252780, S:R, H:0, SP:0, 2D:[(-0.9461, 4.9367)], AtomType(1870252780, FC:0, EV:1, Isotope(1870252780, Element(1870252780, S:R, AN:0))))), ElectronContainer(1849433705EC:2))}, BondRef{Bond(411631404, #O:SINGLE, #S:NONE, #A:2, Atom(314337396, S:C, H:0, SP:0, 2D:[(-2.3263, 5.3066)], AtomType(314337396, FC:0, EV:4, Isotope(314337396, Element(314337396, S:C, AN:6)))), PseudoAtom(1729199940, R1c, Atom(1729199940, S:R, H:0, SP:0, 2D:[(-2.1128, 6.1034)], AtomType(1729199940, FC:0, EV:1, Isotope(1729199940, Element(1729199940, S:R, AN:0))))), ElectronContainer(411631404EC:2))}, BondRef{Bond(897913732, #O:SINGLE, #S:NONE, #A:2, Atom(232824863, S:C, H:0, SP:0, 2D:[(-3.1232, 5.093)], AtomType(232824863, FC:0, EV:4, Isotope(232824863, Element(232824863, S:C, AN:6)))), PseudoAtom(97730845, R1d, Atom(97730845, S:R, H:0, SP:0, 2D:[(-3.7066, 5.6764)], AtomType(97730845, FC:0, EV:1, Isotope(97730845, Element(97730845, S:R, AN:0))))), ElectronContainer(897913732EC:2))}, BondRef{Bond(1688019098, #O:SINGLE, #S:NONE, #A:2, Atom(1282788025, S:C, H:0, SP:0, 2D:[(-3.3367, 4.2961)], AtomType(1282788025, FC:0, EV:4, Isotope(1282788025, Element(1282788025, S:C, AN:6)))), PseudoAtom(611437735, L, Atom(611437735, S:R, H:0, SP:0, 2D:[(-4.1336, 4.0826)], AtomType(611437735, FC:0, EV:2, Isotope(611437735, Element(611437735, S:R, AN:0))))), ElectronContainer(1688019098EC:2))}, BondRef{Bond(1792845110, #O:SINGLE, #S:NONE, #A:2, Atom(519569038, S:C, H:0, SP:0, 2D:[(-2.7534, 3.7128)], AtomType(519569038, FC:0, EV:4, Isotope(519569038, Element(519569038, S:C, AN:6)))), PseudoAtom(100555887, R1a, Atom(100555887, S:R, H:0, SP:0, 2D:[(-2.9669, 2.9159)], AtomType(100555887, FC:0, EV:1, Isotope(100555887, Element(100555887, S:R, AN:0))))), ElectronContainer(1792845110EC:2))}, BondRef{Bond(896681694, #O:SINGLE, #S:NONE, #A:2, PseudoAtom(611437735, L, Atom(611437735, S:R, H:0, SP:0, 2D:[(-4.1336, 4.0826)], AtomType(611437735, FC:0, EV:2, Isotope(611437735, Element(611437735, S:R, AN:0))))), PseudoAtom(1769597131, Z, Atom(1769597131, S:R, H:0, SP:0, 2D:[(-4.9586, 4.0826)], AtomType(1769597131, FC:0, EV:1, Isotope(1769597131, Element(1769597131, S:R, AN:0))))), ElectronContainer(896681694EC:2))}, BondRef{Bond(687241927, #O:SINGLE, #S:DOWN, #A:2, Atom(1919892312, S:C, H:1, SP:2, 2D:[(0.7169, 3.8417)], AtomType(1919892312, FC:0, EV:4, Isotope(1919892312, Element(1919892312, S:C, AN:6)))), Atom(1983747920, S:F, H:0, SP:0, 2D:[(0.7169, 4.6667)], AtomType(1983747920, FC:0, EV:1, Isotope(1983747920, Element(1983747920, S:F, AN:9)))), ElectronContainer(687241927EC:2))}, BondRef{Bond(627185331, #O:SINGLE, #S:NONE, #A:2, Atom(1543727556, S:C, H:3, SP:0, 2D:[(-0.8686, 2.3012)], AtomType(1543727556, FC:0, EV:4, Isotope(1543727556, Element(1543727556, S:C, AN:6)))), PseudoAtom(736709391, (R\S5\n)\sn, Atom(736709391, S:R, H:0, SP:0, 2D:[(-0.8686, 1.4762)], AtomType(736709391, FC:0, EV:1, Isotope(736709391, Element(736709391, S:R, AN:0))))), ElectronContainer(627185331EC:2))}, ST:[#4, Tetrahedral{706277948, CLOCKWISE, c:AtomRef{Atom(476402209, S:C, H:1, SP:1, 2D:[(0.6718, -4.563)], AtomType(476402209, FC:0, EV:4, Isotope(476402209, Element(476402209, S:C, AN:6))))}, 1:AtomRef{Atom(1490180672, S:C, H:1, SP:1, 2D:[(0.6718, -3.738)], AtomType(1490180672, FC:0, EV:4, Isotope(1490180672, Element(1490180672, S:C, AN:6))))}, 2:AtomRef{Atom(317983781, S:C, H:0, SP:0, 2D:[(-0.1128, -4.818)], AtomType(317983781, FC:0, EV:4, Isotope(317983781, Element(317983781, S:C, AN:6))))}, 3:AtomRef{Atom(1451043227, S:O, H:0, SP:0, 2D:[(1.3863, -4.9755)], AtomType(1451043227, FC:0, EV:2, Isotope(1451043227, Element(1451043227, S:O, AN:8))))}, 4:AtomRef{Atom(476402209, S:C, H:1, SP:1, 2D:[(0.6718, -4.563)], AtomType(476402209, FC:0, EV:4, Isotope(476402209, Element(476402209, S:C, AN:6))))}, }, Tetrahedral{226170135, CLOCKWISE, c:AtomRef{Atom(1490180672, S:C, H:1, SP:1, 2D:[(0.6718, -3.738)], AtomType(1490180672, FC:0, EV:4, Isotope(1490180672, Element(1490180672, S:C, AN:6))))}, 1:AtomRef{Atom(476402209, S:C, H:1, SP:1, 2D:[(0.6718, -4.563)], AtomType(476402209, FC:0, EV:4, Isotope(476402209, Element(476402209, S:C, AN:6))))}, 2:AtomRef{Atom(705265961, S:C, H:2, SP:0, 2D:[(-0.1128, -3.4831)], AtomType(705265961, FC:0, EV:4, Isotope(705265961, Element(705265961, S:C, AN:6))))}, 3:AtomRef{Atom(124313277, S:F, H:0, SP:0, 2D:[(0.6718, -2.913)], AtomType(124313277, FC:0, EV:1, Isotope(124313277, Element(124313277, S:F, AN:9))))}, 4:AtomRef{Atom(1490180672, S:C, H:1, SP:1, 2D:[(0.6718, -3.738)], AtomType(1490180672, FC:0, EV:4, Isotope(1490180672, Element(1490180672, S:C, AN:6))))}, }, Tetrahedral{381707837, CLOCKWISE, c:AtomRef{Atom(460332449, S:C, H:1, SP:1, 2D:[(0.7169, 3.0167)], AtomType(460332449, FC:0, EV:4, Isotope(460332449, Element(460332449, S:C, AN:6))))}, 1:AtomRef{Atom(1919892312, S:C, H:1, SP:2, 2D:[(0.7169, 3.8417)], AtomType(1919892312, FC:0, EV:4, Isotope(1919892312, Element(1919892312, S:C, AN:6))))}, 2:AtomRef{Atom(654845766, S:C, H:0, SP:0, 2D:[(-0.0677, 2.7617)], AtomType(654845766, FC:0, EV:4, Isotope(654845766, Element(654845766, S:C, AN:6))))}, 3:AtomRef{Atom(1190524793, S:O, H:0, SP:0, 2D:[(1.4314, 2.6042)], AtomType(1190524793, FC:0, EV:2, Isotope(1190524793, Element(1190524793, S:O, AN:8))))}, 4:AtomRef{Atom(460332449, S:C, H:1, SP:1, 2D:[(0.7169, 3.0167)], AtomType(460332449, FC:0, EV:4, Isotope(460332449, Element(460332449, S:C, AN:6))))}, }, Tetrahedral{589446616, ANTI_CLOCKWISE, c:AtomRef{Atom(1919892312, S:C, H:1, SP:2, 2D:[(0.7169, 3.8417)], AtomType(1919892312, FC:0, EV:4, Isotope(1919892312, Element(1919892312, S:C, AN:6))))}, 1:AtomRef{Atom(460332449, S:C, H:1, SP:1, 2D:[(0.7169, 3.0167)], AtomType(460332449, FC:0, EV:4, Isotope(460332449, Element(460332449, S:C, AN:6))))}, 2:AtomRef{Atom(1151020327, S:C, H:2, SP:0, 2D:[(-0.0677, 4.0966)], AtomType(1151020327, FC:0, EV:4, Isotope(1151020327, Element(1151020327, S:C, AN:6))))}, 3:AtomRef{Atom(1983747920, S:F, H:0, SP:0, 2D:[(0.7169, 4.6667)], AtomType(1983747920, FC:0, EV:1, Isotope(1983747920, Element(1983747920, S:F, AN:9))))}, 4:AtomRef{Atom(1919892312, S:C, H:1, SP:2, 2D:[(0.7169, 3.8417)], AtomType(1919892312, FC:0, EV:4, Isotope(1919892312, Element(1919892312, S:C, AN:6))))}, }]) 0 [main] INFO net.sf.jnati.deploy.artefact.ConfigManager - Loading global configuration 3 [main] DEBUG net.sf.jnati.deploy.artefact.ConfigManager - Loading defaults: jar:file:/C:/Users/-/Desktop/cdk-2.2.jar!/META-INF/jnati/jnati.default-properties 4 [main] INFO net.sf.jnati.deploy.artefact.ConfigManager - Loading artefact configuration: jniinchi-1.03_1 5 [main] DEBUG net.sf.jnati.deploy.artefact.ConfigManager - Loading instance defaults: jar:file:/C:/Users/-/Desktop/cdk-2.2.jar!/META-INF/jnati/jnati.instance.default-properties 7 [main] INFO net.sf.jnati.deploy.repository.ClasspathRepository - Searching classpath for: jniinchi-1.03_1-WINDOWS-AMD64 8 [main] INFO net.sf.jnati.deploy.repository.LocalRepository - Searching local repository for: jniinchi-1.03_1-WINDOWS-AMD64 8 [main] DEBUG net.sf.jnati.deploy.repository.LocalRepository - Artefact path: C:\Users-.jnati\repo\jniinchi\1.03_1\WINDOWS-AMD64 9 [main] INFO net.sf.jnati.deploy.artefact.ManifestReader - Reading manifest 96 [main] INFO net.sf.jnati.deploy.NativeArtefactLocator - Artefact (jniinchi-1.03_1-WINDOWS-AMD64) location: C:\Users-.jnati\repo\jniinchi\1.03_1\WINDOWS-AMD64 97 [main] DEBUG net.sf.jnati.deploy.NativeLibraryLoader - Loading library: C:\Users-.jnati\repo\jniinchi\1.03_1\WINDOWS-AMD64\JniInchi-1.03_1-WINDOWS-AMD64.dll Inchi Result null

johnmay commented 5 years ago

InChI does not support "pseudo atoms", which you have in your structure. This is not a CDK problem but just a limitation of the InChI. Can you attach the MOLfile?

In any case, normally you would check the InChI return result:

InChIGeneratorFactory fact = InChIGeneratorFactory.getInstance();
InChIGenerator        gen  = fact.getInChIGenerator(molecule);
switch (gen.getReturnStatus()) {
  case INCHI_RET.ERROR:
    System.err.println("InChI Error: " + gen.getMessage());
    break;
  case INCHI_RET.WARNING:
    System.err.println("InChI Warning: " + gen.getMessage());
  default:
    System.out.println(gen.getInChI());
    break;
}
likusta commented 5 years ago

Sure, in attachments molFile1 and molFile2. Also i have problems with files like molFile3, it's format problem? molFile3.txt molFile1.txt molFile2.txt

johnmay commented 5 years ago

Yes none of those are supported by InChI, let's take a step back why are you trying to generate InChIs as this might be an XY Problem?

molFile1 and 2 has positional variation and with frequency variation on the deutriums molfile3 looks like it was at some point a reaction before it got mangled. However if you copy the structures out one by one you should be able to get an InChI.