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106 lines
3.4 KiB
C++
106 lines
3.4 KiB
C++
//
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// Copyright (C) 2022 Greg Landrum and other RDKit contributors
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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 "catch.hpp"
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#include "AlignMolecules.h"
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/ROMol.h>
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#include <GraphMol/Conformer.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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using namespace RDKit;
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TEST_CASE("symmetric functional groups") {
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SECTION("basics") {
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auto m1 =
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"CCC(=O)[O-] "
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"|(-1.11,0.08,-0.29;0.08,-0.18,0.58;1.34,0.03,-0.16;1.74,1.22,-0.32;2.06,-1.04,-0.66)|"_smiles;
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REQUIRE(m1);
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// swap the bond orders to the Os
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RWMol m2(*m1);
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m2.getAtomWithIdx(3)->setFormalCharge(-1);
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m2.getAtomWithIdx(4)->setFormalCharge(0);
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m2.getBondBetweenAtoms(2, 3)->setBondType(Bond::BondType::SINGLE);
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m2.getBondBetweenAtoms(2, 4)->setBondType(Bond::BondType::DOUBLE);
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{
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auto rmsd = MolAlign::getBestRMS(m2, *m1);
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CHECK(rmsd == Approx(0.0).margin(1e-3));
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}
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{
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// previous behavior
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int probeId = -1;
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int refId = -1;
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std::vector<MatchVectType> mp;
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int maxMatches = 1e6;
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bool symmetrize = false;
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auto rmsd = MolAlign::getBestRMS(m2, *m1, probeId, refId, mp, maxMatches,
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symmetrize);
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CHECK(rmsd == Approx(0.747).margin(1e-3));
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}
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}
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SECTION("terminal sulfate1") {
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auto m1 =
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"CS(=O)(=O)[O-] |(-0.93,-0.06,-0.04;0.82,0.07,0.13;1.27,-0.04,1.54;1.21,1.40,-0.48;1.53,-1.11,-0.82)|"_smiles;
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REQUIRE(m1);
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// swap the bond orders to the Os
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RWMol m2(*m1);
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m2.getAtomWithIdx(2)->setFormalCharge(-1);
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m2.getAtomWithIdx(4)->setFormalCharge(0);
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m2.getBondBetweenAtoms(1, 2)->setBondType(Bond::BondType::SINGLE);
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m2.getBondBetweenAtoms(1, 4)->setBondType(Bond::BondType::DOUBLE);
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{
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auto rmsd = MolAlign::getBestRMS(m2, *m1);
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CHECK(rmsd == Approx(0.0).margin(1e-3));
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}
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{
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// previous behavior
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int probeId = -1;
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int refId = -1;
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std::vector<MatchVectType> mp;
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int maxMatches = 1e6;
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bool symmetrize = false;
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auto rmsd = MolAlign::getBestRMS(m2, *m1, probeId, refId, mp, maxMatches,
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symmetrize);
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CHECK(rmsd == Approx(0.097).margin(1e-3));
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}
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}
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SECTION("terminal sulfate2") {
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auto m1 =
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"CS(=O)(=O)[O-] |(-0.93,-0.06,-0.04;0.82,0.07,0.13;1.27,-0.04,1.54;1.21,1.40,-0.48;1.53,-1.11,-0.82)|"_smiles;
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REQUIRE(m1);
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// swap the bond orders to the Os
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RWMol m2(*m1);
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m2.getAtomWithIdx(3)->setFormalCharge(-1);
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m2.getAtomWithIdx(4)->setFormalCharge(0);
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m2.getBondBetweenAtoms(1, 3)->setBondType(Bond::BondType::SINGLE);
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m2.getBondBetweenAtoms(1, 4)->setBondType(Bond::BondType::DOUBLE);
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{
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auto rmsd = MolAlign::getBestRMS(m2, *m1);
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CHECK(rmsd == Approx(0.0).margin(1e-3));
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}
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{
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// previous behavior
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int probeId = -1;
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int refId = -1;
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std::vector<MatchVectType> mp;
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int maxMatches = 1e6;
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bool symmetrize = false;
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auto rmsd = MolAlign::getBestRMS(m2, *m1, probeId, refId, mp, maxMatches,
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symmetrize);
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CHECK(rmsd == Approx(0.097).margin(1e-3));
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}
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}
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} |