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5c5de2f78b
* add test for conformer canonicalization inverting stereo * Fix problem with canonicalizeConformer inverting stereo * response to review cleanup fix the other tests affected by this change
106 lines
2.8 KiB
C++
106 lines
2.8 KiB
C++
//
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// Copyright (c) 2024 Greg Landrum
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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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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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///
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#include <catch2/catch_all.hpp>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <algorithm>
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#include <regex>
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using namespace RDKit;
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using std::unique_ptr;
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TEST_CASE("chirality flip in canonicalizeMolConformer") {
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SECTION("first discovery") {
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auto m1 = R"CTAB(
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RDKit 3D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 11 10 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -1.533948 2.465972 -1.220733 0
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M V30 2 C -1.361222 1.165424 -1.939720 0 CFG=2
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M V30 3 C -2.694145 0.606596 -2.153754 0
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M V30 4 N -3.766061 0.178135 -2.319155 0
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M V30 5 C -0.566772 0.289201 -1.072783 0
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M V30 6 C 0.084234 -0.420637 -0.345400 0
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M V30 7 C 0.867082 -1.237691 0.508367 0
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M V30 8 C 1.549171 -1.919699 1.232613 0
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M V30 9 C 2.339643 -2.731169 2.106347 0
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M V30 10 C 2.993349 -3.411935 2.854815 0
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M V30 11 O 3.747921 -4.178375 3.716269 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 2 1 CFG=1
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M V30 2 1 2 3
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M V30 3 3 3 4
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M V30 4 1 2 5
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M V30 5 3 5 6
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M V30 6 1 6 7
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M V30 7 3 7 8
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M V30 8 1 8 9
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M V30 9 3 9 10
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M V30 10 1 10 11
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M V30 END BOND
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M V30 END CTAB
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M END)CTAB"_ctab;
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REQUIRE(m1);
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auto m2 = R"CTAB(
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RDKit 3D
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0 0 0 0 0 0 0 0 0 0999 V3000
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M V30 BEGIN CTAB
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M V30 COUNTS 11 10 0 0 0
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M V30 BEGIN ATOM
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M V30 1 C -3.278200 0.712725 -0.066592 0
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M V30 2 C -2.682025 -0.648154 -0.271665 0 CFG=1
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M V30 3 C -2.915612 -1.059871 -1.656844 0
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M V30 4 N -3.080403 -1.390524 -2.739848 0
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M V30 5 C -1.232937 -0.539032 -0.023304 0
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M V30 6 C -0.029030 -0.463778 0.167869 0
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M V30 7 C 1.366183 -0.398546 0.377840 0
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M V30 8 C 2.562372 -0.361417 0.548269 0
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M V30 9 C 3.973502 -0.322846 0.772691 0
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M V30 10 C 5.164230 -0.269523 0.960648 0
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M V30 11 O 6.516239 -0.218493 1.152837 0
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M V30 END ATOM
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M V30 BEGIN BOND
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M V30 1 1 2 1 CFG=3
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M V30 2 1 2 3
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M V30 3 3 3 4
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M V30 4 1 2 5
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M V30 5 3 5 6
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M V30 6 1 6 7
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M V30 7 3 7 8
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M V30 8 1 8 9
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M V30 9 3 9 10
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M V30 10 1 10 11
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M V30 END BOND
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M V30 END CTAB
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M END)CTAB"_ctab;
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REQUIRE(m2);
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auto m1_cp = ROMol(*m1);
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auto m2_cp = ROMol(*m2);
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MolTransforms::canonicalizeConformer(m1_cp.getConformer());
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MolTransforms::canonicalizeConformer(m2_cp.getConformer());
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MolOps::assignChiralTypesFrom3D(m1_cp);
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MolOps::assignChiralTypesFrom3D(m2_cp);
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CHECK(m1_cp.getAtomWithIdx(1)->getChiralTag() ==
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m1->getAtomWithIdx(1)->getChiralTag());
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CHECK(m2_cp.getAtomWithIdx(1)->getChiralTag() ==
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m2->getAtomWithIdx(1)->getChiralTag());
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}
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}
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