mirror of
https://github.com/rdkit/rdkit.git
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cd74dc2207
* very basics: actually parsing the new atom stereochem features * add some input verification for the chiral permutations * fix a typo add quadruple bond SMILES/SMARTS extension * add forgotten files * patch from Roger * add Roger's parsing examples * typo * new tests * adjusted version of next PR from Roger: - add SP2D hybridization for square planar (this may change) - some modernizationof Chirality.cpp - stop using < HybridizationType in Chirality.cpp (should probably do this elsewhere too) - improved handling of hybridization assignment for new stereochem - handle new stereo/hybridization in UFF - tests for the above * perception of non-tetrahedral stereo from 3D (from Roger S) Basic testing of SP and TB based on opensmiles docs * potential fixes for octahedral assignment more tests * docs update need way more! * map the TH tags directly to @ tags * very basics of SMILES writing this does not work with anything that changes the permutation order like canonicalization or writing things in rings. * start to support the getChiralAcross API * more testing * consistency * add hasNonTetrahedralStereo() and getIdealAngleBetweenLigands() * assignStereochemistry should only remove non-tetrahedral stereo * re-simplify those tests * cleanup matrix stream output * initial pass at supporting nontet stereo in distgeom * backup * start on the reference docs * TBP reference * first pass at Oh finished * update SP section * more doc updates * fix a typo * add param to not remove Hs connected to non-tetrahedral atoms * VERY basic coord generation for square planar * TBP basics * basic OH depiction * start testing missing ligands allow non-tet stereo in rings (ugly, but correct) * add new TBP functions from Roger * update depiction code for new API * backup, the new tests work so far * Finish the TB tests * OH tests pass too * cleanup * first pass at getting correct SMILES with reordering need way more testing than this * ensure permutation 0 is correctly preserved * some progress towards adding non-tetrahedral stereo to StereoInfo * doc update * add non-tet chiral classes to python wrappers * make sure removeAllHs also gets neighbors of non-tetrahedral centers more testing * a bit of depictor cleanup * make the assignment from 3D more tolerant more testing * improve the bulk testing * cleanup * remove a bit of redundant code * ensure we don't write bogus permutation values to SMILES * fix some rebase problems * allow assignStereochemistryFrom3D() to be called without sanitization * allow disabling the non-tetrahedral stereo when it's not explicit * get that working on windows too
377 lines
15 KiB
C++
377 lines
15 KiB
C++
//
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// Copyright (C) 2021 Greg Landrum and other RDKit contributors
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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 <RDGeneral/test.h>
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#include "catch.hpp"
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#include <RDGeneral/RDLog.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Chirality.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h>
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#include "Embedder.h"
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#include "BoundsMatrixBuilder.h"
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#include <tuple>
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using namespace RDKit;
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TEST_CASE("Torsions not found in fused macrocycles", "[macrocycles]") {
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RDLog::InitLogs();
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SECTION("reported") {
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// this is 6VY8 from the PDB
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auto mol1 =
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"CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](CCCC[NH3+])NC(=O)[C@H]([C@@H](C)O)NC(O)[C@@H]2CN3NNC[C@H]3C[C@H](NC1=O)C(O)N[C@@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@@H](CCCNC(N)=[NH2+])C(=O)N2"_smiles;
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REQUIRE(mol1);
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MolOps::addHs(*mol1);
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ForceFields::CrystalFF::CrystalFFDetails details;
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bool useExpTorsions = true;
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bool useSmallRingTorsions = false;
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bool useMacrocycleTorsions = true;
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bool useBasicKnowledge = true;
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unsigned int version = 2;
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bool verbose = true;
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std::stringstream sstrm;
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rdInfoLog->SetTee(sstrm);
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ForceFields::CrystalFF::getExperimentalTorsions(
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*mol1, details, useExpTorsions, useSmallRingTorsions,
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useMacrocycleTorsions, useBasicKnowledge, version, verbose);
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rdInfoLog->ClearTee();
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auto txt = sstrm.str();
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CHECK(txt.find("{9-}") != std::string::npos);
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}
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SECTION("edges") {
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std::vector<std::tuple<std::string, bool, unsigned int>> tests{
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{"O=C1CNC(=O)C2CCC(N1)NC(=O)CNC2=O", true, 15}, // 9-9
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{"O=C1NC2CCC(C(=O)N1)C(=O)NCC(=O)N2", true, 4}, // 9-8
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{"O=C1NC2CCC(C(=O)N1)C(=O)NC(=O)N2", false, 0}, // 8-8
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{"O=C1CC(=O)NC2NC(=O)CC(=O)NC(N1)NC(=O)CC(=O)N2", true,
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18}}; // 12-12-12
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for (const auto &tpl : tests) {
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std::unique_ptr<RWMol> m{SmilesToMol(std::get<0>(tpl))};
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REQUIRE(m);
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MolOps::addHs(*m);
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ForceFields::CrystalFF::CrystalFFDetails details;
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bool useExpTorsions = true;
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bool useSmallRingTorsions = false;
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bool useMacrocycleTorsions = true;
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bool useBasicKnowledge = true;
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unsigned int version = 2;
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bool verbose = true;
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std::stringstream sstrm;
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rdInfoLog->SetTee(sstrm);
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std::cerr << "-----------" << std::endl;
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ForceFields::CrystalFF::getExperimentalTorsions(
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*m, details, useExpTorsions, useSmallRingTorsions,
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useMacrocycleTorsions, useBasicKnowledge, version, verbose);
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rdInfoLog->ClearTee();
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auto txt = sstrm.str();
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if (std::get<1>(tpl)) {
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CHECK(txt.find("{9-}") != std::string::npos);
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} else {
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CHECK(txt.find("{9-}") == std::string::npos);
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}
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CHECK(details.expTorsionAngles.size() == std::get<2>(tpl));
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}
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}
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}
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namespace {
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void compareConfs(const ROMol *m, const ROMol *expected, int molConfId = -1,
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int expectedConfId = -1) {
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PRECONDITION(m, "bad pointer");
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PRECONDITION(expected, "bad pointer");
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TEST_ASSERT(m->getNumAtoms() == expected->getNumAtoms());
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const Conformer &conf1 = m->getConformer(molConfId);
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const Conformer &conf2 = expected->getConformer(expectedConfId);
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for (unsigned int i = 0; i < m->getNumAtoms(); i++) {
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TEST_ASSERT(m->getAtomWithIdx(i)->getAtomicNum() ==
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expected->getAtomWithIdx(i)->getAtomicNum());
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RDGeom::Point3D pt1i = conf1.getAtomPos(i);
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RDGeom::Point3D pt2i = conf2.getAtomPos(i);
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TEST_ASSERT((pt1i - pt2i).length() < 0.05);
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}
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}
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} // namespace
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TEST_CASE("update parameters from JSON") {
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std::string rdbase = getenv("RDBASE");
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SECTION("DG") {
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std::string fname =
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rdbase +
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"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.dg.mol";
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std::unique_ptr<RWMol> ref{MolFileToMol(fname, true, false)};
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REQUIRE(ref);
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std::unique_ptr<RWMol> mol{SmilesToMol("OCCC")};
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REQUIRE(mol);
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MolOps::addHs(*mol);
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CHECK(ref->getNumAtoms() == mol->getNumAtoms());
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DGeomHelpers::EmbedParameters params;
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std::string json = R"JSON({"randomSeed":42})JSON";
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DGeomHelpers::updateEmbedParametersFromJSON(params, json);
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CHECK(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
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compareConfs(ref.get(), mol.get());
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}
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SECTION("ETKDG") {
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std::string fname =
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rdbase +
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"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.etkdg.mol";
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std::unique_ptr<RWMol> ref{MolFileToMol(fname, true, false)};
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REQUIRE(ref);
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std::unique_ptr<RWMol> mol{SmilesToMol("OCCC")};
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REQUIRE(mol);
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MolOps::addHs(*mol);
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CHECK(ref->getNumAtoms() == mol->getNumAtoms());
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DGeomHelpers::EmbedParameters params;
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std::string json = R"JSON({"randomSeed":42,
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"useExpTorsionAnglePrefs":true,
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"useBasicKnowledge":true})JSON";
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DGeomHelpers::updateEmbedParametersFromJSON(params, json);
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CHECK(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
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compareConfs(ref.get(), mol.get());
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}
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SECTION("ETKDGv2") {
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std::string fname =
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rdbase +
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"/Code/GraphMol/DistGeomHelpers/test_data/torsion.etkdg.v2.mol";
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std::unique_ptr<RWMol> ref{MolFileToMol(fname, true, false)};
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REQUIRE(ref);
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std::unique_ptr<RWMol> mol{SmilesToMol("n1cccc(C)c1ON")};
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REQUIRE(mol);
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MolOps::addHs(*mol);
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CHECK(ref->getNumAtoms() == mol->getNumAtoms());
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DGeomHelpers::EmbedParameters params;
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std::string json = R"JSON({"randomSeed":42,
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"useExpTorsionAnglePrefs":true,
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"useBasicKnowledge":true,
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"ETversion":2})JSON";
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DGeomHelpers::updateEmbedParametersFromJSON(params, json);
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CHECK(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
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compareConfs(ref.get(), mol.get());
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}
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SECTION("setting atommap") {
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std::unique_ptr<RWMol> mol{SmilesToMol("OCCC")};
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REQUIRE(mol);
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MolOps::addHs(*mol);
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{
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DGeomHelpers::EmbedParameters params;
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std::string json = R"JSON({"randomSeed":42,
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"coordMap":{"0":[0,0,0],"1":[0,0,1.5],"2":[0,1.5,1.5]}})JSON";
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DGeomHelpers::updateEmbedParametersFromJSON(params, json);
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CHECK(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
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delete params.coordMap;
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auto conf = mol->getConformer();
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auto v1 = conf.getAtomPos(0) - conf.getAtomPos(1);
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auto v2 = conf.getAtomPos(2) - conf.getAtomPos(1);
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CHECK(v1.angleTo(v2) == Approx(M_PI / 2).margin(0.15));
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}
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}
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}
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TEST_CASE(
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"github #4346: Specified cis/trans stereo being ignored during "
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"conformation generation in macrocycles") {
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SECTION("basics 1") {
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auto m1 = "C1C/C=C/CCCCCCCC1"_smiles;
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REQUIRE(m1);
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CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
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Bond::BondStereo::STEREOE);
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MolOps::addHs(*m1);
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DGeomHelpers::EmbedParameters params = DGeomHelpers::KDG;
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params.randomSeed = 0xf00d;
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CHECK(DGeomHelpers::EmbedMolecule(*m1, params) != -1);
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MolOps::assignStereochemistryFrom3D(*m1);
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CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
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Bond::BondStereo::STEREOE);
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}
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SECTION("basics 2") {
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auto m1 = "C1C/C=C\\CCCCCCCC1"_smiles;
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REQUIRE(m1);
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CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
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Bond::BondStereo::STEREOZ);
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MolOps::addHs(*m1);
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DGeomHelpers::EmbedParameters params = DGeomHelpers::KDG;
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params.randomSeed = 0xf00d;
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CHECK(DGeomHelpers::EmbedMolecule(*m1, params) != -1);
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MolOps::assignStereochemistryFrom3D(*m1);
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CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
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Bond::BondStereo::STEREOZ);
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}
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}
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TEST_CASE("nontetrahedral stereo", "[nontetrahedral]") {
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SECTION("bounds matrix basics") {
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{
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auto m = "Cl[Pt@SP1]([35Cl])([36Cl])[37Cl]"_smiles;
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REQUIRE(m);
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CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(0))
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->getIdx() == 3);
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CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(2))
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->getIdx() == 4);
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
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Catch::Matchers::WithinAbs(180, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(90, 0.001));
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DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(m->getNumAtoms())};
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DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
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DGeomHelpers::setTopolBounds(*m, bm);
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// std::cerr << *bm << std::endl;
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CHECK(bm->getLowerBound(0, 3) - bm->getLowerBound(0, 2) > 1.0);
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CHECK(bm->getUpperBound(0, 3) - bm->getUpperBound(0, 2) > 1.0);
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}
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{
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auto m = "Cl[Pt@SP1]([35Cl])[36Cl]"_smiles;
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REQUIRE(m);
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CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(0))
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->getIdx() == 3);
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CHECK(!Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(2)));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
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Catch::Matchers::WithinAbs(180, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(90, 0.001));
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DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(m->getNumAtoms())};
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DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
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DGeomHelpers::setTopolBounds(*m, bm);
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// std::cerr << *bm << std::endl;
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CHECK(bm->getLowerBound(0, 3) - bm->getLowerBound(0, 2) > 1.0);
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CHECK(bm->getUpperBound(0, 3) - bm->getUpperBound(0, 2) > 1.0);
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}
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{
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// note that things aren't quite as nice here since we don't actually have
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// TBP UFF parameters
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auto m = "Cl[Pt@TB1]([35Cl])([36Cl])([37Cl])[38Cl]"_smiles;
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REQUIRE(m);
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CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(0))
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->getIdx() == 5);
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CHECK(!Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(2)));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(5)),
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Catch::Matchers::WithinAbs(180, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(90, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(3), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(120, 0.001));
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DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(m->getNumAtoms())};
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DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
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DGeomHelpers::setTopolBounds(*m, bm);
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CHECK(bm->getLowerBound(0, 5) - bm->getLowerBound(0, 2) > 0.5);
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CHECK(bm->getUpperBound(0, 5) - bm->getUpperBound(0, 2) > 0.5);
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CHECK(bm->getLowerBound(0, 5) - bm->getLowerBound(2, 3) > 0.5);
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CHECK(bm->getUpperBound(0, 5) - bm->getUpperBound(2, 3) > 0.5);
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CHECK(bm->getLowerBound(2, 3) - bm->getLowerBound(0, 2) > 0.5);
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CHECK(bm->getUpperBound(2, 3) - bm->getUpperBound(0, 2) > 0.5);
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}
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{
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auto m = "Cl[Th@OH1]([35Cl])([36Cl])([37Cl])([38Cl])[39Cl]"_smiles;
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REQUIRE(m);
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CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(0))
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->getIdx() == 6);
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CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(2))
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->getIdx() == 4);
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CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
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m->getAtomWithIdx(3))
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->getIdx() == 5);
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(6)),
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Catch::Matchers::WithinAbs(180, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(90, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(4), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(180, 0.001));
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CHECK_THAT(
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Chirality::getIdealAngleBetweenLigands(
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m->getAtomWithIdx(1), m->getAtomWithIdx(3), m->getAtomWithIdx(2)),
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Catch::Matchers::WithinAbs(90, 0.001));
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DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(m->getNumAtoms())};
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DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
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DGeomHelpers::setTopolBounds(*m, bm);
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CHECK(bm->getLowerBound(0, 6) - bm->getLowerBound(0, 2) > 0.5);
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CHECK(bm->getUpperBound(0, 6) - bm->getUpperBound(0, 3) > 0.5);
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CHECK(bm->getLowerBound(0, 6) - bm->getLowerBound(2, 3) > 0.5);
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CHECK(bm->getUpperBound(0, 6) - bm->getUpperBound(2, 4) < 0.01);
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CHECK(bm->getLowerBound(2, 4) - bm->getLowerBound(2, 3) > 0.5);
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}
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}
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#if 1
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SECTION("Embedding") {
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{
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auto m = "Cl[Pt@SP1](<-N)(<-N)[Cl]"_smiles;
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REQUIRE(m);
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m->setProp("_Name", "cis platin");
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MolOps::addHs(*m);
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CHECK(DGeomHelpers::EmbedMolecule(*m) == 0);
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auto mb = MolToV3KMolBlock(*m);
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// std::cerr << mb << std::endl;
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std::unique_ptr<RWMol> m2(MolBlockToMol(mb));
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MolOps::assignStereochemistryFrom3D(*m2);
|
|
CHECK(m2->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_SQUAREPLANAR);
|
|
unsigned int perm = 100;
|
|
CHECK(m2->getAtomWithIdx(1)->getPropIfPresent(
|
|
common_properties::_chiralPermutation, perm));
|
|
CHECK(perm == 1);
|
|
}
|
|
{
|
|
auto m = "Cl[Pt@SP3](<-N)(<-N)[Cl]"_smiles;
|
|
REQUIRE(m);
|
|
m->setProp("_Name", "trans platin");
|
|
MolOps::addHs(*m);
|
|
CHECK(DGeomHelpers::EmbedMolecule(*m) == 0);
|
|
auto mb = MolToV3KMolBlock(*m);
|
|
// std::cerr << mb << std::endl;
|
|
std::unique_ptr<RWMol> m2(MolBlockToMol(mb));
|
|
MolOps::assignStereochemistryFrom3D(*m2);
|
|
CHECK(m2->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_SQUAREPLANAR);
|
|
unsigned int perm = 100;
|
|
CHECK(m2->getAtomWithIdx(1)->getPropIfPresent(
|
|
common_properties::_chiralPermutation, perm));
|
|
CHECK(perm == 3);
|
|
}
|
|
}
|
|
#endif
|
|
} |