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ea0e8f674e
* Sketch of a solution to preserve bond direction in fragmentOnBonds * A bit of cleanup work based on Andrew's original commit for #1039 Add a couple of tests too * forgot to save a file before the commit
58 lines
2.3 KiB
C++
58 lines
2.3 KiB
C++
//
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// Copyright (c) 2019 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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#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
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// this in one cpp file
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#include "catch.hpp"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/ChemTransforms/ChemTransforms.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolSupplier.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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using namespace RDKit;
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using std::unique_ptr;
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TEST_CASE("Github #1039", "[]") {
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SECTION("double bond") {
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auto m1 = "C/C=C/C=C/C"_smiles;
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REQUIRE(m1);
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std::vector<unsigned int> bonds = {2};
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std::unique_ptr<ROMol> pieces(MolFragmenter::fragmentOnBonds(*m1, bonds));
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REQUIRE(pieces);
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CHECK(pieces->getNumAtoms() == 8);
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REQUIRE(pieces->getBondBetweenAtoms(3, 6));
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REQUIRE(pieces->getBondBetweenAtoms(2, 7));
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CHECK(pieces->getBondBetweenAtoms(3, 6)->getBondType() == Bond::SINGLE);
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CHECK(pieces->getBondBetweenAtoms(3, 6)->getBondDir() == Bond::ENDUPRIGHT);
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CHECK(pieces->getBondBetweenAtoms(2, 7)->getBondType() == Bond::SINGLE);
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CHECK(pieces->getBondBetweenAtoms(2, 7)->getBondDir() == Bond::ENDUPRIGHT);
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CHECK(MolToSmiles(*pieces) == "[2*]/C=C/C.[3*]/C=C/C");
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}
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SECTION("atomic stereo") {
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auto m1 = "C(C)(F)(Cl)O"_smiles;
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REQUIRE(m1);
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m1->getBondWithIdx(0)->setBondDir(Bond::BEGINWEDGE);
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std::vector<unsigned int> bonds = {0};
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std::unique_ptr<ROMol> pieces(MolFragmenter::fragmentOnBonds(*m1, bonds));
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REQUIRE(pieces);
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CHECK(pieces->getNumAtoms() == 7);
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REQUIRE(pieces->getBondBetweenAtoms(0, 6));
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REQUIRE(pieces->getBondBetweenAtoms(1, 5));
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CHECK(pieces->getBondBetweenAtoms(0, 6)->getBondDir() == Bond::BEGINWEDGE);
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CHECK(pieces->getBondBetweenAtoms(1, 5)->getBondDir() == Bond::NONE);
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// no actual stereo in the SMILES here since we haven't assigned it (need a
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// conformer to do that using wedging)
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CHECK(MolToSmiles(*pieces) == "*C.[1*]C(O)(F)Cl");
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}
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}
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