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da6cd73168
* run clang-format-18 across Code/*.cpp and Code/*.h * run clang-format-18 across External
582 lines
17 KiB
C++
582 lines
17 KiB
C++
//
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// Copyright (C) 2017-2020 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 <iostream>
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#include <fstream>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <GraphMol/MolAlign/AlignMolecules.h>
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#include <GraphMol/MolTransforms/MolTransforms.h>
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#include <GraphMol/ChemTransforms/ChemTransforms.h>
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#include <RDGeneral/RDLog.h>
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#include "coordgen/sketcherMinimizer.h"
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#include <CoordGen/CoordGen.h>
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using namespace RDKit;
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void test1() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "test1: basics" << std::endl;
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#if 1
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{
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ROMol *m = SmilesToMol("c1cc(CC)cnc1CC(=O)O");
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TEST_ASSERT(m);
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m->setProp("_Name", "test1");
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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auto mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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delete m;
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}
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{
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// ROMol* m = SmilesToMol("c1ccncc1");
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ROMol *m = SmilesToMol("ClC(O)(F)C");
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TEST_ASSERT(m);
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m->setProp("_Name", "test2");
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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auto mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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delete m;
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}
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{
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ROMol *m = SmilesToMol(
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"CC[C@H]1C(=O)N(CC(=O)N([C@H](C(=O)N[C@H](C(=O)N([C@H](C(=O)N[C@H](C(="
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"O)N[C@@H](C(=O)N([C@H](C(=O)N([C@H](C(=O)N([C@H](C(=O)N([C@H](C(=O)N1)"
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"[C@@H]([C@H](C)C/C=C/"
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"C)O)C)C(C)C)C)CC(C)C)C)CC(C)C)C)C)C)CC(C)C)C)C(C)C)CC(C)C)C)C");
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TEST_ASSERT(m);
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m->setProp("_Name", "cyclosporine a");
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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auto mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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delete m;
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}
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{
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// ROMol* m = SmilesToMol("c1ccncc1");
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ROMol *m = SmilesToMol("CCCNC=CNCOC=CC=CC=COC");
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TEST_ASSERT(m);
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m->setProp("_Name", "single-double");
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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auto mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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delete m;
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}
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#endif
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{
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ROMol *m = SmilesToMol("O/C=C/C=C/C=C\\C=C/N");
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TEST_ASSERT(m);
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m->setProp("_Name", "cis-trans");
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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auto mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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delete m;
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}
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{
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ROMol *m = SmilesToMol("C1C3CC2CC(CC1C2)C3");
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TEST_ASSERT(m);
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m->setProp("_Name", "admntn");
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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auto mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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delete m;
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}
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{
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SmilesParserParams params;
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params.removeHs = false;
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ROMol *m = SmilesToMol(
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"[H]C([H])=C1C#C/C2=C(/C#C/C3=C(\\C#CC2=C([H])[H])C(=C([H])[H])C#CCC(=C=O)C#C3)C(=C([H])[H])C#CC(=O)C1=C([H])[H]",
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params);
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TEST_ASSERT(m);
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m->setProp("_Name", "github 4845 - nan coordinates but no crash");
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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auto mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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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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namespace {
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bool compareConfs(const ROMol *m, ROMol *templ, const MatchVectType &mv,
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bool alignFirst = false, int molConfId = -1,
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int templateConfId = -1, double postol = 1e-2,
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double rmstol = 0.1) {
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PRECONDITION(m, "bad pointer");
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PRECONDITION(templ, "bad pointer");
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TEST_ASSERT(m->getNumAtoms() >= templ->getNumAtoms());
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if (alignFirst) {
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double rmsd =
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MolAlign::alignMol(*templ, *m, molConfId, templateConfId, &mv);
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if (rmsd > rmstol) {
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return false;
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}
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}
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const Conformer &conf1 = m->getConformer(molConfId);
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const Conformer &conf2 = templ->getConformer(templateConfId);
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for (unsigned int i = 0; i < templ->getNumAtoms(); i++) {
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TEST_ASSERT(m->getAtomWithIdx(mv[i].second)->getAtomicNum() ==
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templ->getAtomWithIdx(mv[i].first)->getAtomicNum());
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RDGeom::Point3D pt1i = conf1.getAtomPos(mv[i].second);
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RDGeom::Point3D pt2i = conf2.getAtomPos(mv[i].first);
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if ((pt1i - pt2i).length() >= postol) {
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return false;
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}
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}
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return true;
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}
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} // namespace
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void test2() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog) << "test2: using templates" << std::endl;
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{
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ROMol *core = SmilesToMol("C1CON1");
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TEST_ASSERT(core);
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core->setProp("_Name", "core");
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TEST_ASSERT(CoordGen::addCoords(*core) == 0);
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TEST_ASSERT(core->getNumConformers() == 1);
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auto mb = MolToMolBlock(*core);
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std::cerr << mb << std::endl;
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ROMol *m = SmilesToMol("C1C(CCC)ON1");
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TEST_ASSERT(m);
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m->setProp("_Name", "core+sidechain");
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MatchVectType mv;
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SubstructMatch(*m, *core, mv);
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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TEST_ASSERT(!compareConfs(m, core, mv));
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{
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auto coreConf = core->getConformer();
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RDGeom::INT_POINT2D_MAP coordMap;
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for (auto &i : mv) {
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coordMap[i.second] = RDGeom::Point2D(coreConf.getAtomPos(i.first).x,
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coreConf.getAtomPos(i.first).y);
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}
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CoordGen::CoordGenParams params;
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params.coordMap = coordMap;
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params.dbg_useFixed = true;
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TEST_ASSERT(CoordGen::addCoords(*m, ¶ms) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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// m->setProp("_Name", "templated");
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// mb = MolToMolBlock(*m);
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// std::cerr << mb << std::endl;
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TEST_ASSERT(compareConfs(m, core, mv));
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}
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{
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CoordGen::CoordGenParams params;
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params.templateMol = core;
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params.dbg_useFixed = true;
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TEST_ASSERT(CoordGen::addCoords(*m, ¶ms) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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m->setProp("_Name", "templated");
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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TEST_ASSERT(compareConfs(m, core, mv));
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}
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delete m;
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delete core;
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}
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{
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ROMol *core = SmilesToMol("C1CCCCCONCN1");
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TEST_ASSERT(core);
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core->setProp("_Name", "core");
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TEST_ASSERT(CoordGen::addCoords(*core) == 0);
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TEST_ASSERT(core->getNumConformers() == 1);
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auto mb = MolToMolBlock(*core);
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std::cerr << mb << std::endl;
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ROMol *m = SmilesToMol("C1CCCCONC(CC)NC1");
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TEST_ASSERT(m);
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m->setProp("_Name", "core+sidechain");
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MatchVectType mv;
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SubstructMatch(*m, *core, mv);
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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TEST_ASSERT(!compareConfs(m, core, mv));
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{
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auto coreConf = core->getConformer();
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RDGeom::INT_POINT2D_MAP coordMap;
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for (auto &i : mv) {
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coordMap[i.second] = RDGeom::Point2D(coreConf.getAtomPos(i.first).x,
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coreConf.getAtomPos(i.first).y);
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}
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CoordGen::CoordGenParams params;
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params.coordMap = coordMap;
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params.dbg_useFixed = true;
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TEST_ASSERT(CoordGen::addCoords(*m, ¶ms) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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// m->setProp("_Name", "templated");
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// mb = MolToMolBlock(*m);
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// std::cerr << mb << std::endl;
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TEST_ASSERT(compareConfs(m, core, mv));
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}
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{
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CoordGen::CoordGenParams params;
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params.templateMol = core;
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params.dbg_useFixed = true;
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TEST_ASSERT(CoordGen::addCoords(*m, ¶ms) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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m->setProp("_Name", "templated");
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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TEST_ASSERT(compareConfs(m, core, mv));
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}
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delete m;
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delete core;
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}
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{
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ROMol *core = SmilesToMol("C1CCCCCONCN1");
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TEST_ASSERT(core);
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core->setProp("_Name", "core");
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TEST_ASSERT(CoordGen::addCoords(*core) == 0);
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TEST_ASSERT(core->getNumConformers() == 1);
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auto mb = MolToMolBlock(*core);
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std::cerr << mb << std::endl;
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ROMol *m = SmilesToMol("C1CCCCONC(CCCCCC)NC1");
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TEST_ASSERT(m);
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m->setProp("_Name", "core+sidechain");
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MatchVectType mv;
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SubstructMatch(*m, *core, mv);
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TEST_ASSERT(CoordGen::addCoords(*m) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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TEST_ASSERT(!compareConfs(m, core, mv));
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{
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auto coreConf = core->getConformer();
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RDGeom::INT_POINT2D_MAP coordMap;
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for (auto &i : mv) {
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coordMap[i.second] = RDGeom::Point2D(coreConf.getAtomPos(i.first).x,
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coreConf.getAtomPos(i.first).y);
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}
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CoordGen::CoordGenParams params;
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params.coordMap = coordMap;
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params.dbg_useFixed = true;
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TEST_ASSERT(CoordGen::addCoords(*m, ¶ms) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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// m->setProp("_Name", "templated");
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// mb = MolToMolBlock(*m);
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// std::cerr << mb << std::endl;
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TEST_ASSERT(compareConfs(m, core, mv));
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}
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{
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CoordGen::CoordGenParams params;
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params.templateMol = core;
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params.dbg_useFixed = true;
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TEST_ASSERT(CoordGen::addCoords(*m, ¶ms) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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m->setProp("_Name", "templated");
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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TEST_ASSERT(compareConfs(m, core, mv));
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}
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delete m;
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delete core;
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}
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{
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ROMol *core = SmilesToMol("C1CCCC2C1NCC2");
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TEST_ASSERT(core);
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core->setProp("_Name", "core");
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CoordGen::addCoords(*core);
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TEST_ASSERT(core->getNumConformers() == 1);
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auto mb = MolToMolBlock(*core);
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std::cerr << mb << std::endl;
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ROMol *m = SmilesToMol("C1C(CCC)CC(CC3CC3)C2C1N(C(C)C)CC2");
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TEST_ASSERT(m);
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m->setProp("_Name", "core+sidechain");
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MatchVectType mv;
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SubstructMatch(*m, *core, mv);
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CoordGen::addCoords(*m);
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TEST_ASSERT(m->getNumConformers() == 1);
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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// This is a rigid core: if we provide the matching substructure,
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// and do alignment, the conformations will still match.
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TEST_ASSERT(!compareConfs(m, core, mv, false));
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{
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CoordGen::CoordGenParams params;
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params.templateMol = core;
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CoordGen::addCoords(*m, ¶ms);
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TEST_ASSERT(m->getNumConformers() == 1);
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m->setProp("_Name", "templated");
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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TEST_ASSERT(compareConfs(m, core, mv, true, -1, -1, 0.3));
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}
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delete m;
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delete core;
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}
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{
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ROMol *core = SmilesToMol("CC(N)CC");
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TEST_ASSERT(core);
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core->setProp("_Name", "core");
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CoordGen::addCoords(*core);
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TEST_ASSERT(core->getNumConformers() == 1);
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auto mb = MolToMolBlock(*core);
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std::cerr << mb << std::endl;
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ROMol *m = SmilesToMol("CC(N)CC(O)C");
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TEST_ASSERT(m);
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m->setProp("_Name", "core+sidechain");
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MatchVectType mv;
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SubstructMatch(*m, *core, mv);
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CoordGen::addCoords(*m);
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TEST_ASSERT(m->getNumConformers() == 1);
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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// This mol is just slightly bigger than the core, providing
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// the matching substructure and doing alignment will cause
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// the conformations to match.
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TEST_ASSERT(!compareConfs(m, core, mv, false));
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{
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CoordGen::CoordGenParams params;
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params.templateMol = core;
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CoordGen::addCoords(*m, ¶ms);
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TEST_ASSERT(m->getNumConformers() == 1);
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m->setProp("_Name", "templated");
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mb = MolToMolBlock(*m);
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std::cerr << mb << std::endl;
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TEST_ASSERT(compareConfs(m, core, mv, true, -1, -1, 0.05));
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}
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delete m;
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delete core;
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}
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BOOST_LOG(rdInfoLog) << "done" << std::endl;
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}
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void testGithub1929() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog)
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<< "testing github1929: make sure coordgen works with bogus file names"
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<< std::endl;
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{
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ROMol *m = SmilesToMol("c1cc(CC)cnc1CC(=O)O");
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TEST_ASSERT(m);
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m->setProp("_Name", "test1");
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CoordGen::CoordGenParams params;
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params.templateFileDir = "I_do_not_exist";
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TEST_ASSERT(CoordGen::addCoords(*m, ¶ms) == 0);
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TEST_ASSERT(m->getNumConformers() == 1);
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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 testGithub3131() {
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BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
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BOOST_LOG(rdInfoLog)
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<< "testing github3131: results from coordgen are sometimes not centered"
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<< std::endl;
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{
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auto m1 =
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"CC1=C(C=C(C=C1)NC(=O)C2=CC=C(C=C2)CN3CCN(CC3)C)NC4=NC=CC(=N4)C5=CN=CC="
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"C5"_smiles;
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TEST_ASSERT(m1);
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TEST_ASSERT(CoordGen::addCoords(*m1) == 0);
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TEST_ASSERT(m1->getNumConformers() == 1);
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auto center = MolTransforms::computeCentroid(m1->getConformer());
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TEST_ASSERT(feq(center.x, 0.0));
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TEST_ASSERT(feq(center.y, 0.0));
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}
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{
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auto m1 =
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"CCC1=C2N=C(C=C(N2N=C1)NCC3=C[N+](=CC=C3)[O-])N4CCCC[C@H]4CCO"_smiles;
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TEST_ASSERT(m1);
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TEST_ASSERT(CoordGen::addCoords(*m1) == 0);
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TEST_ASSERT(m1->getNumConformers() == 1);
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auto center = MolTransforms::computeCentroid(m1->getConformer());
|
|
TEST_ASSERT(feq(center.x, 0.0));
|
|
TEST_ASSERT(feq(center.y, 0.0));
|
|
}
|
|
|
|
{
|
|
// make sure that it's not recentered if we provide a coordmap:
|
|
auto m1 =
|
|
"CCC1=C2N=C(C=C(N2N=C1)NCC3=C[N+](=CC=C3)[O-])N4CCCC[C@H]4CCO"_smiles;
|
|
TEST_ASSERT(m1);
|
|
CoordGen::CoordGenParams params;
|
|
params.coordMap[0] = {10.0, 10.0};
|
|
params.coordMap[1] = {11.0, 10.0};
|
|
TEST_ASSERT(CoordGen::addCoords(*m1, ¶ms) == 0);
|
|
TEST_ASSERT(m1->getNumConformers() == 1);
|
|
auto center = MolTransforms::computeCentroid(m1->getConformer());
|
|
TEST_ASSERT(!feq(center.x, 0.0));
|
|
TEST_ASSERT(!feq(center.y, 0.0));
|
|
}
|
|
|
|
{
|
|
// make sure that it's not recentered if we provide a template:
|
|
auto templateMol =
|
|
"C1=C2N=C(C=C(N2N=C1)NCC3=C[N+](=CC=C3))N4CCCC[C@H]4"_smiles;
|
|
TEST_ASSERT(templateMol);
|
|
TEST_ASSERT(CoordGen::addCoords(*templateMol) == 0);
|
|
TEST_ASSERT(templateMol->getNumConformers() == 1);
|
|
|
|
auto center = MolTransforms::computeCentroid(templateMol->getConformer());
|
|
TEST_ASSERT(feq(center.x, 0.0));
|
|
TEST_ASSERT(feq(center.y, 0.0));
|
|
|
|
auto m1 =
|
|
"CCC1=C2N=C(C=C(N2N=C1)NCC3=C[N+](=CC=C3)[O-])N4CCCC[C@H]4CCO"_smiles;
|
|
TEST_ASSERT(m1);
|
|
CoordGen::CoordGenParams params;
|
|
params.templateMol = templateMol.get();
|
|
TEST_ASSERT(CoordGen::addCoords(*m1, ¶ms) == 0);
|
|
TEST_ASSERT(m1->getNumConformers() == 1);
|
|
center = MolTransforms::computeCentroid(m1->getConformer());
|
|
TEST_ASSERT(!feq(center.x, 0.0));
|
|
TEST_ASSERT(!feq(center.y, 0.0));
|
|
}
|
|
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
}
|
|
|
|
void testZOBs() {
|
|
BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
|
|
BOOST_LOG(rdInfoLog) << "testing the zero-order bond setting with coordgen"
|
|
<< std::endl;
|
|
{
|
|
auto m1 =
|
|
R"CTAB(
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 7 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 Al 0.108450 -0.062175 0.000000 0 VAL=3
|
|
M V30 2 C 0.976250 -0.558975 0.000000 0
|
|
M V30 3 C 0.104850 0.937825 0.000000 0
|
|
M V30 4 C -0.755750 -0.565175 0.000000 0
|
|
M V30 5 C 1.840650 -0.055775 0.000000 0
|
|
M V30 6 C -1.623550 -0.068375 0.000000 0
|
|
M V30 7 C -2.487750 -0.571375 0.000000 0
|
|
M V30 8 C 1.836850 0.944025 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 1 3
|
|
M V30 3 1 1 4
|
|
M V30 4 2 2 5
|
|
M V30 5 2 4 6
|
|
M V30 6 1 6 7
|
|
M V30 7 1 5 8
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
TEST_ASSERT(m1);
|
|
TEST_ASSERT(m1->getNumConformers() == 1);
|
|
CoordGen::addCoords(*m1);
|
|
TEST_ASSERT(m1->getNumConformers() == 1);
|
|
{
|
|
std::unique_ptr<ROMol> nm{MolBlockToMol(MolToMolBlock(*m1))};
|
|
TEST_ASSERT(nm);
|
|
TEST_ASSERT(nm->getBondWithIdx(3)->getStereo() ==
|
|
m1->getBondWithIdx(3)->getStereo());
|
|
TEST_ASSERT(nm->getBondWithIdx(4)->getStereo() ==
|
|
m1->getBondWithIdx(4)->getStereo());
|
|
}
|
|
|
|
CoordGen::CoordGenParams ps;
|
|
ps.treatNonterminalBondsToMetalAsZeroOrder = true;
|
|
CoordGen::addCoords(*m1, &ps);
|
|
{
|
|
// the ZOB behavior screws up the double bond stereo here... detect that
|
|
std::unique_ptr<ROMol> nm{MolBlockToMol(MolToMolBlock(*m1))};
|
|
TEST_ASSERT(nm);
|
|
TEST_ASSERT(nm->getBondWithIdx(3)->getStereo() !=
|
|
m1->getBondWithIdx(3)->getStereo());
|
|
TEST_ASSERT(nm->getBondWithIdx(4)->getStereo() !=
|
|
m1->getBondWithIdx(4)->getStereo());
|
|
}
|
|
}
|
|
BOOST_LOG(rdInfoLog) << "done" << std::endl;
|
|
}
|
|
|
|
int main(int argc, char *argv[]) {
|
|
(void)argc;
|
|
(void)argv;
|
|
RDLog::InitLogs();
|
|
#if 1
|
|
test2();
|
|
test1();
|
|
testGithub1929();
|
|
testGithub3131();
|
|
#endif
|
|
testZOBs();
|
|
}
|