mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-03 21:44:30 +08:00
Greg Landrum
@@ -1,6 +1,5 @@
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// $Id$
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//
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// Copyright (C) 2004-2014 Greg Landrum and Rational Discovery LLC
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// Copyright (C) 2004-2017 Greg Landrum and Rational Discovery LLC
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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@@ -656,7 +655,7 @@ void DetectAtomStereoChemistry(RWMol &mol, const Conformer *conf) {
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if (dir == Bond::BEGINWEDGE || dir == Bond::BEGINDASH) {
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Atom *atom = bond->getBeginAtom();
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if (atom->getImplicitValence() == -1) {
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atom->calcExplicitValence();
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atom->calcExplicitValence(false);
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atom->calcImplicitValence(false);
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}
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Atom::ChiralType code = FindAtomStereochemistry(mol, bond, conf);
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@@ -4765,6 +4765,24 @@ void testGithub1049() {
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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void testGithub1251() {
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BOOST_LOG(rdInfoLog)
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<< "Test github 1251: MolFromMolBlock sanitizing when it should not be"
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<< std::endl;
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std::string rdbase = getenv("RDBASE");
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rdbase += "/Code/GraphMol/FileParsers/test_data/";
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{
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std::string fName = rdbase + "github1251.mol";
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RWMol *m = MolFileToMol(fName, false);
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TEST_ASSERT(m);
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TEST_ASSERT(m->getNumAtoms() == 39);
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TEST_ASSERT(m->getNumBonds() == 44);
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delete m;
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}
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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void RunTests() {
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#if 1
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test1();
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@@ -4848,11 +4866,12 @@ void RunTests() {
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testGithub1023();
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testGithub1034();
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testGithub1049();
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#endif
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testPDBFile();
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testSequences();
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// testSequenceReaders();
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// testSequenceReaders();
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#endif
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testGithub1251();
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}
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// must be in German Locale for test...
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90
Code/GraphMol/FileParsers/test_data/github1251.mol
Normal file
90
Code/GraphMol/FileParsers/test_data/github1251.mol
Normal file
@@ -0,0 +1,90 @@
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58
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-OEChem-07261613412D
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39 44 0 1 0 0 0 0 0999 V2000
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2.7797 3.3689 0.0000 Tc 2 3 3 0 0 0 0 0 0 0 0 0
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3.0867 2.2535 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
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1.1617 2.3585 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
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2.1936 4.6289 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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1.0917 6.3485 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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10.9562 2.0346 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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12.3693 4.3178 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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16.3490 0.7000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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3.1917 4.4235 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
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1.1967 4.5285 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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7.1879 4.3897 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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13.7824 1.9757 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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1.6517 5.4735 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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3.0517 5.3685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.3701 3.9098 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.4414 5.1451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.0000 4.1389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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4.2238 2.5175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.0000 2.7389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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5.2567 4.5635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.0617 5.0885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.7757 2.9178 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
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7.0767 0.9585 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0
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9.5431 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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8.0711 2.4467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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8.7776 1.1514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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5.5393 2.0934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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6.3047 1.2691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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5.3626 0.7392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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12.3693 2.9178 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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15.1366 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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16.3490 2.1000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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15.1366 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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16.3490 4.9000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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17.5615 2.8000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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17.5615 4.2000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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16.3490 6.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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17.5615 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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9.5431 4.2131 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
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1 2 1 0 0 0 0
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1 3 1 0 0 0 0
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1 4 2 0 0 0 0
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1 9 1 0 0 0 0
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1 10 1 0 0 0 0
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2 18 1 0 0 0 0
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3 19 1 0 0 0 0
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5 13 2 0 0 0 0
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6 24 1 0 0 0 0
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6 30 1 0 0 0 0
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7 30 2 0 0 0 0
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8 32 1 0 0 0 0
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8 38 1 0 0 0 0
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9 14 1 0 0 0 0
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9 15 1 0 0 0 0
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9 16 1 1 0 0 0
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10 13 1 0 0 0 0
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10 17 1 0 0 0 0
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11 21 1 0 0 0 0
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11 22 1 0 0 0 0
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11 23 1 0 0 0 0
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12 30 1 0 0 0 0
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12 31 1 0 0 0 0
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13 14 1 0 0 0 0
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15 18 1 0 0 0 0
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16 20 1 0 0 0 0
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17 19 1 0 0 0 0
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20 21 1 0 0 0 0
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22 25 1 0 0 0 0
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22 27 1 0 0 0 0
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23 26 1 0 0 0 0
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23 28 1 0 0 0 0
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24 25 1 0 0 0 0
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24 26 1 0 0 0 0
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24 39 1 0 0 0 0
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27 29 1 0 0 0 0
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28 29 1 0 0 0 0
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31 32 2 0 0 0 0
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31 33 1 0 0 0 0
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32 35 1 0 0 0 0
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33 34 2 0 0 0 0
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34 36 1 0 0 0 0
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34 37 1 0 0 0 0
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35 36 2 0 0 0 0
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M CHG 1 1 1
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M ISO 1 1 99
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M END
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