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7a9265b103
* Fixes #8420 * Update Code/GraphMol/Chirality.cpp Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com> --------- Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
6160 lines
209 KiB
C++
6160 lines
209 KiB
C++
//
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// Copyright (C) 2020-2025 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 <cstdlib>
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#include <catch2/catch_all.hpp>
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#include <boost/noncopyable.hpp>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/StereoGroup.h>
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#include <GraphMol/Chirality.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/test_fixtures.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/FileParsers/MolFileStereochem.h>
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#include <GraphMol/FileParsers/MolSupplier.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/CIPLabeler/CIPLabeler.h>
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using namespace RDKit;
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unsigned count_wedged_bonds(const ROMol &mol) {
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unsigned nWedged = 0;
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for (const auto bond : mol.bonds()) {
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if (bond->getBondDir() != Bond::BondDir::NONE) {
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++nWedged;
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}
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}
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return nWedged;
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}
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TEST_CASE("bond StereoInfo", "[unittest]") {
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SECTION("basics") {
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{
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auto mol = "CC=C(C#C)C=C"_smiles;
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REQUIRE(mol);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 4);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
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CHECK(sinfo.controllingAtoms[2] == 3);
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CHECK(sinfo.controllingAtoms[3] == 5);
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CHECK(sinfo.specified == Chirality::StereoSpecified::Unspecified);
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CHECK(sinfo.descriptor == Chirality::StereoDescriptor::None);
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}
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{
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auto mol = "CC=NC=N"_smiles;
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REQUIRE(mol);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 4);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
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CHECK(sinfo.controllingAtoms[2] == 3);
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CHECK(sinfo.controllingAtoms[3] == Chirality::StereoInfo::NOATOM);
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}
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}
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SECTION("stereo") {
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{
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auto mol = "C/C=C(/C#C)C"_smiles;
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REQUIRE(mol);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms().size() == 2);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[0] == 0);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[1] == 3);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 4);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
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CHECK(sinfo.controllingAtoms[2] == 3);
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CHECK(sinfo.controllingAtoms[3] == 5);
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CHECK(sinfo.specified == Chirality::StereoSpecified::Specified);
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CHECK(sinfo.descriptor == Chirality::StereoDescriptor::Bond_Trans);
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}
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{ // check an example where one of the stereo atoms isn't the first
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// neighbor
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auto mol = "C/C=C(/C)C#C"_smiles;
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REQUIRE(mol);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms().size() == 2);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[0] == 0);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[1] == 4);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 4);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
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CHECK(sinfo.controllingAtoms[2] == 3);
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CHECK(sinfo.controllingAtoms[3] == 4);
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CHECK(sinfo.specified == Chirality::StereoSpecified::Specified);
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CHECK(sinfo.descriptor == Chirality::StereoDescriptor::Bond_Trans);
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}
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{
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auto mol = "C/C=C(\\C#C)C"_smiles;
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REQUIRE(mol);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms().size() == 2);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[0] == 0);
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CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[1] == 3);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 4);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
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CHECK(sinfo.controllingAtoms[2] == 3);
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CHECK(sinfo.controllingAtoms[3] == 5);
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CHECK(sinfo.specified == Chirality::StereoSpecified::Specified);
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CHECK(sinfo.descriptor == Chirality::StereoDescriptor::Bond_Cis);
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}
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{ // any bonds
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auto mol = "CC=C(C#C)C"_smiles;
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REQUIRE(mol);
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mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 4);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
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CHECK(sinfo.controllingAtoms[2] == 3);
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CHECK(sinfo.controllingAtoms[3] == 5);
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CHECK(sinfo.specified == Chirality::StereoSpecified::Unknown);
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CHECK(sinfo.descriptor == Chirality::StereoDescriptor::None);
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}
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}
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}
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TEST_CASE("isBondPotentialStereoBond", "[unittest]") {
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SECTION("basics") {
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{
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auto mol = "CC=C(C#C)C=C"_smiles;
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REQUIRE(mol);
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CHECK(
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Chirality::detail::isBondPotentialStereoBond(mol->getBondWithIdx(1)));
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CHECK(!Chirality::detail::isBondPotentialStereoBond(
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mol->getBondWithIdx(5)));
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CHECK(!Chirality::detail::isBondPotentialStereoBond(
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mol->getBondWithIdx(3)));
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CHECK(!Chirality::detail::isBondPotentialStereoBond(
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mol->getBondWithIdx(4)));
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}
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{
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auto mol = "CC=NC=N"_smiles;
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REQUIRE(mol);
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CHECK(
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Chirality::detail::isBondPotentialStereoBond(mol->getBondWithIdx(1)));
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CHECK(
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Chirality::detail::isBondPotentialStereoBond(mol->getBondWithIdx(3)));
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}
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{
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SmilesParserParams ps;
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ps.removeHs = false;
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std::unique_ptr<ROMol> mol{SmilesToMol("[H]C=CC=C([H])[H]", ps)};
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REQUIRE(mol);
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CHECK(!Chirality::detail::isBondPotentialStereoBond(
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mol->getBondWithIdx(1)));
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CHECK(!Chirality::detail::isBondPotentialStereoBond(
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mol->getBondWithIdx(3)));
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}
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}
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SECTION("ring size") {
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{
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auto m = "C1=CCCCC1"_smiles;
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REQUIRE(m);
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CHECK(
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!Chirality::detail::isBondPotentialStereoBond(m->getBondWithIdx(0)));
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}
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{
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auto m = "C1=CCCCCC1"_smiles;
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REQUIRE(m);
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CHECK(
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!Chirality::detail::isBondPotentialStereoBond(m->getBondWithIdx(0)));
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}
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{
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auto m = "C12=C(CCCC2)CCCCCC1"_smiles;
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REQUIRE(m);
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CHECK(
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!Chirality::detail::isBondPotentialStereoBond(m->getBondWithIdx(0)));
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}
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}
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}
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TEST_CASE("atom StereoInfo", "[unittest]") {
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SECTION("basics") {
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{
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auto mol = "CC(F)(Cl)CNC(C)C"_smiles;
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REQUIRE(mol);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 4);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == 2);
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CHECK(sinfo.controllingAtoms[2] == 3);
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CHECK(sinfo.controllingAtoms[3] == 4);
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CHECK(sinfo.specified == Chirality::StereoSpecified::Unspecified);
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CHECK(sinfo.descriptor == Chirality::StereoDescriptor::None);
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sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(6));
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CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(sinfo.centeredOn == 6);
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REQUIRE(sinfo.controllingAtoms.size() == 3);
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CHECK(sinfo.controllingAtoms[0] == 5);
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CHECK(sinfo.controllingAtoms[1] == 7);
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CHECK(sinfo.controllingAtoms[2] == 8);
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CHECK(sinfo.specified == Chirality::StereoSpecified::Unspecified);
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CHECK(sinfo.descriptor == Chirality::StereoDescriptor::None);
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}
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{
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auto mol = "C[C@](F)(Cl)CNC(C)C"_smiles;
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REQUIRE(mol);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 4);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == 2);
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CHECK(sinfo.controllingAtoms[2] == 3);
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CHECK(sinfo.controllingAtoms[3] == 4);
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CHECK(sinfo.specified == Chirality::StereoSpecified::Specified);
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CHECK(sinfo.descriptor == Chirality::StereoDescriptor::Tet_CCW);
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}
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{
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auto mol = "CN1CC1N(F)C"_smiles;
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REQUIRE(mol);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 3);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == 2);
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CHECK(sinfo.controllingAtoms[2] == 3);
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}
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{
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auto mol = "O[As](F)C[As]C[As]"_smiles;
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REQUIRE(mol);
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auto sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(1));
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CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(sinfo.centeredOn == 1);
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REQUIRE(sinfo.controllingAtoms.size() == 3);
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CHECK(sinfo.controllingAtoms[0] == 0);
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CHECK(sinfo.controllingAtoms[1] == 2);
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CHECK(sinfo.controllingAtoms[2] == 3);
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sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(4));
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CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(sinfo.centeredOn == 4);
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REQUIRE(sinfo.controllingAtoms.size() == 2);
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CHECK(sinfo.controllingAtoms[0] == 3);
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CHECK(sinfo.controllingAtoms[1] == 5);
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}
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}
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}
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TEST_CASE("isAtomPotentialTetrahedralCenter", "[unittest]") {
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SECTION("basics") {
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{
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auto mol = "CC(F)(Cl)CNC(C)(C)C"_smiles;
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REQUIRE(mol);
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(1)));
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CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(0)));
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CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(4)));
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(6)));
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}
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{
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auto mol = "CN1CC1N(F)C"_smiles;
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REQUIRE(mol);
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(1)));
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CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(4)));
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}
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{
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auto mol = "O=S(F)CC[S+]([O-])CS=O"_smiles;
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REQUIRE(mol);
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(1)));
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(5)));
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CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(8)));
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}
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{
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auto mol = "O=[Se](F)CC[Se+]([O-])C[Se]=O"_smiles;
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REQUIRE(mol);
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(1)));
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(5)));
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CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(8)));
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}
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{
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auto mol = "OP(F)CPCP"_smiles;
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REQUIRE(mol);
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(1)));
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(4)));
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CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(6)));
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}
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{
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auto mol = "O[As](F)C[As]C[As]"_smiles;
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REQUIRE(mol);
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(1)));
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(4)));
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CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(6)));
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}
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{
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auto mol = "O[P]([O-])(=O)OC"_smiles;
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REQUIRE(mol);
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
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mol->getAtomWithIdx(1)));
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}
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}
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}
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TEST_CASE("isAtomPotentialStereoAtom", "[unittest]") {
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SECTION("basics") {
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{
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auto mol = "CC(F)(Cl)CNC(C)(C)C"_smiles;
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REQUIRE(mol);
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for (const auto atom : mol->atoms()) {
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(atom) ==
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Chirality::detail::isAtomPotentialStereoAtom(atom));
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}
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}
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{
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auto mol = "CN1CC1N(F)C"_smiles;
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REQUIRE(mol);
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for (const auto atom : mol->atoms()) {
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(atom) ==
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Chirality::detail::isAtomPotentialStereoAtom(atom));
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}
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}
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{
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auto mol = "O=S(F)CC[S+]([O-])CS=O"_smiles;
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REQUIRE(mol);
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for (const auto atom : mol->atoms()) {
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CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(atom) ==
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Chirality::detail::isAtomPotentialStereoAtom(atom));
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}
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}
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}
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}
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TEST_CASE("possible stereochemistry on atoms", "[chirality]") {
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SECTION("specified") {
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{
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auto mol = "CC(C)(O)[C@](Cl)(F)I"_smiles;
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REQUIRE(mol);
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auto stereoInfo = Chirality::findPotentialStereo(*mol);
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REQUIRE(stereoInfo.size() == 1);
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CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
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CHECK(stereoInfo[0].centeredOn == 4);
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std::vector<unsigned> catoms = {1, 5, 6, 7};
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CHECK(stereoInfo[0].controllingAtoms == catoms);
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}
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{
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auto mol = "C[C@@H](O)[C@H](C)[C@H](C)O"_smiles;
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REQUIRE(mol);
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auto stereoInfo = Chirality::findPotentialStereo(*mol);
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REQUIRE(stereoInfo.size() == 3);
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CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
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CHECK(stereoInfo[0].centeredOn == 1);
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CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
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CHECK(stereoInfo[1].centeredOn == 3);
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CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
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CHECK(stereoInfo[2].specified == Chirality::StereoSpecified::Specified);
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CHECK(stereoInfo[2].centeredOn == 5);
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}
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{
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auto mol = "FC(F)(F)[C@@H](O)[C@H](C)[C@H](C(F)(F)F)O"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 3);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(stereoInfo[0].centeredOn == 4);
|
|
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(stereoInfo[1].centeredOn == 6);
|
|
|
|
CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[2].specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(stereoInfo[2].centeredOn == 8);
|
|
}
|
|
}
|
|
SECTION("simple unspecified") {
|
|
{
|
|
auto mol = "CC(C)(O)C(Cl)(F)I"_smiles;
|
|
REQUIRE(mol);
|
|
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[0].centeredOn == 4);
|
|
std::vector<unsigned> catoms = {1, 5, 6, 7};
|
|
CHECK(stereoInfo[0].controllingAtoms == catoms);
|
|
}
|
|
}
|
|
SECTION("atoms with unknown set, real") {
|
|
auto mol = "FC(O)C"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BondDir::UNKNOWN);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
}
|
|
SECTION("atoms with unknown set, not real") {
|
|
auto mol = "CC(O)C"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BondDir::UNKNOWN);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
SECTION("Isotopes") {
|
|
{
|
|
auto mol = "O[C@H](F)[18OH]"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
std::vector<unsigned> catoms = {0, 2, 3};
|
|
CHECK(stereoInfo[0].controllingAtoms == catoms);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("possible stereochemistry on bonds", "[chirality]") {
|
|
SECTION("simplest") {
|
|
{
|
|
auto mol = "CC=CC"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
std::vector<unsigned> catoms = {0, Chirality::StereoInfo::NOATOM, 3,
|
|
Chirality::StereoInfo::NOATOM};
|
|
CHECK(stereoInfo[0].controllingAtoms == catoms);
|
|
}
|
|
{
|
|
auto mol = "CC=C(C)C"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
{
|
|
auto mol = "CC=C"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
{
|
|
auto mol = "CC(F)=C(Cl)C"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 2);
|
|
std::vector<unsigned> catoms = {2, 0, 4, 5};
|
|
CHECK(stereoInfo[0].controllingAtoms == catoms);
|
|
}
|
|
{
|
|
auto mol = "CC=C(Cl)C"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
std::vector<unsigned> catoms = {0, Chirality::StereoInfo::NOATOM, 3, 4};
|
|
CHECK(stereoInfo[0].controllingAtoms == catoms);
|
|
}
|
|
}
|
|
SECTION("bond with unknown set, real") {
|
|
auto mol = "CC=C(C)F"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
}
|
|
SECTION("bond with unknown set, not real") {
|
|
auto mol = "CC=C(C)C"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("para-stereocenters and assignStereochemistry", "[chirality]") {
|
|
SECTION("simplest") {
|
|
auto mol = "CC(F)C(C)C(C)F"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 3);
|
|
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].controllingAtoms.size() == 3);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 3);
|
|
CHECK(stereoInfo[1].controllingAtoms.size() == 3);
|
|
CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[2].centeredOn == 5);
|
|
CHECK(stereoInfo[2].controllingAtoms.size() == 3);
|
|
}
|
|
|
|
SECTION("including bonds") {
|
|
// thanks to Salome Rieder for this nasty example
|
|
auto mol = "CC=CC(C=CC)C(C)C(C=CC)C=CC"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.size() == 7);
|
|
|
|
std::sort(stereoInfo.begin(), stereoInfo.end(),
|
|
[](const Chirality::StereoInfo &a,
|
|
const Chirality::StereoInfo &b) -> bool {
|
|
return (a.type < b.type) && (a.centeredOn < b.centeredOn) &&
|
|
(a.specified < b.specified) &&
|
|
(a.descriptor < b.descriptor) &&
|
|
(a.controllingAtoms < b.controllingAtoms);
|
|
});
|
|
REQUIRE(stereoInfo.size() == 7);
|
|
|
|
CHECK(stereoInfo[6].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[6].centeredOn == 13);
|
|
CHECK(stereoInfo[5].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[5].centeredOn == 10);
|
|
CHECK(stereoInfo[4].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[4].centeredOn == 4);
|
|
CHECK(stereoInfo[3].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[3].centeredOn == 1);
|
|
|
|
CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[2].centeredOn == 9);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 7);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 3);
|
|
}
|
|
|
|
SECTION("sugar fun") {
|
|
auto mol = "C1(O)C(O)C(O)C(O)C(O)C1O"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 6);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.centeredOn % 2 == 0);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("ring stereochemistry", "[chirality]") {
|
|
SECTION("partially specified") {
|
|
SmilesParserParams ps;
|
|
ps.sanitize = false;
|
|
std::unique_ptr<RWMol> mol{SmilesToMol("C[C@H]1CCC(C)CC1", ps)};
|
|
REQUIRE(mol);
|
|
// std::cerr << "------------ 3 -------------" << std::endl;
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 4);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
SECTION("specified") {
|
|
auto mol = "C[C@H]1CC[C@@H](C)CC1"_smiles;
|
|
REQUIRE(mol);
|
|
// std::cerr << "------------ 1 -------------" << std::endl;
|
|
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 4);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
SECTION("unspecified") {
|
|
auto mol = "CC1CCC(C)CC1"_smiles;
|
|
REQUIRE(mol);
|
|
// std::cerr << "------------ 2 -------------" << std::endl;
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 4);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
SECTION("four ring") {
|
|
auto mol = "C[C@H]1C[C@@H](C)C1"_smiles;
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
|
|
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 3);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
SECTION("four ring unspecified") {
|
|
auto mol = "CC1CC(C)C1"_smiles;
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 3);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("tricky recursive example from Dan Nealschneider", "[chirality]") {
|
|
SECTION("adapted") {
|
|
auto mol = "CC=C1CCC(O)CC1"_smiles;
|
|
REQUIRE(mol);
|
|
mol->updatePropertyCache();
|
|
MolOps::setBondStereoFromDirections(*mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 5);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[1].centeredOn == 1);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
SECTION("simplified") {
|
|
// can't sanitize this because the current (2020.03) assignStereochemistry
|
|
// code doesn't recognize the stereo here and removes it
|
|
SmilesParserParams ps;
|
|
ps.sanitize = false;
|
|
ps.removeHs = false;
|
|
std::unique_ptr<ROMol> mol(SmilesToMol("C/C=C1/C[C@H](O)C1", ps));
|
|
REQUIRE(mol);
|
|
mol->updatePropertyCache();
|
|
MolOps::setBondStereoFromDirections(*mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 4);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[1].centeredOn == 1);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
// FIX this still isn't working
|
|
SECTION("unspecified") {
|
|
auto mol = "CC=C1C[CH](O)C1"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 4);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[1].centeredOn == 1);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("unknown stereo", "[chirality]") {
|
|
SECTION("atoms") {
|
|
auto mol = "CC(O)C[C@@H](O)F"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getBondBetweenAtoms(0, 1));
|
|
mol->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BondDir::UNKNOWN);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 4);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
SECTION("atoms2") {
|
|
// artificial situation: "squiggly bond" overrides the specified atomic
|
|
// stereo
|
|
auto mol = "C[C@H](O)C[C@@H](O)F"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getBondBetweenAtoms(0, 1));
|
|
mol->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BondDir::UNKNOWN);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 4);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
SECTION("bonds") {
|
|
{
|
|
auto mol = "CC=CC"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getBondBetweenAtoms(1, 2));
|
|
mol->getBondBetweenAtoms(1, 2)->setBondDir(Bond::BondDir::EITHERDOUBLE);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
}
|
|
{
|
|
auto mol = "CC=CC=C"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getBondBetweenAtoms(1, 2));
|
|
mol->getBondBetweenAtoms(1, 2)->setBondDir(Bond::BondDir::EITHERDOUBLE);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
}
|
|
}
|
|
SECTION("bonds with squiggle bonds") {
|
|
{ // to begin atom
|
|
auto mol = "CC=CC"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getBondBetweenAtoms(0, 1));
|
|
mol->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BondDir::UNKNOWN);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
}
|
|
{ // to end atom
|
|
auto mol = "CC=CC"_smiles;
|
|
REQUIRE(mol);
|
|
REQUIRE(mol->getBondBetweenAtoms(2, 3));
|
|
mol->getBondBetweenAtoms(2, 3)->setBondDir(Bond::BondDir::UNKNOWN);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("cleaning chirality", "[chirality]") {
|
|
SECTION("atoms") {
|
|
auto mol = "CC(O)C"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getAtomWithIdx(1)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
{
|
|
// by default we don't clean up, so the chiral center survives even though
|
|
// we don't get any results:
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.size() == 0);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
}
|
|
{
|
|
bool cleanIt = true;
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol, cleanIt);
|
|
CHECK(stereoInfo.size() == 0);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("bonds") {
|
|
auto mol = "CC=C(C)C"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(1)->setStereoAtoms(0, 3);
|
|
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOCIS);
|
|
{
|
|
// by default we don't clean up, so the stereo bond survives even though
|
|
// we don't get any results:
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.size() == 0);
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOCIS);
|
|
}
|
|
{
|
|
bool cleanIt = true;
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol, cleanIt);
|
|
CHECK(stereoInfo.size() == 0);
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() ==
|
|
Bond::BondStereo::STEREONONE);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("flagPossible", "[chirality]") {
|
|
SECTION("atoms") {
|
|
auto mol = "CC(O)[C@H](F)O"_smiles;
|
|
REQUIRE(mol);
|
|
{
|
|
// by default we do use flagPossible:
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 3);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
{
|
|
bool cleanIt = false;
|
|
bool flagPossible = false;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 3);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
}
|
|
SECTION("bonds") {
|
|
auto mol = "CC=C/C=C/C"_smiles;
|
|
REQUIRE(mol);
|
|
{
|
|
// by default we do use flagPossible
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[1].centeredOn == 3);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = false;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
|
|
CHECK(stereoInfo[0].centeredOn == 3);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("cleanup after removing possible centers", "[chirality]") {
|
|
SECTION("atoms1") {
|
|
auto mol = "FC(Cl)(F)C(C(Cl)(F)F)I"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.empty());
|
|
}
|
|
SECTION("bonds1") {
|
|
auto mol = "FC(Cl)(F)C(C(Cl)(F)F)=CF"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.empty());
|
|
}
|
|
SECTION("atoms2") {
|
|
auto mol = "ClC(F)(F)C(=CC(F)C=C(C(F)(F)Cl)C(F)(F)Cl)C(Cl)(F)F"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.empty());
|
|
}
|
|
}
|
|
|
|
TEST_CASE("findPotentialStereo problems related to #3490", "[chirality][bug]") {
|
|
SECTION("example 1") {
|
|
auto mol = "CC1CC(O)C1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 3);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
SECTION("example 2a") {
|
|
auto mol = "C(C(C)C1)C12CCN2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
SECTION("example 2b") {
|
|
auto mol = "CC(C1)CC12CCN2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
SECTION("example 2c") {
|
|
auto mol = "C([C@H](C)C1)[C@]12CCN2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
SECTION("example 2d") {
|
|
auto mol = "C[C@H](C1)C[C@]12CCN2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
SECTION("example 3") {
|
|
auto mol = "C(C(C)C1)C12CN(C3)CCCCC23"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 4); // [1, 4, 6, 12]
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 4);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[2].centeredOn == 6);
|
|
CHECK(stereoInfo[2].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[3].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[3].centeredOn == 12);
|
|
CHECK(stereoInfo[3].specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
}
|
|
TEST_CASE("ring stereo finding is overly aggressive", "[chirality][bug]") {
|
|
SECTION("Finding too much 1a") {
|
|
auto mol = "CC1CCCCC1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
SECTION("Finding too much 1b") {
|
|
auto mol = "CC1CCC(C)CC1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
SECTION("Finding too much 1c") {
|
|
auto mol = "C[C@H]1CCC(C)CC1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
SECTION("Finding too much 1d") {
|
|
auto mol = "CC1(C)CCCCC1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
SECTION("Finding too much 1e") {
|
|
auto mol = "CC1(C)CCC(C)CC1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
SECTION("Finding too much 1f") {
|
|
auto mol = "C2CC2C1(C2CC2)CCCCC1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
SECTION("Finding too much 1g") {
|
|
auto mol = "CC1CC2(CCC2)C1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
SECTION("Finding too much 1h") {
|
|
auto mol = "CC1CC2(CC(C)C2)C1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 3);
|
|
}
|
|
|
|
SECTION("Finding too much 2a") {
|
|
auto mol = "CC1CCNCC1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
SECTION("Finding too much 2b") {
|
|
auto mol = "CC1CCN(C)CC1"_smiles; // 3-coordinate N is not stereogenic
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
SECTION("Finding too much 3a") {
|
|
auto mol = "CC1CCC1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
|
|
SECTION("Finding too much 3b") {
|
|
auto mol = "CC1CC(C)C1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
SECTION("fused rings 1") {
|
|
auto mol = "C1CCC2CCCCC2C1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
|
|
SECTION("fused rings 2") {
|
|
auto mol = "C1CC2CCCC2C1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
|
|
SECTION("cages 1") {
|
|
auto mol = "CC1CN2CCC1CC2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 3);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[1].centeredOn == 3);
|
|
CHECK(stereoInfo[2].centeredOn == 6);
|
|
}
|
|
SECTION("cages 1b") {
|
|
auto mol = "O1CN2CCC1CC2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].centeredOn == 2);
|
|
CHECK(stereoInfo[1].centeredOn == 5);
|
|
}
|
|
SECTION("cages 2") {
|
|
auto mol = "C1CC2(O)CCC1(C)CC2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].centeredOn == 2);
|
|
CHECK(stereoInfo[1].centeredOn == 6);
|
|
}
|
|
SECTION("cages 3") {
|
|
auto mol = "C1CC2(O)CCC1CC2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].centeredOn == 2);
|
|
CHECK(stereoInfo[1].centeredOn == 6);
|
|
}
|
|
SECTION("adamantyl") {
|
|
auto mol = "CC12CC3CC(CC(C3)C1)C2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 4);
|
|
}
|
|
SECTION("bug 1a") {
|
|
// example that came up during testing
|
|
auto mol = "C(=O)C(C(C)N2C=C2)C(=O)"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].centeredOn == 3);
|
|
}
|
|
SECTION("bug 1b") {
|
|
// example that came up during testing
|
|
auto mol = "C(=O)C(C(CC)c2ccc(Cl)cc2)C(=O)"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].centeredOn == 3);
|
|
}
|
|
|
|
SECTION("bug 1c") {
|
|
// example that came up during testing
|
|
auto mol = "O=CC(C=O)C(C)n2cccc2"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].centeredOn == 5);
|
|
}
|
|
|
|
SECTION("bug 1c") {
|
|
// example that came up during testing
|
|
auto mol = "C(=O)C(C(C)n2cccc2)C(=O)"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].centeredOn == 3);
|
|
}
|
|
|
|
SECTION("bug 1d") {
|
|
// example that came up during testing
|
|
auto mol = "C(O)C(C(C)n2cccc2)C(O)"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].centeredOn == 3);
|
|
}
|
|
SECTION("just a bug") {
|
|
// example that came up during testing
|
|
|
|
auto mol = "CC1=CN(C2OC(CNC(=O)C3c4ccccc4Sc4ccccc43)CC2)C(=O)NC1=O"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 2);
|
|
}
|
|
SECTION(
|
|
"Removal of stereoatoms requires removing CIS/TRANS when using legacy stereo") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
|
|
{
|
|
auto mol = "N/C=C/C"_smiles;
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() ==
|
|
Bond::BondStereo::STEREOTRANS);
|
|
auto rwmol = dynamic_cast<RWMol *>(mol.get());
|
|
rwmol->removeBond(0, 1);
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() ==
|
|
Bond::BondStereo::STEREONONE);
|
|
}
|
|
{
|
|
auto mol = "N/C=C/C"_smiles;
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() ==
|
|
Bond::BondStereo::STEREOTRANS);
|
|
auto rwmol = dynamic_cast<RWMol *>(mol.get());
|
|
rwmol->removeBond(2, 3);
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() ==
|
|
Bond::BondStereo::STEREONONE);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"github #3631: Ring stereochemistry not properly removed from N atoms",
|
|
"[chirality][bug]") {
|
|
SECTION("basics") {
|
|
SmilesParserParams ps;
|
|
ps.sanitize = false;
|
|
ps.removeHs = false;
|
|
std::unique_ptr<RWMol> mol{SmilesToMol("C[N@]1C[C@@](F)(Cl)C1", ps)};
|
|
REQUIRE(mol);
|
|
MolOps::sanitizeMol(*mol);
|
|
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol->getAtomWithIdx(3)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
bool force = true;
|
|
{
|
|
RWMol mol2(*mol);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(mol2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
{
|
|
RWMol mol2(*mol);
|
|
MolOps::assignStereochemistry(mol2, cleanIt, force, flagPossible);
|
|
CHECK(mol2.getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol2.getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("default behavior") {
|
|
auto mol = "C[N@]1C[C@@](F)(Cl)C1"_smiles;
|
|
REQUIRE(mol);
|
|
auto smiles = MolToSmiles(*mol);
|
|
CHECK(smiles == "CN1CC(F)(Cl)C1");
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
bool force = true;
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol->getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
{
|
|
RWMol mol2(*mol);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(mol2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 0);
|
|
}
|
|
{
|
|
RWMol mol2(*mol);
|
|
MolOps::assignStereochemistry(mol2, cleanIt, force, flagPossible);
|
|
CHECK(mol2.getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol2.getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("don't overcorrect") {
|
|
auto mol = "C[N@]1O[C@@](F)(Cl)C1"_smiles;
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
bool force = true;
|
|
{
|
|
RWMol mol2(*mol);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(mol2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 1);
|
|
CHECK(stereoInfo[0].centeredOn == 3);
|
|
}
|
|
{
|
|
RWMol mol2(*mol);
|
|
MolOps::assignStereochemistry(mol2, cleanIt, force, flagPossible);
|
|
CHECK(mol2.getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol2.getAtomWithIdx(3)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("N Chirality in rings") {
|
|
SECTION("basics 4 coordinate") {
|
|
{
|
|
auto mol = "CC1CC2CC[N@@+]1(C)OC2"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(6)->getAtomicNum() == 7);
|
|
CHECK(mol->getAtomWithIdx(6)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
{
|
|
auto mol = "C[N@@+](F)(Cl)O"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(1)->getAtomicNum() == 7);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("basics 3 coordinate") {
|
|
{
|
|
auto mol = "CC1CC2CC[N@@]1OC2"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(6)->getAtomicNum() == 7);
|
|
CHECK(mol->getAtomWithIdx(6)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
{
|
|
auto mol = "C1CC[N@]2OCCCC2C1"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(3)->getAtomicNum() == 7);
|
|
CHECK(mol->getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("ring stereo") {
|
|
{ // real chirality
|
|
auto mol = "C[C@H]1CC[N@@+](C)(O)OC1"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(4)->getAtomicNum() == 7);
|
|
CHECK(mol->getAtomWithIdx(4)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol->getAtomWithIdx(1)->getAtomicNum() == 6);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
{ // ring stereo
|
|
auto mol = "C[C@H]1CC[N@@+](C)(O)CC1"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(4)->getAtomicNum() == 7);
|
|
CHECK(mol->getAtomWithIdx(4)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol->getAtomWithIdx(1)->getAtomicNum() == 6);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
{ // three-ring degree-three ring stereo
|
|
auto mol = "C[C@H]1[C@@H](C)[N@]1C"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(4)->getAtomicNum() == 7);
|
|
CHECK(mol->getAtomWithIdx(4)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
{ // CHEMBL79374
|
|
auto mol = "Cn1ncc([C@]23CC[N@](CC2)C3)n1"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(8)->getAtomicNum() == 7);
|
|
CHECK(mol->getAtomWithIdx(8)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
{ // derived from CHEMBL79374
|
|
auto mol = "Cn1ncc([C@]23CC[C@](CC2)C3)n1"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(8)->getAtomicNum() == 6);
|
|
CHECK(mol->getAtomWithIdx(8)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #4115: RemoveStereochemistry should also remove stereogroups") {
|
|
SECTION("basics") {
|
|
auto mol = "C[C@H](O)[C@@H](C)F |o1:1,3,r|"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol->getAtomWithIdx(3)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol->getStereoGroups().size() == 1);
|
|
MolOps::removeStereochemistry(*mol);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol->getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol->getStereoGroups().empty());
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #4155: Problem finding stereocenters in bridged bicyclics with "
|
|
"4-rings") {
|
|
SECTION("specified") {
|
|
std::vector<std::string> smis = {
|
|
"C[C@H]1CC[C@H](CC1)C(N)=O", "C[C@]12CC[C@](CC1)(C2)C(N)=O",
|
|
"C[C@H]1C[C@H](C1)C(N)=O", "C[C@]12C[C@](C1)(CC2)C(N)=O"};
|
|
for (const auto &smi : smis) {
|
|
std::unique_ptr<ROMol> mol(SmilesToMol(smi));
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
}
|
|
}
|
|
SECTION("unspecified") {
|
|
std::vector<std::string> smis = {
|
|
"CC1CCC(CC1)C(N)=O", "CC12CCC(CC1)(C2)C(N)=O", "CC1CC(C1)C(N)=O",
|
|
"CC12CC(C1)(CC2)C(N)=O"};
|
|
for (const auto &smi : smis) {
|
|
std::unique_ptr<ROMol> mol(SmilesToMol(smi));
|
|
REQUIRE(mol);
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("pickBondsToWedge() should avoid double bonds") {
|
|
SECTION("simplest") {
|
|
auto mol = "OC=C[C@H](C1CC1)C2CCC2"_smiles;
|
|
REQUIRE(mol);
|
|
auto wedgedBonds = Chirality::pickBondsToWedge(*mol);
|
|
REQUIRE(wedgedBonds.size() == 1);
|
|
auto head = wedgedBonds.begin();
|
|
CHECK(head->first == 3);
|
|
CHECK(head->second->getIdx() == 3);
|
|
}
|
|
SECTION("simplest, specified double bond") {
|
|
auto mol = "OC=C[C@H](C1CC1)C2CCC2"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondBetweenAtoms(1, 2)->setStereoAtoms(0, 3);
|
|
mol->getBondBetweenAtoms(1, 2)->setStereo(Bond::BondStereo::STEREOCIS);
|
|
auto wedgedBonds = Chirality::pickBondsToWedge(*mol);
|
|
REQUIRE(wedgedBonds.size() == 1);
|
|
auto head = wedgedBonds.begin();
|
|
CHECK(head->first == 3);
|
|
CHECK(head->second->getIdx() == 3);
|
|
}
|
|
SECTION("prefer unspecified bond stereo") {
|
|
auto mol = "OC=C[C@H](C=CF)(C=CC)"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondBetweenAtoms(1, 2)->setStereoAtoms(0, 3);
|
|
mol->getBondBetweenAtoms(1, 2)->setStereo(Bond::BondStereo::STEREOCIS);
|
|
mol->getBondBetweenAtoms(4, 5)->setStereoAtoms(3, 6);
|
|
mol->getBondBetweenAtoms(4, 5)->setStereo(Bond::BondStereo::STEREOANY);
|
|
auto wedgedBonds = Chirality::pickBondsToWedge(*mol);
|
|
REQUIRE(wedgedBonds.size() == 1);
|
|
auto head = wedgedBonds.begin();
|
|
CHECK(head->first == 6);
|
|
CHECK(head->second->getIdx() == 3);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("addWavyBondsForStereoAny()") {
|
|
SECTION("simplest") {
|
|
auto mol = "CC=CC"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(1)->setStereoAtoms(0, 3);
|
|
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
|
|
addWavyBondsForStereoAny(*mol);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::BondDir::UNKNOWN);
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("don't reset flags") {
|
|
auto mol = "CC=CC"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(1)->setStereoAtoms(0, 3);
|
|
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
|
|
bool clearFlags = false;
|
|
addWavyBondsForStereoAny(*mol, clearFlags);
|
|
CHECK(mol->getBondWithIdx(0)->getBondDir() == Bond::BondDir::UNKNOWN);
|
|
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOANY);
|
|
}
|
|
SECTION("avoid double bonds") {
|
|
auto mol = "CC=CC(CC)=CC"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(5)->setStereoAtoms(2, 7);
|
|
mol->getBondWithIdx(5)->setStereo(Bond::BondStereo::STEREOANY);
|
|
addWavyBondsForStereoAny(*mol);
|
|
CHECK(mol->getBondWithIdx(6)->getBondDir() == Bond::BondDir::UNKNOWN);
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("avoid chiral atoms") {
|
|
auto mol = "C[C@](F)(Cl)C(C)=CC"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(5)->setStereoAtoms(1, 7);
|
|
mol->getBondWithIdx(5)->setStereo(Bond::BondStereo::STEREOANY);
|
|
addWavyBondsForStereoAny(*mol);
|
|
CHECK(mol->getBondWithIdx(4)->getBondDir() == Bond::BondDir::UNKNOWN);
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("prefer atoms with less neighbors") {
|
|
auto mol = "CC(F)(Cl)C(CF)=CC"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(6)->setStereoAtoms(1, 8);
|
|
mol->getBondWithIdx(6)->setStereo(Bond::BondStereo::STEREOANY);
|
|
addWavyBondsForStereoAny(*mol);
|
|
CHECK(mol->getBondWithIdx(7)->getBondDir() == Bond::BondDir::UNKNOWN);
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("more complex") {
|
|
auto mol = "CC=CC(C=CO)=CC"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(6)->setStereoAtoms(2, 8);
|
|
mol->getBondWithIdx(6)->setStereo(Bond::BondStereo::STEREOANY);
|
|
addWavyBondsForStereoAny(*mol);
|
|
CHECK(mol->getBondWithIdx(7)->getBondDir() == Bond::BondDir::UNKNOWN);
|
|
CHECK(mol->getBondWithIdx(6)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("no solution without changing threshold") {
|
|
auto mol = "CC=CC=CC=CC"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(1)->setStereoAtoms(0, 3);
|
|
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOCIS);
|
|
mol->getBondWithIdx(3)->setStereoAtoms(2, 5);
|
|
mol->getBondWithIdx(3)->setStereo(Bond::BondStereo::STEREOANY);
|
|
mol->getBondWithIdx(5)->setStereoAtoms(4, 7);
|
|
mol->getBondWithIdx(5)->setStereo(Bond::BondStereo::STEREOCIS);
|
|
addWavyBondsForStereoAny(*mol);
|
|
// we didn't actually do anything:
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::BondStereo::STEREOANY);
|
|
|
|
bool clearDoubleBondFlags = true;
|
|
addWavyBondsForStereoAny(*mol, clearDoubleBondFlags,
|
|
StereoBondThresholds::DBL_BOND_SPECIFIED_STEREO);
|
|
CHECK(mol->getBondWithIdx(2)->getBondDir() == Bond::BondDir::UNKNOWN);
|
|
CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("multiple bonds to wedge") {
|
|
auto mol = "CCC(C)=CC=C(CC)C=CC(C)=CC"_smiles;
|
|
REQUIRE(mol);
|
|
mol->getBondWithIdx(3)->setStereoAtoms(3, 5);
|
|
mol->getBondWithIdx(3)->setStereo(Bond::BondStereo::STEREOCIS);
|
|
mol->getBondWithIdx(9)->setStereoAtoms(6, 11);
|
|
mol->getBondWithIdx(9)->setStereo(Bond::BondStereo::STEREOANY);
|
|
mol->getBondWithIdx(5)->setStereoAtoms(4, 7);
|
|
mol->getBondWithIdx(5)->setStereo(Bond::BondStereo::STEREOANY);
|
|
addWavyBondsForStereoAny(*mol);
|
|
CHECK(mol->getBondWithIdx(9)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(5)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
CHECK(mol->getBondWithIdx(8)->getBondDir() == Bond::BondDir::UNKNOWN);
|
|
for (const auto bond : mol->bonds()) {
|
|
if (bond->getBondType() == Bond::BondType::SINGLE &&
|
|
bond->getIdx() != 8) {
|
|
CHECK(bond->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Github #4215: Ring stereo being discarded in spiro systems") {
|
|
// Note: this bug is still there when using the legacy stereochemistry
|
|
// assignment. It's "non-trivial" to fix there and we've opted not to
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
|
|
SECTION("original failing example") {
|
|
auto m = "C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
}
|
|
SECTION("original failing example, findPossible") {
|
|
// UseLegacyStereoPerceptionFixture inner_reset_stereo_perception(true);
|
|
SmilesParserParams ps2;
|
|
ps2.sanitize = false;
|
|
std::unique_ptr<RWMol> m{
|
|
SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2", ps2)};
|
|
REQUIRE(m);
|
|
MolOps::sanitizeMol(*m);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(11)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
REQUIRE(stereoInfo.size() == 4);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
if (si.centeredOn != 9) {
|
|
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
|
|
} else {
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
}
|
|
SECTION("original passing example") {
|
|
auto m = "C[C@H]1CCC2(CC1)CC[C@H](C)CC2"_smiles;
|
|
REQUIRE(m);
|
|
// if the middle is unspecified, the two ends can't be specified
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 3);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = false;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.empty());
|
|
}
|
|
}
|
|
SECTION("specified chirality on spiro atom") {
|
|
auto m = "C[C@H]1CC[C@@]2(CC[C@H](C)CC2)CC1"_smiles;
|
|
REQUIRE(m);
|
|
// now the middle is specified, so the two ends are as well
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(7)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 3);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = false;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 3);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
}
|
|
SECTION("three spiro rings, unspecified spiro links") {
|
|
auto m = "C[C@H]1CCC2(CC1)CCC1(CC[C@H](C)CC1)CC2"_smiles;
|
|
REQUIRE(m);
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 4);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
}
|
|
SECTION("three spiro rings, specified spiro links") {
|
|
auto m = "C[C@H]1CC[C@@]2(CC1)CC[C@]1(CC[C@H](C)CC1)CC2"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(12)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 4);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #4215: Ring stereo being discarded in spiro systems, using deprecated useLegacyStereo option") {
|
|
// Note: this bug is still there when using the legacy stereochemistry
|
|
// assignment. It's "non-trivial" to fix there and we've opted not to
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
SECTION("original failing example") {
|
|
std::unique_ptr<RWMol> m{SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2")};
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
}
|
|
SECTION("original failing example, findPossible") {
|
|
SmilesParserParams ps2;
|
|
ps2.sanitize = false;
|
|
std::unique_ptr<RWMol> m{
|
|
SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2", ps2)};
|
|
REQUIRE(m);
|
|
MolOps::sanitizeMol(*m);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(11)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
REQUIRE(stereoInfo.size() == 4);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
if (si.centeredOn != 9) {
|
|
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
|
|
} else {
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
}
|
|
SECTION("original passing example") {
|
|
std::unique_ptr<RWMol> m{SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)CC2")};
|
|
REQUIRE(m);
|
|
// if the middle is unspecified, the two ends can't be specified
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 3);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = false;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.empty());
|
|
}
|
|
}
|
|
SECTION("specified chirality on spiro atom") {
|
|
std::unique_ptr<RWMol> m{SmilesToMol("C[C@H]1CC[C@@]2(CC[C@H](C)CC2)CC1")};
|
|
REQUIRE(m);
|
|
// now the middle is specified, so the two ends are as well
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(7)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 3);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = false;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 3);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
}
|
|
SECTION("three spiro rings, unspecified spiro links") {
|
|
std::unique_ptr<RWMol> m{
|
|
SmilesToMol("C[C@H]1CCC2(CC1)CCC1(CC[C@H](C)CC1)CC2")};
|
|
REQUIRE(m);
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 4);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
}
|
|
SECTION("three spiro rings, specified spiro links") {
|
|
std::unique_ptr<RWMol> m{
|
|
SmilesToMol("C[C@H]1CC[C@@]2(CC1)CC[C@]1(CC[C@H](C)CC1)CC2")};
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(12)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
{
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
RWMol m2(*m);
|
|
auto stereoInfo =
|
|
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
|
|
CHECK(stereoInfo.size() == 4);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #4279: FindPotentialStereo() doesn't find *marked* ring stereo "
|
|
"when flagPossible=False") {
|
|
SECTION("base") {
|
|
std::unique_ptr<RWMol> m{SmilesToMol("C[C@H]1CC[C@@H](C)CC1")};
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
bool cleanIt = true;
|
|
bool flagPossible = false;
|
|
auto stereoInfo = Chirality::findPotentialStereo(*m, cleanIt, flagPossible);
|
|
for (const auto &si : stereoInfo) {
|
|
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(si.specified == Chirality::StereoSpecified::Specified);
|
|
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
|
|
}
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("StereoInfo comparisons") {
|
|
Chirality::StereoInfo si1;
|
|
si1.centeredOn = 3;
|
|
CHECK(si1.type == Chirality::StereoType::Unspecified);
|
|
si1.type = Chirality::StereoType::Atom_Tetrahedral;
|
|
Chirality::StereoInfo si2;
|
|
si2.centeredOn = 3;
|
|
si2.type = Chirality::StereoType::Atom_Tetrahedral;
|
|
CHECK(si1 == si2);
|
|
si2.descriptor = Chirality::StereoDescriptor::Tet_CCW;
|
|
CHECK(si1 != si2);
|
|
}
|
|
|
|
TEST_CASE("StereoGroup Testing") {
|
|
SECTION("basics") {
|
|
auto mol = "C[C@H](O)[C@@H](C)[C@H](F)Cl |o1:1,3,&2:5,r|"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getStereoGroups().size() == 2);
|
|
StereoGroup cp(mol->getStereoGroups()[0]);
|
|
CHECK(cp == mol->getStereoGroups()[0]);
|
|
CHECK(cp != mol->getStereoGroups()[1]);
|
|
|
|
std::vector<Atom *> toRemove{mol->getAtomWithIdx(1)};
|
|
std::vector<StereoGroup> &sgs =
|
|
const_cast<std::vector<StereoGroup> &>(mol->getStereoGroups());
|
|
removeGroupsWithAtoms(toRemove, sgs);
|
|
CHECK(mol->getStereoGroups().size() == 1);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Removing stereogroups from unspecified atoms") {
|
|
SECTION("basics") {
|
|
auto mol = "C[C@](O)(Cl)F |o1:1|"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getStereoGroups().size() == 1);
|
|
mol->getAtomWithIdx(1)->setChiralTag(Atom::ChiralType::CHI_UNSPECIFIED);
|
|
Chirality::cleanupStereoGroups(*mol);
|
|
CHECK(mol->getStereoGroups().empty());
|
|
}
|
|
SECTION("parsing") {
|
|
auto mol = "C[C@](C)(Cl)F |o1:1|"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getStereoGroups().empty());
|
|
}
|
|
SECTION("partial group removal") {
|
|
auto mol = "C[C@](C)(Cl)[C@H](F)Cl |o1:1,4|"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getStereoGroups().size() == 1);
|
|
CHECK(mol->getStereoGroups()[0].getAtoms().size() == 1);
|
|
CHECK(mol->getStereoGroups()[0].getAtoms()[0]->getIdx() == 4);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("replaceAtom and StereoGroups") {
|
|
SECTION("basics") {
|
|
auto mol = "C[C@](O)(Cl)[C@H](F)Cl |o1:1,4|"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getStereoGroups().size() == 1);
|
|
CHECK(mol->getStereoGroups()[0].getAtoms().size() == 2);
|
|
CHECK(mol->getStereoGroups()[0].getAtoms()[0] == mol->getAtomWithIdx(1));
|
|
|
|
Atom acp(*mol->getAtomWithIdx(1));
|
|
mol->replaceAtom(1, &acp);
|
|
CHECK(mol->getStereoGroups().size() == 1);
|
|
CHECK(mol->getStereoGroups()[0].getAtoms().size() == 2);
|
|
CHECK(mol->getStereoGroups()[0].getAtoms()[0] == mol->getAtomWithIdx(1));
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #5200: FindPotentialStereo does not clean stereoflags from atoms "
|
|
"which cannot be stereocenters") {
|
|
auto m = "CCF"_smiles;
|
|
REQUIRE(m);
|
|
m->getAtomWithIdx(1)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
bool cleanIt = true;
|
|
auto sinfo = Chirality::findPotentialStereo(*m, cleanIt);
|
|
CHECK(sinfo.empty());
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #5196: Zero & coordinate bonds are being taken into account for "
|
|
"chirality") {
|
|
RDLog::LogStateSetter setter; // disable irritating warning messages
|
|
auto mol = R"CTAB(
|
|
RDKit 3D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 15 18 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.136359 0.025241 -0.986870 0
|
|
M V30 2 C 0.211183 -0.810922 0.138318 0
|
|
M V30 3 C -0.446638 -0.713741 1.305561 0
|
|
M V30 4 C -1.141107 0.914647 -0.916429 0
|
|
M V30 5 R -1.628248 -0.983190 -0.411960 0
|
|
M V30 6 H 0.392055 -0.106505 -1.920607 0
|
|
M V30 7 H 0.974038 -1.568492 0.017171 0
|
|
M V30 8 H -0.209921 -1.406535 2.084966 0
|
|
M V30 9 H -1.378909 1.482059 -1.807349 0
|
|
M V30 10 C -1.544607 0.306162 1.588191 0
|
|
M V30 11 C -1.946856 1.186683 0.358271 0
|
|
M V30 12 H -1.207983 0.944410 2.407927 0
|
|
M V30 13 H -2.419549 -0.225146 1.965589 0
|
|
M V30 14 H -3.006492 1.040978 0.144313 0
|
|
M V30 15 H -1.830875 2.240146 0.620809 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1
|
|
M V30 2 2 3 2
|
|
M V30 3 2 4 1
|
|
M V30 4 0 1 5
|
|
M V30 5 0 2 5
|
|
M V30 6 0 3 5
|
|
M V30 7 0 4 5
|
|
M V30 8 1 1 6
|
|
M V30 9 1 2 7
|
|
M V30 10 1 3 8
|
|
M V30 11 1 4 9
|
|
M V30 12 1 10 3
|
|
M V30 13 1 11 4
|
|
M V30 14 1 11 10
|
|
M V30 15 1 12 10
|
|
M V30 16 1 13 10
|
|
M V30 17 1 14 11
|
|
M V30 18 1 15 11
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
SECTION("as reported") {
|
|
MolOps::assignStereochemistryFrom3D(*mol);
|
|
for (auto aidx : {0, 1, 2, 3}) {
|
|
CHECK(mol->getAtomWithIdx(aidx)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("as reported - ZOBs") {
|
|
for (auto bidx : {3, 4, 5, 6}) {
|
|
mol->getBondWithIdx(bidx)->setBondType(Bond::BondType::ZERO);
|
|
}
|
|
MolOps::assignStereochemistryFrom3D(*mol);
|
|
for (auto idx : {0, 1, 2, 3}) {
|
|
CHECK(mol->getAtomWithIdx(idx)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("as reported - datives") {
|
|
for (auto bidx : {3, 4, 5, 6}) {
|
|
mol->getBondWithIdx(bidx)->setBondType(Bond::BondType::DATIVE);
|
|
}
|
|
MolOps::assignStereochemistryFrom3D(*mol);
|
|
for (auto idx : {0, 1, 2, 3}) {
|
|
CHECK(mol->getAtomWithIdx(idx)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("as reported - reversed datives") {
|
|
// structure is bogus, but we want to test
|
|
for (auto bidx : {3, 4, 5, 6}) {
|
|
auto bond = mol->getBondWithIdx(bidx);
|
|
bond->setEndAtomIdx(bond->getBeginAtomIdx());
|
|
bond->setBeginAtomIdx(4);
|
|
bond->setBondType(Bond::BondType::DATIVE);
|
|
}
|
|
MolOps::assignStereochemistryFrom3D(*mol);
|
|
for (auto idx : {0, 1, 2, 3}) {
|
|
CHECK(mol->getAtomWithIdx(idx)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("as reported - singles") {
|
|
// structure is bogus, but we want to test
|
|
for (auto bidx : {3, 4, 5, 6}) {
|
|
mol->getBondWithIdx(bidx)->setBondType(Bond::BondType::SINGLE);
|
|
}
|
|
MolOps::assignStereochemistryFrom3D(*mol);
|
|
for (auto idx : {0, 1, 2, 3}) {
|
|
CHECK(mol->getAtomWithIdx(idx)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("assignStereochemistry") {
|
|
auto mol = "[Fe]C(=C)O |C:1.0|"_smiles;
|
|
REQUIRE(mol);
|
|
for (auto bt : {Bond::BondType::DATIVE, Bond::BondType::ZERO,
|
|
Bond::BondType::UNSPECIFIED}) {
|
|
mol->getAtomWithIdx(1)->setChiralTag(
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
mol->getBondWithIdx(0)->setBondType(bt);
|
|
bool cleanit = true;
|
|
bool force = true;
|
|
MolOps::assignStereochemistry(*mol, cleanit, force);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("isAtomPotentialTetrahedralCenter() and getStereoInfo()") {
|
|
auto mol = "[Fe]C(=C)O |C:1.0|"_smiles;
|
|
REQUIRE(mol);
|
|
for (auto bt : {Bond::BondType::DATIVE, Bond::BondType::ZERO,
|
|
Bond::BondType::UNSPECIFIED}) {
|
|
mol->getAtomWithIdx(1)->setChiralTag(
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
mol->getBondWithIdx(0)->setBondType(bt);
|
|
CHECK(!Chirality::detail::isAtomPotentialStereoAtom(
|
|
mol->getAtomWithIdx(1)));
|
|
bool cleanit = true;
|
|
auto sinfo = Chirality::findPotentialStereo(*mol, cleanit);
|
|
CHECK(sinfo.empty());
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #5239: Precondition violation on chiral Atoms with zero order "
|
|
"bonds") {
|
|
RDLog::LogStateSetter setter; // disable irritating warning messages
|
|
auto molblock = R"CTAB(
|
|
RDKit 3D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 5 4 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.446600 -0.713700 1.305600 0
|
|
M V30 2 Fe -1.628200 -0.983200 -0.412000 0
|
|
M V30 3 Cl -0.049300 -1.876700 2.613900 0
|
|
M V30 4 C -1.544600 0.306200 1.588200 0
|
|
M V30 5 F 0.673700 0.029200 0.993700 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 3
|
|
M V30 2 1 1 4 CFG=1
|
|
M V30 3 1 1 5
|
|
M V30 4 0 2 1
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END)CTAB";
|
|
bool sanitize = false;
|
|
std::unique_ptr<ROMol> mol(MolBlockToMol(molblock, sanitize));
|
|
REQUIRE(mol);
|
|
MolOps::assignStereochemistryFrom3D(*mol);
|
|
|
|
CHECK(mol->getAtomWithIdx(0)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
TEST_CASE("nontetrahedral stereo from 3D", "[nontetrahedral]") {
|
|
std::string pathName = getenv("RDBASE");
|
|
pathName += "/Code/GraphMol/test_data/nontetrahedral_3d.sdf";
|
|
SECTION("basics") {
|
|
SDMolSupplier suppl(pathName);
|
|
while (!suppl.atEnd()) {
|
|
std::unique_ptr<ROMol> m{suppl.next()};
|
|
REQUIRE(m);
|
|
MolOps::assignChiralTypesFrom3D(*m);
|
|
auto ct = m->getProp<std::string>("ChiralType");
|
|
auto cp = m->getProp<unsigned>("ChiralPermutation");
|
|
auto atom = m->getAtomWithIdx(0);
|
|
|
|
if (ct == "SP") {
|
|
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_SQUAREPLANAR);
|
|
} else if (ct == "TB") {
|
|
CHECK(atom->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
|
|
} else if (ct == "TH") {
|
|
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL);
|
|
} else if (ct == "OH") {
|
|
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_OCTAHEDRAL);
|
|
}
|
|
|
|
CHECK(atom->getProp<unsigned>(common_properties::_chiralPermutation) ==
|
|
cp);
|
|
}
|
|
}
|
|
SECTION("disable nontetrahedral stereo") {
|
|
AllowNontetrahedralChiralityFixture reset_non_tetrahedral_allowed;
|
|
Chirality::setAllowNontetrahedralChirality(false);
|
|
SDMolSupplier suppl(pathName);
|
|
while (!suppl.atEnd()) {
|
|
std::unique_ptr<ROMol> m{suppl.next()};
|
|
REQUIRE(m);
|
|
MolOps::assignChiralTypesFrom3D(*m);
|
|
auto ct = m->getProp<std::string>("ChiralType");
|
|
auto atom = m->getAtomWithIdx(0);
|
|
|
|
if (ct == "TH") {
|
|
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL);
|
|
} else {
|
|
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("assignStereochemistry shouldn't remove nontetrahedral stereo",
|
|
"[nontetrahedral]") {
|
|
SECTION("basics") {
|
|
SmilesParserParams parseps;
|
|
parseps.sanitize = false;
|
|
parseps.removeHs = false;
|
|
std::unique_ptr<RWMol> m{SmilesToMol("F[Pt@TB1](O)(Br)(N)Cl", parseps)};
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
|
|
bool cleanIt = true;
|
|
bool force = true;
|
|
MolOps::assignStereochemistry(*m, cleanIt, force);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
|
|
}
|
|
SECTION("standard SMILES parsing") {
|
|
std::unique_ptr<RWMol> m{SmilesToMol("F[Pt@TB1](O)(Br)(N)Cl")};
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
|
|
}
|
|
SECTION("SMILES parsing w/o sanitization") {
|
|
SmilesParserParams parseps;
|
|
// we need to skip stereo assignment
|
|
parseps.sanitize = false;
|
|
std::unique_ptr<RWMol> m{SmilesToMol("F[Pt@TB1](O)(Br)(N)Cl", parseps)};
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("remove hs and non-tetrahedral stereo", "[nontetrahedral]") {
|
|
SmilesParserParams parseps;
|
|
parseps.sanitize = false;
|
|
parseps.removeHs = false;
|
|
std::vector<std::string> smiles = {"F[Pt@TB1]([H])(Br)(N)Cl",
|
|
"F[Pt@TB]([H])(Br)(N)Cl"};
|
|
for (const auto &smi : smiles) {
|
|
std::unique_ptr<RWMol> m{SmilesToMol(smi, parseps)};
|
|
REQUIRE(m);
|
|
CHECK(m->getNumAtoms(6));
|
|
{
|
|
// the default is to not remove Hs to non-tetrahedral stereocenters
|
|
RWMol molcp(*m);
|
|
MolOps::removeHs(molcp);
|
|
CHECK(molcp.getNumAtoms() == 6);
|
|
}
|
|
{
|
|
// but we can enable it
|
|
RWMol molcp(*m);
|
|
MolOps::RemoveHsParameters ps;
|
|
ps.removeNontetrahedralNeighbors = true;
|
|
MolOps::removeHs(molcp, ps);
|
|
CHECK(molcp.getNumAtoms() == 5);
|
|
}
|
|
{
|
|
// but we can enable it
|
|
RWMol molcp(*m);
|
|
MolOps::removeAllHs(molcp);
|
|
CHECK(molcp.getNumAtoms() == 5);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("getIdealAngle", "[nontetrahedral]") {
|
|
SECTION("TB1") {
|
|
auto m = "S[As@TB1](F)(Cl)(Br)N"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(0)));
|
|
CHECK(Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(5)));
|
|
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(2)));
|
|
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(3)));
|
|
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(4)));
|
|
CHECK(Chirality::getTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1))
|
|
->getIdx() == 0);
|
|
CHECK(Chirality::getTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1), -1)
|
|
->getIdx() == 5);
|
|
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(4)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(2), m->getAtomWithIdx(3)),
|
|
Catch::Matchers::WithinAbs(120, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(5)),
|
|
Catch::Matchers::WithinAbs(180, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(5), m->getAtomWithIdx(2)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(5), m->getAtomWithIdx(3)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(5), m->getAtomWithIdx(4)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
}
|
|
SECTION("TB1 missing 1") {
|
|
// S[As@TB1](F)(Cl)(Br)* => S[As@TB7](*)(F)(Cl)Br
|
|
auto m = "S[As@TB7](F)(Cl)Br"_smiles;
|
|
REQUIRE(m);
|
|
|
|
CHECK(Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(0)));
|
|
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(2)));
|
|
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(3)));
|
|
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
m->getAtomWithIdx(4)));
|
|
CHECK(Chirality::getTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1))
|
|
->getIdx() == 0);
|
|
CHECK(Chirality::getTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
|
|
-1) == nullptr);
|
|
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(4)),
|
|
Catch::Matchers::WithinAbs(90, 0.001));
|
|
CHECK_THAT(
|
|
Chirality::getIdealAngleBetweenLigands(
|
|
m->getAtomWithIdx(1), m->getAtomWithIdx(2), m->getAtomWithIdx(3)),
|
|
Catch::Matchers::WithinAbs(120, 0.001));
|
|
}
|
|
}
|
|
|
|
TEST_CASE("getChiralPermutation", "[nontetrahedral]") {
|
|
SECTION("TB1") {
|
|
// clang-format off
|
|
std::vector<std::pair<std::list<int>, unsigned int>> data = {
|
|
{{2, 3, 4, 5, 6}, 1},
|
|
{{2, 3, 5, 4, 6}, 2},
|
|
|
|
{{2, 3, 4, 6, 5}, 3},
|
|
{{2, 3, 5, 6, 4}, 4},
|
|
|
|
{{2, 3, 6, 4, 5}, 5},
|
|
{{2, 3, 6, 5, 4}, 6},
|
|
|
|
{{2, 6, 3, 4, 5}, 7},
|
|
{{2, 6, 3, 5, 4}, 8},
|
|
|
|
{{3, 2, 4, 5, 6}, 9},
|
|
{{3, 2, 5, 4, 6}, 11},
|
|
|
|
{{3, 2, 4, 6, 5}, 10},
|
|
{{3, 2, 5, 6, 4}, 12},
|
|
|
|
{{3, 2, 6, 4, 5}, 13},
|
|
{{3, 2, 6, 5, 4}, 14},
|
|
|
|
{{3, 4, 2, 5, 6}, 15},
|
|
{{3, 5, 2, 4, 6}, 20},
|
|
|
|
{{3, 4, 2, 6, 5}, 16},
|
|
{{3, 5, 2, 6, 4}, 19},
|
|
|
|
{{3, 4, 5, 2, 6}, 17},
|
|
{{3, 5, 4, 2, 6}, 18},
|
|
|
|
|
|
};
|
|
// clang-format on
|
|
auto m = "CCS[As@TB1](F)(Cl)(Br)N"_smiles;
|
|
REQUIRE(m);
|
|
const auto atm = m->getAtomWithIdx(3);
|
|
for (const auto &pr : data) {
|
|
// std::cerr << "---- " << pr.second << std::endl;
|
|
CHECK(Chirality::getChiralPermutation(atm, pr.first) == pr.second);
|
|
}
|
|
}
|
|
|
|
SECTION("SP1") {
|
|
// clang-format off
|
|
std::vector<std::pair<std::list<int>, unsigned int>> data = {
|
|
{{2, 3, 4, 5}, 1},
|
|
{{2, 4, 3, 5}, 2},
|
|
{{2, 3, 5, 4}, 3},
|
|
};
|
|
// clang-format on
|
|
auto m = "CCC[Pt@SP1](F)(Cl)N"_smiles;
|
|
REQUIRE(m);
|
|
const auto atm = m->getAtomWithIdx(3);
|
|
for (const auto &pr : data) {
|
|
// std::cerr << "---- " << pr.second << std::endl;
|
|
CHECK(Chirality::getChiralPermutation(atm, pr.first) == pr.second);
|
|
}
|
|
}
|
|
SECTION("OH1") {
|
|
// clang-format off
|
|
std::vector<std::pair<std::list<int>, unsigned int>> data = {
|
|
{{2, 3, 4, 5, 6, 7}, 1},
|
|
{{2, 3, 6, 5, 4, 7}, 2},
|
|
|
|
{{2, 3, 4, 5, 7, 6}, 3},
|
|
{{2, 3, 6, 5, 7, 4}, 16},
|
|
|
|
{{2, 3, 4, 7, 5, 6}, 6},
|
|
{{2, 3, 6, 7, 5, 4}, 18},
|
|
|
|
{{2, 3, 7, 4, 5, 6}, 19},
|
|
{{2, 3, 7, 6, 5, 4}, 24},
|
|
|
|
{{2, 7, 3, 4, 5, 6}, 25},
|
|
{{2, 7, 3, 6, 5, 4}, 30},
|
|
|
|
{{2, 3, 4, 6, 5, 7}, 4},
|
|
{{2, 3, 6, 4, 5, 7}, 14},
|
|
|
|
{{2, 3, 4, 6, 7, 5}, 5},
|
|
{{2, 3, 6, 4, 7, 5}, 15},
|
|
|
|
{{2, 3, 4, 7, 6, 5}, 7},
|
|
{{2, 3, 6, 7, 4, 5}, 17},
|
|
|
|
{{2, 3, 7, 4, 6, 5}, 20},
|
|
{{2, 3, 7, 6, 4, 5}, 23},
|
|
|
|
{{2, 7, 3, 4, 6, 5}, 26},
|
|
{{2, 7, 3, 6, 4, 5}, 29},
|
|
|
|
{{2, 3, 5, 6, 4, 7}, 10},
|
|
{{2, 3, 5, 4, 6, 7}, 8},
|
|
|
|
{{2, 3, 5, 6, 7, 4}, 11},
|
|
{{2, 3, 5, 4, 7, 6}, 9},
|
|
|
|
{{2, 3, 5, 7, 6, 4}, 13},
|
|
{{2, 3, 5, 7, 4, 6}, 12},
|
|
|
|
{{2, 3, 7, 5, 6, 4}, 22},
|
|
{{2, 3, 7, 5, 4, 6}, 21},
|
|
|
|
{{2, 7, 3, 5, 6, 4}, 28},
|
|
{{2, 7, 3, 5, 4, 6}, 27},
|
|
|
|
};
|
|
// clang-format on
|
|
auto m = "CCO[Co@OH1](Cl)(C)(N)(F)P"_smiles;
|
|
REQUIRE(m);
|
|
const auto atm = m->getAtomWithIdx(3);
|
|
for (const auto &pr : data) {
|
|
// std::cerr << "---- " << pr.second << std::endl;
|
|
CHECK(Chirality::getChiralPermutation(atm, pr.first) == pr.second);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("isAtomPotentialNontetrahedralCenter", "[nontetrahedral]") {
|
|
SECTION("basics") {
|
|
{
|
|
auto mol = "C[S+](O)F"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(!Chirality::detail::isAtomPotentialNontetrahedralCenter(
|
|
mol->getAtomWithIdx(1)));
|
|
}
|
|
{
|
|
auto mol = "C[SH](O)F"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(Chirality::detail::isAtomPotentialNontetrahedralCenter(
|
|
mol->getAtomWithIdx(1)));
|
|
}
|
|
{
|
|
auto mol = "C[S@SP](O)F"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(Chirality::detail::isAtomPotentialNontetrahedralCenter(
|
|
mol->getAtomWithIdx(1)));
|
|
}
|
|
}
|
|
}
|
|
TEST_CASE("nontetrahedral StereoInfo", "[nontetrahedral]") {
|
|
SECTION("SP") {
|
|
auto m = "C[Pt@SP1](F)(Cl)O"_smiles;
|
|
REQUIRE(m);
|
|
auto sinfo = Chirality::findPotentialStereo(*m);
|
|
REQUIRE(sinfo.size() == 1);
|
|
CHECK(sinfo[0].centeredOn == 1);
|
|
CHECK(sinfo[0].type == Chirality::StereoType::Atom_SquarePlanar);
|
|
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
|
|
CHECK(sinfo[0].permutation == 1);
|
|
CHECK(sinfo[0].controllingAtoms == std::vector<unsigned int>{0, 2, 3, 4});
|
|
}
|
|
SECTION("TB") {
|
|
auto m = "C[Fe@TB4](F)(Cl)(O)N"_smiles;
|
|
REQUIRE(m);
|
|
auto sinfo = Chirality::findPotentialStereo(*m);
|
|
REQUIRE(sinfo.size() == 1);
|
|
CHECK(sinfo[0].centeredOn == 1);
|
|
CHECK(sinfo[0].type == Chirality::StereoType::Atom_TrigonalBipyramidal);
|
|
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
|
|
CHECK(sinfo[0].permutation == 4);
|
|
CHECK(sinfo[0].controllingAtoms ==
|
|
std::vector<unsigned int>{0, 2, 3, 4, 5});
|
|
}
|
|
SECTION("TB0") {
|
|
auto m = "C[Fe@TB](F)(Cl)(O)N"_smiles;
|
|
REQUIRE(m);
|
|
auto sinfo = Chirality::findPotentialStereo(*m);
|
|
REQUIRE(sinfo.size() == 1);
|
|
CHECK(sinfo[0].centeredOn == 1);
|
|
CHECK(sinfo[0].specified == Chirality::StereoSpecified::Unknown);
|
|
CHECK(sinfo[0].type == Chirality::StereoType::Atom_TrigonalBipyramidal);
|
|
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
|
|
CHECK(sinfo[0].permutation == 0);
|
|
CHECK(sinfo[0].controllingAtoms ==
|
|
std::vector<unsigned int>{0, 2, 3, 4, 5});
|
|
}
|
|
SECTION("perceived as possible") {
|
|
auto m = "C[Fe](F)(Cl)(O)N"_smiles;
|
|
REQUIRE(m);
|
|
auto sinfo = Chirality::findPotentialStereo(*m);
|
|
REQUIRE(sinfo.size() == 1);
|
|
CHECK(sinfo[0].centeredOn == 1);
|
|
CHECK(sinfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
CHECK(sinfo[0].type == Chirality::StereoType::Atom_TrigonalBipyramidal);
|
|
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
|
|
CHECK(sinfo[0].permutation == 0);
|
|
CHECK(sinfo[0].controllingAtoms ==
|
|
std::vector<unsigned int>{0, 2, 3, 4, 5});
|
|
}
|
|
|
|
SECTION("OH") {
|
|
auto m = "C[Fe@OH9](F)(Cl)(O)(N)Br"_smiles;
|
|
REQUIRE(m);
|
|
auto sinfo = Chirality::findPotentialStereo(*m);
|
|
REQUIRE(sinfo.size() == 1);
|
|
CHECK(sinfo[0].centeredOn == 1);
|
|
CHECK(sinfo[0].type == Chirality::StereoType::Atom_Octahedral);
|
|
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
|
|
CHECK(sinfo[0].permutation == 9);
|
|
CHECK(sinfo[0].controllingAtoms ==
|
|
std::vector<unsigned int>{0, 2, 3, 4, 5, 6});
|
|
}
|
|
SECTION("OH missing ligand") {
|
|
// C[Fe@OH9](F)(Cl)(O)(N)* => C[Fe@OH4](*)(F)(Cl)(O)N
|
|
auto m = "C[Fe@OH4](F)(Cl)(O)N"_smiles;
|
|
REQUIRE(m);
|
|
auto sinfo = Chirality::findPotentialStereo(*m);
|
|
REQUIRE(sinfo.size() == 1);
|
|
CHECK(sinfo[0].centeredOn == 1);
|
|
CHECK(sinfo[0].type == Chirality::StereoType::Atom_Octahedral);
|
|
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
|
|
CHECK(sinfo[0].permutation == 9);
|
|
CHECK(sinfo[0].controllingAtoms ==
|
|
std::vector<unsigned int>{0, 2, 3, 4, 5});
|
|
}
|
|
}
|
|
|
|
TEST_CASE("github #5328: assignChiralTypesFrom3D() ignores wiggly bonds") {
|
|
SECTION("basics") {
|
|
auto m = R"CTAB(
|
|
RDKit 3D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 5 4 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 0.900794 -0.086835 0.009340 0
|
|
M V30 2 C -0.552652 0.319534 0.077502 0
|
|
M V30 3 F -0.861497 0.413307 1.437370 0
|
|
M V30 4 Cl -0.784572 1.925710 -0.672698 0
|
|
M V30 5 O -1.402227 -0.583223 -0.509512 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 2 4 CFG=2
|
|
M V30 4 1 2 5
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
MolOps::assignChiralTypesFrom3D(*m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
SECTION("non-tetrahedral") {
|
|
auto m = R"CTAB(
|
|
Mrv2108 05252216313D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 6 5 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -1.7191 0.2488 -3.5085 0
|
|
M V30 2 As -1.0558 1.9209 -2.6345 0
|
|
M V30 3 F -0.4636 3.422 -1.7567 0
|
|
M V30 4 O -2.808 2.4243 -2.1757 0
|
|
M V30 5 Cl -0.1145 2.6609 -4.5048 0
|
|
M V30 6 Br 0.2255 0.6458 -1.079 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 2 4
|
|
M V30 4 1 2 5 CFG=2
|
|
M V30 5 1 2 6
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
MolOps::assignChiralTypesFrom3D(*m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("useLegacyStereoPerception feature flag") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(true);
|
|
|
|
SECTION("original failing example") {
|
|
Chirality::setUseLegacyStereoPerception(true);
|
|
auto m = "C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
}
|
|
SECTION("use new code") {
|
|
Chirality::setUseLegacyStereoPerception(false);
|
|
auto m = "C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
}
|
|
std::string molblock = R"CTAB(
|
|
Mrv2108 05202206352D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 14 15 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -4.5417 3.165 0 0
|
|
M V30 2 C -5.8753 2.395 0 0
|
|
M V30 3 C -5.8753 0.855 0 0
|
|
M V30 4 C -4.5417 0.085 0 0 CFG=1
|
|
M V30 5 C -3.208 0.855 0 0
|
|
M V30 6 C -3.208 2.395 0 0
|
|
M V30 7 C -4.5417 -1.455 0 0
|
|
M V30 8 C -1.8743 0.085 0 0
|
|
M V30 9 C -4.5417 6.2451 0 0 CFG=2
|
|
M V30 10 C -5.8753 5.4751 0 0
|
|
M V30 11 C -5.8753 3.9351 0 0
|
|
M V30 12 C -3.208 3.9351 0 0
|
|
M V30 13 C -3.208 5.4751 0 0
|
|
M V30 14 C -4.5417 7.7851 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 1 4 5
|
|
M V30 5 1 5 6
|
|
M V30 6 1 1 6
|
|
M V30 7 1 4 7 CFG=1
|
|
M V30 8 1 5 8
|
|
M V30 9 1 9 10
|
|
M V30 10 1 10 11
|
|
M V30 11 1 12 13
|
|
M V30 12 1 9 13
|
|
M V30 13 1 11 1
|
|
M V30 14 1 1 12
|
|
M V30 15 1 9 14 CFG=1
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB";
|
|
SECTION("original example, from mol block") {
|
|
Chirality::setUseLegacyStereoPerception(true);
|
|
std::unique_ptr<RWMol> m{MolBlockToMol(molblock)};
|
|
CHECK(m->getAtomWithIdx(3)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(8)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
}
|
|
SECTION("original example, from mol block, new code") {
|
|
Chirality::setUseLegacyStereoPerception(false);
|
|
std::unique_ptr<RWMol> m{MolBlockToMol(molblock)};
|
|
CHECK(m->getAtomWithIdx(3)->getChiralTag() != Atom::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(8)->getChiralTag() == Atom::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("wedgeMolBonds to aromatic rings") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 10 11 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 2.948889 -2.986305 0.000000 0
|
|
M V30 2 C 2.560660 -4.435194 0.000000 0
|
|
M V30 3 N 1.111771 -4.046965 0.000000 0
|
|
M V30 4 C 1.500000 -2.598076 0.000000 0
|
|
M V30 5 C 0.750000 -1.299038 0.000000 0
|
|
M V30 6 C 1.500000 0.000000 0.000000 0
|
|
M V30 7 C 0.750000 1.299038 0.000000 0
|
|
M V30 8 C -0.750000 1.299038 0.000000 0
|
|
M V30 9 C -1.500000 0.000000 0.000000 0
|
|
M V30 10 C -0.750000 -1.299038 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 1 4 5 CFG=1
|
|
M V30 5 2 5 6
|
|
M V30 6 1 6 7
|
|
M V30 7 2 7 8
|
|
M V30 8 1 8 9
|
|
M V30 9 2 9 10
|
|
M V30 10 1 4 1
|
|
M V30 11 1 10 5
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(3)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(m->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE);
|
|
|
|
SECTION("generating mol blocks") {
|
|
auto mb = MolToV3KMolBlock(*m);
|
|
CHECK(mb.find("M V30 10 1 4 1 CFG=1") == std::string::npos);
|
|
CHECK(mb.find("M V30 4 1 4 5 CFG=1") != std::string::npos);
|
|
}
|
|
|
|
SECTION("details: pickBondsWedge()") {
|
|
// this is with aromatic bonds
|
|
auto wedgedBonds = Chirality::pickBondsToWedge(*m);
|
|
CHECK(wedgedBonds.at(3)->getIdx() == 3);
|
|
RWMol cp(*m);
|
|
|
|
// now try kekulized:
|
|
MolOps::Kekulize(cp);
|
|
wedgedBonds = Chirality::pickBondsToWedge(cp);
|
|
CHECK(wedgedBonds.at(3)->getIdx() == 3);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("github 5307: AssignAtomChiralTagsFromStructure ignores Hydrogens") {
|
|
std::string mb = R"CTAB(
|
|
RDKit 3D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 5 4 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.022097 0.003215 0.016520 0
|
|
M V30 2 H -0.669009 0.889360 -0.100909 0
|
|
M V30 3 H -0.377788 -0.857752 -0.588296 0
|
|
M V30 4 H 0.096421 -0.315125 1.063781 0
|
|
M V30 5 H 0.972473 0.280302 -0.391096 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 1 1 5
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB";
|
|
bool sanitize = true;
|
|
bool removeHs = false;
|
|
std::unique_ptr<RWMol> m{MolBlockToMol(mb, sanitize, removeHs)};
|
|
REQUIRE(m);
|
|
MolOps::assignChiralTypesFrom3D(*m);
|
|
CHECK(m->getAtomWithIdx(0)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
// assignStereochemistryFrom3D() actually checks:
|
|
MolOps::assignStereochemistryFrom3D(*m);
|
|
CHECK(m->getAtomWithIdx(0)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
|
|
TEST_CASE(
|
|
"github 5403: Incorrect perception of pseudoasymmetric centers on "
|
|
"non-canonical molecules") {
|
|
SECTION("basics") {
|
|
auto mol1 = "N[C@@]12CC[C@@](CC1)(C2)C(F)F"_smiles;
|
|
REQUIRE(mol1);
|
|
|
|
bool clean = true;
|
|
|
|
auto stereoInfo1 = Chirality::findPotentialStereo(*mol1, clean);
|
|
REQUIRE(stereoInfo1.size() == 2);
|
|
REQUIRE(stereoInfo1[0].centeredOn == 1);
|
|
REQUIRE(stereoInfo1[1].centeredOn == 4);
|
|
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol1->getAtomWithIdx(4)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
|
|
auto mol2 = "C1C[C@]2(C(F)F)CC[C@@]1(N)C2"_smiles;
|
|
REQUIRE(mol2);
|
|
|
|
auto stereoInfo2 = Chirality::findPotentialStereo(*mol2, clean);
|
|
REQUIRE(stereoInfo2.size() == 2);
|
|
CHECK(stereoInfo2[0].centeredOn == 2);
|
|
CHECK(stereoInfo2[1].centeredOn == 8);
|
|
{
|
|
RWMol cp(*mol2);
|
|
Chirality::findPotentialStereo(cp, true, false);
|
|
CHECK(cp.getAtomWithIdx(2)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(cp.getAtomWithIdx(8)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
SECTION("new stereo") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
|
|
auto mol1 = "N[C@@]12CC[C@@](CC1)(C2)C(F)F"_smiles;
|
|
REQUIRE(mol1);
|
|
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(mol1->getAtomWithIdx(4)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
TEST_CASE("assignStereochemistry sets bond stereo with new stereo perception") {
|
|
SECTION("basics") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
{
|
|
auto m = "C/C=C/C"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
|
|
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
|
|
}
|
|
{
|
|
auto m = "C/C=C\\C"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOCIS);
|
|
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
|
|
}
|
|
{
|
|
auto m = "C(/C)=C/C"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOCIS);
|
|
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{1, 3});
|
|
}
|
|
{
|
|
auto m = "FC(/C)=C/C"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREOTRANS);
|
|
CHECK(m->getBondWithIdx(2)->getStereoAtoms() == std::vector<int>{0, 4});
|
|
}
|
|
{
|
|
auto m = "FC(/C)=C(F)/C"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREOCIS);
|
|
CHECK(m->getBondWithIdx(2)->getStereoAtoms() == std::vector<int>{0, 4});
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("chiral duplicates") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
SECTION("atom basics") {
|
|
auto mol = "C[C@](F)([C@H](F)Cl)[C@H](F)Cl"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(mol->getAtomWithIdx(6)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
SECTION("double bonds and atoms") {
|
|
auto mol = "C/C(O)=C([C@H](F)Cl)/[C@H](F)Cl"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(4)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(mol->getAtomWithIdx(7)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("double bonds and atoms 2") {
|
|
auto mol = "C/C(O)=C([C@H](F)Cl)/[C@@H](F)Cl"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getAtomWithIdx(4)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(mol->getAtomWithIdx(7)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() != Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("double bonds and double bonds") {
|
|
auto mol = "C/C(O)=C(/C=C/C)/C=C/C"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::BondStereo::STEREOTRANS);
|
|
CHECK(mol->getBondWithIdx(7)->getStereo() == Bond::BondStereo::STEREOTRANS);
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("double bonds and double bonds 2") {
|
|
auto mol = "C/C(O)=C(/C=C/C)/C=C\\C"_smiles;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::BondStereo::STEREOTRANS);
|
|
CHECK(mol->getBondWithIdx(7)->getStereo() == Bond::BondStereo::STEREOCIS);
|
|
CHECK(mol->getBondWithIdx(2)->getStereo() != Bond::BondStereo::STEREONONE);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("more findPotential") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
SECTION("basics") {
|
|
{
|
|
auto m = "O[C@H](C)CC(C)C[C@@H](C)O"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 2);
|
|
}
|
|
{
|
|
auto m = "O[C@H](C)CC(C)C[C@H](C)O"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
{
|
|
auto m = "O[CH](C)C[C@H](C)C[CH](C)O"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
{
|
|
auto m = "O[CH](C)C[CH](C)C[CH](C)O"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
}
|
|
SECTION("double bond impact on atoms") {
|
|
{
|
|
auto m = "C[CH](/C=C/C)/C=C\\C"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
{
|
|
auto m = "C[CH](/C=C/C)/C=C/C"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 2);
|
|
}
|
|
{
|
|
auto m = "C[CH](C=CC)C=CC"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
{
|
|
auto m = "C[CH](C=CC)C=CC"_smiles;
|
|
REQUIRE(m);
|
|
m->getBondWithIdx(2)->setStereo(Bond::BondStereo::STEREOANY);
|
|
m->getBondWithIdx(5)->setStereo(Bond::BondStereo::STEREOANY);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
}
|
|
SECTION("atom impact on double bonds") {
|
|
{
|
|
auto m = "CC=C([C@H](F)Cl)[C@@H](F)Cl"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
{
|
|
auto m = "CC=C([C@H](F)Cl)[C@H](F)Cl"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 2);
|
|
}
|
|
{
|
|
auto m = "CC=C([CH](F)Cl)[CH](F)Cl"_smiles;
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
{
|
|
auto m = "CC=C([CH](F)Cl)[CH](F)Cl"_smiles;
|
|
REQUIRE(m);
|
|
m->getBondBetweenAtoms(2, 3)->setBondDir(Bond::UNKNOWN);
|
|
m->getBondBetweenAtoms(2, 6)->setBondDir(Bond::UNKNOWN);
|
|
auto si = Chirality::findPotentialStereo(*m, true, true);
|
|
CHECK(si.size() == 3);
|
|
}
|
|
}
|
|
}
|
|
TEST_CASE("more findPotential and ring stereo") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
SECTION("simple") {
|
|
{
|
|
auto m = "CC1CCC(C)CC1"_smiles;
|
|
REQUIRE(m);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*m, true, true);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].centeredOn == 1);
|
|
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
|
|
|
|
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].centeredOn == 4);
|
|
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"github 2984: RDKit misplaces stereochemistry/chirality information for "
|
|
"small ring") {
|
|
using namespace RDKit::Chirality;
|
|
|
|
// UseLegacyStereoPerceptionFixture reset_stereo_perception(true);
|
|
|
|
SECTION("The mol with the issue") {
|
|
for (auto use_legacy : {false, true}) {
|
|
Chirality::setUseLegacyStereoPerception(use_legacy);
|
|
|
|
// With Legacy stereo, parsing the SMILES string will discard the
|
|
// problematic stereo features, so findPotentialStereo (which uses
|
|
// the new algorithm) will still find them, but they will be unspecified.
|
|
// Parsing with the new algorithm will preserve the features, so they
|
|
// can be correctly resolved.
|
|
|
|
auto specified_status = use_legacy ? StereoSpecified::Unspecified
|
|
: StereoSpecified::Specified;
|
|
|
|
auto mol = R"SMI(CC/C=C1\C[C@H](O)C1)SMI"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].centeredOn == 5);
|
|
CHECK(stereoInfo[0].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == specified_status);
|
|
CHECK(stereoInfo[1].centeredOn == 2);
|
|
CHECK(stereoInfo[1].type == StereoType::Bond_Double);
|
|
CHECK(stereoInfo[1].specified == specified_status);
|
|
}
|
|
}
|
|
|
|
// The other sections should yield the same results independently
|
|
// of which stereo algoritm is used, new or legacy
|
|
|
|
SECTION("Unspecified, but still potentially stereo") {
|
|
for (auto use_legacy : {false, true}) {
|
|
Chirality::setUseLegacyStereoPerception(use_legacy);
|
|
|
|
auto mol = R"SMI(CCC=C1CC(O)C1)SMI"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].centeredOn == 5);
|
|
CHECK(stereoInfo[0].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[1].centeredOn == 2);
|
|
CHECK(stereoInfo[1].type == StereoType::Bond_Double);
|
|
CHECK(stereoInfo[1].specified == StereoSpecified::Unspecified);
|
|
}
|
|
}
|
|
|
|
SECTION("Specified") {
|
|
for (auto use_legacy : {false, true}) {
|
|
Chirality::setUseLegacyStereoPerception(use_legacy);
|
|
|
|
auto mol = R"SMI(CC/C=C1\CC[C@H]1O)SMI"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 2);
|
|
CHECK(stereoInfo[0].centeredOn == 6);
|
|
CHECK(stereoInfo[0].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == StereoSpecified::Specified);
|
|
CHECK(stereoInfo[1].centeredOn == 2);
|
|
CHECK(stereoInfo[1].type == StereoType::Bond_Double);
|
|
CHECK(stereoInfo[1].specified == StereoSpecified::Specified);
|
|
}
|
|
}
|
|
|
|
SECTION("More than one ring (1)") {
|
|
for (auto use_legacy : {false, true}) {
|
|
Chirality::setUseLegacyStereoPerception(use_legacy);
|
|
|
|
auto mol = R"SMI(CC\C=C/1C2CCC1[C@H]2O)SMI"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 4);
|
|
CHECK(stereoInfo[0].centeredOn == 4);
|
|
CHECK(stereoInfo[0].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[1].centeredOn == 7);
|
|
CHECK(stereoInfo[1].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].specified == StereoSpecified::Unspecified);
|
|
CHECK(stereoInfo[2].centeredOn == 8);
|
|
CHECK(stereoInfo[2].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[2].specified == (use_legacy
|
|
? StereoSpecified::Unspecified
|
|
: StereoSpecified::Specified));
|
|
CHECK(stereoInfo[3].centeredOn == 2);
|
|
CHECK(stereoInfo[3].type == StereoType::Bond_Double);
|
|
CHECK(stereoInfo[3].specified == (use_legacy
|
|
? StereoSpecified::Unspecified
|
|
: StereoSpecified::Specified));
|
|
}
|
|
}
|
|
|
|
SECTION("More than one ring (2)") {
|
|
for (auto use_legacy : {false, true}) {
|
|
Chirality::setUseLegacyStereoPerception(use_legacy);
|
|
|
|
// This is the same structure as previos section, but
|
|
// the rings are defined in the opposite order
|
|
auto mol = R"SMI(CC\C=C/1C2[C@H](O)C1CC2)SMI"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
REQUIRE(stereoInfo.size() == 4);
|
|
CHECK(stereoInfo[0].centeredOn == 4);
|
|
CHECK(stereoInfo[0].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[0].specified == StereoSpecified::Unspecified);
|
|
|
|
CHECK(stereoInfo[1].centeredOn == 5);
|
|
CHECK(stereoInfo[1].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[1].specified == (use_legacy
|
|
? StereoSpecified::Unspecified
|
|
: StereoSpecified::Specified));
|
|
|
|
CHECK(stereoInfo[2].centeredOn == 7);
|
|
CHECK(stereoInfo[2].type == StereoType::Atom_Tetrahedral);
|
|
CHECK(stereoInfo[2].specified == StereoSpecified::Unspecified);
|
|
|
|
CHECK(stereoInfo[3].centeredOn == 2);
|
|
CHECK(stereoInfo[3].type == StereoType::Bond_Double);
|
|
CHECK(stereoInfo[3].specified == (use_legacy
|
|
? StereoSpecified::Unspecified
|
|
: StereoSpecified::Specified));
|
|
}
|
|
}
|
|
|
|
SECTION("Stereo not possible: symmetric opposite atom") {
|
|
for (auto use_legacy : {false, true}) {
|
|
Chirality::setUseLegacyStereoPerception(use_legacy);
|
|
|
|
auto mol = R"SMI(CCC=C1CC(O)(O)C1)SMI"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.empty());
|
|
}
|
|
}
|
|
|
|
SECTION("Stereo not possible: odd-sized ring") {
|
|
for (auto use_legacy : {false, true}) {
|
|
Chirality::setUseLegacyStereoPerception(use_legacy);
|
|
|
|
auto mol = R"SMI(CCC=C1CCCC1)SMI"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
CHECK(stereoInfo.empty());
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("double bond stereo with new chirality perception") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
SECTION("chain bonds") {
|
|
{
|
|
auto m = "C/C=C/C"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
|
|
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
|
|
}
|
|
}
|
|
SECTION("ring bonds") {
|
|
{
|
|
auto m = "C1/C=C/CCCCCCC1"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
|
|
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("false positives from new stereo code") {
|
|
SECTION("elements") {
|
|
std::vector<std::string> examples{"P", "PC", "S", "SC", "S(F)C"};
|
|
for (auto &smi : examples) {
|
|
INFO(smi);
|
|
std::unique_ptr<RWMol> m{SmilesToMol(smi)};
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m);
|
|
CHECK(si.empty());
|
|
}
|
|
}
|
|
SECTION("non-tetrahedral and implicit Hs") {
|
|
std::vector<std::string> examples{
|
|
"[SiH4]", "[SiH3]C", "[SH4]", "[PH5]",
|
|
"[PH4]C", "[SH6]", "[SH5]C", //"[SiH2](C)C",
|
|
"[PH3](C)C", "[PH2](C)(C)C", "[SH4](C)C", "[SH3](C)(C)C",
|
|
"[SH2](C)(C)(C)C"};
|
|
{
|
|
AllowNontetrahedralChiralityFixture reset_non_tetrahedral_allowed;
|
|
Chirality::setAllowNontetrahedralChirality(false);
|
|
for (auto &smi : examples) {
|
|
INFO(smi);
|
|
std::unique_ptr<RWMol> m{SmilesToMol(smi)};
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m);
|
|
CHECK(si.empty());
|
|
}
|
|
}
|
|
{
|
|
AllowNontetrahedralChiralityFixture reset_non_tetrahedral_allowed;
|
|
Chirality::setAllowNontetrahedralChirality(true);
|
|
for (auto &smi : examples) {
|
|
INFO(smi);
|
|
std::unique_ptr<RWMol> m{SmilesToMol(smi)};
|
|
REQUIRE(m);
|
|
auto si = Chirality::findPotentialStereo(*m);
|
|
CHECK(si.size() == 1);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #6049: Cyclobutyl group in a macrocycle triggers a stereo center") {
|
|
SECTION("as reported") {
|
|
auto mol = "O=S1(=O)C=CC=C2CCCCC3CC(C3)N21"_smiles;
|
|
REQUIRE(mol);
|
|
auto stereoInfo = Chirality::findPotentialStereo(*mol);
|
|
for (const auto &sg : stereoInfo) {
|
|
CHECK(sg.centeredOn != 15);
|
|
}
|
|
}
|
|
}
|
|
|
|
void testStereoValidationFromMol(std::string molBlock,
|
|
std::string expectedSmiles, bool legacyFlag,
|
|
bool canonicalFlag = false) {
|
|
RDKit::Chirality::setUseLegacyStereoPerception(legacyFlag);
|
|
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(molBlock, true, false, false));
|
|
REQUIRE(mol);
|
|
|
|
// CHECK(CIPLabeler::validateStereochem(*mol, validationFlags));
|
|
|
|
RDKit::SmilesWriteParams smilesWriteParams;
|
|
smilesWriteParams.doIsomericSmiles = true;
|
|
smilesWriteParams.doKekule = false;
|
|
smilesWriteParams.canonical = canonicalFlag;
|
|
|
|
unsigned int flags = 0 |
|
|
RDKit::SmilesWrite::CXSmilesFields::CX_MOLFILE_VALUES |
|
|
RDKit::SmilesWrite::CXSmilesFields::CX_ATOM_PROPS |
|
|
RDKit::SmilesWrite::CXSmilesFields::CX_BOND_CFG |
|
|
RDKit::SmilesWrite::CXSmilesFields::CX_ENHANCEDSTEREO |
|
|
RDKit::SmilesWrite::CXSmilesFields::CX_SGROUPS |
|
|
RDKit::SmilesWrite::CXSmilesFields::CX_POLYMER;
|
|
|
|
auto outSmiles = MolToCXSmiles(*mol, smilesWriteParams, flags);
|
|
RDKit::Chirality::setUseLegacyStereoPerception(false);
|
|
|
|
CHECK(outSmiles == expectedSmiles);
|
|
}
|
|
|
|
std::string validateStereoMolBlockSpiro = R"(
|
|
Mrv2308 06232316112D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 13 14 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -4.2921 0.9158 0 0
|
|
M V30 2 C -4.2921 -0.6244 0 0
|
|
M V30 3 C -2.9583 -1.3942 0 0 CFG=1
|
|
M V30 4 C -1.6246 -0.6244 0 0
|
|
M V30 5 C -1.6246 0.9158 0 0
|
|
M V30 6 C -2.9583 4.7658 0 0 CFG=2
|
|
M V30 7 C -4.2921 3.9958 0 0
|
|
M V30 8 C -4.2921 2.4556 0 0
|
|
M V30 9 C -2.9583 1.6858 0 0 CFG=2
|
|
M V30 10 C -1.6246 2.4556 0 0
|
|
M V30 11 C -1.6246 3.9958 0 0
|
|
M V30 12 C -2.9583 6.3058 0 0
|
|
M V30 13 Cl -2.9583 -2.9342 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 1 4 5
|
|
M V30 5 1 6 7
|
|
M V30 6 1 6 11
|
|
M V30 7 1 7 8
|
|
M V30 8 1 9 8 CFG=1
|
|
M V30 9 1 9 10
|
|
M V30 10 1 10 11
|
|
M V30 11 1 9 1
|
|
M V30 12 1 9 5
|
|
M V30 13 1 6 12 CFG=1
|
|
M V30 14 1 3 13 CFG=1
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
|
|
)";
|
|
|
|
std::string validateStereoMolBlockDoubleBondNoStereo = R"(
|
|
Mrv2308 06232316392D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 9 9 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 0.8498 2.3564 0 0
|
|
M V30 2 C 2.1835 1.5864 0 0
|
|
M V30 3 C 2.1835 0.0464 0 0
|
|
M V30 4 C -0.4839 1.5864 0 0
|
|
M V30 5 O -1.8176 2.3564 0 0
|
|
M V30 6 C -1.8176 3.8964 0 0
|
|
M V30 7 C -3.3342 3.629 0 0
|
|
M V30 8 O -0.4839 4.6664 0 0
|
|
M V30 9 C 0.8498 3.8964 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 1 4
|
|
M V30 4 1 4 5
|
|
M V30 5 1 5 6
|
|
M V30 6 1 6 7
|
|
M V30 7 1 6 8
|
|
M V30 8 1 8 9
|
|
M V30 9 1 1 9
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)";
|
|
|
|
std::string validateStereoMolBlockDoubleBondNoStereo2 = R"(
|
|
Mrv0541 07011416342D
|
|
|
|
21 22 0 0 0 0 999 V2000
|
|
-1.9814 1.4834 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9581 -2.7980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.3658 -2.0787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.8189 1.5764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.5800 0.7796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.9760 2.3967 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.1333 -2.7836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.9581 -1.3592 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7256 -2.0690 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4882 -1.3401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8471 2.4140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7304 -0.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.9007 -0.6351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.4834 0.0700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.1333 -1.3497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.3658 0.9831 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.9814 0.0525 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7598 0.7854 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.3410 0.0700 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.6556 2.2396 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.2722 2.7980 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
20 1 1 0 0 0 0
|
|
4 1 2 0 0 0 0
|
|
5 1 1 0 0 0 0
|
|
2 7 2 0 0 0 0
|
|
3 2 1 0 0 0 0
|
|
3 8 2 0 0 0 0
|
|
6 4 1 0 0 0 0
|
|
16 4 1 0 0 0 0
|
|
18 5 1 0 0 0 0
|
|
17 5 2 0 0 0 0
|
|
21 6 2 0 0 0 0
|
|
7 9 1 0 0 0 0
|
|
8 15 1 0 0 0 0
|
|
9 15 2 0 0 0 0
|
|
10 13 1 0 0 0 0
|
|
11 20 1 0 0 0 0
|
|
13 12 2 0 0 0 0
|
|
15 12 1 0 0 0 0
|
|
14 13 1 0 0 0 0
|
|
19 14 2 0 0 0 0
|
|
19 18 1 0 0 0 0
|
|
21 20 1 0 0 0 0
|
|
M END
|
|
> <Compound Name>
|
|
VM-0411129
|
|
|
|
> <CDD Number>
|
|
CDD-2839271
|
|
|
|
$$$$
|
|
|
|
)";
|
|
|
|
std::string validateStereoError1 = R"(
|
|
-ISIS- -- StrEd --
|
|
|
|
29 32 0 0 0 0 0 0 0 0999 V2000
|
|
-1.2050 -4.7172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8959 -3.7660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0823 -3.5582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7514 -4.3013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7296 -4.0934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.0385 -3.1425 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3694 -2.3993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.6785 -1.4481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0094 -0.7050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0312 -0.9129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.9470 -1.1209 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3183 0.2461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2694 0.5550 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2694 1.5549 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3183 1.8641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0094 2.8151 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.6785 3.5582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.3694 4.5093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3912 4.7172 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.2777 3.9739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0312 3.0230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7305 1.0550 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.2694 1.0550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7694 1.9210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7695 1.9210 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.2694 1.0550 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7695 0.1889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7694 0.1889 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3912 -2.6071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0 0 0 0
|
|
2 3 1 0 0 0 0
|
|
3 4 1 0 0 0 0
|
|
4 5 2 0 0 0 0
|
|
5 6 1 0 0 0 0
|
|
6 7 2 0 0 0 0
|
|
7 8 1 0 0 0 0
|
|
8 9 2 0 0 0 0
|
|
9 10 1 0 0 0 0
|
|
10 11 3 0 0 0 0
|
|
9 12 1 0 0 0 0
|
|
12 13 2 0 0 0 0
|
|
13 14 1 0 0 0 0
|
|
14 15 2 0 0 0 0
|
|
15 16 1 0 0 0 0
|
|
16 17 1 0 0 0 0
|
|
17 18 1 0 0 0 0
|
|
18 19 1 0 0 0 0
|
|
19 20 1 0 0 0 0
|
|
20 21 1 0 0 0 0
|
|
16 21 1 0 0 0 0
|
|
15 22 1 0 0 0 0
|
|
12 22 1 0 0 0 0
|
|
22 23 1 0 0 0 0
|
|
23 24 1 0 0 0 0
|
|
24 25 2 0 0 0 0
|
|
25 26 1 0 0 0 0
|
|
26 27 2 0 0 0 0
|
|
27 28 1 0 0 0 0
|
|
23 28 2 0 0 0 0
|
|
7 29 1 0 0 0 0
|
|
3 29 2 0 0 0 0
|
|
M END
|
|
> <Compound Name>
|
|
Z362114294
|
|
|
|
> <CDD Number>
|
|
CDD-3164311
|
|
|
|
$$$$
|
|
|
|
)";
|
|
|
|
std::string validateStereoUniq1 = R"(
|
|
Mrv0541 06301412152D
|
|
|
|
15 15 0 0 0 0 999 V2000
|
|
1.0464 -0.3197 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.0464 -1.1460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7601 -1.5571 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.4739 -1.1460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.4739 -0.3197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7601 0.0914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.3309 -1.5706 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.1912 0.0976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.9103 -0.3114 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.1853 0.9197 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.9115 -1.1336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7601 0.9135 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.6215 -1.5447 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7601 -2.3793 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.1894 -1.5665 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 6 1 0 0 0 0
|
|
1 2 1 0 0 0 0
|
|
2 3 1 0 0 0 0
|
|
2 7 2 0 0 0 0
|
|
3 4 1 0 0 0 0
|
|
3 14 1 0 0 0 0
|
|
4 15 1 0 0 0 0
|
|
4 5 2 0 0 0 0
|
|
5 6 1 0 0 0 0
|
|
5 8 1 0 0 0 0
|
|
6 12 1 0 0 0 0
|
|
8 9 1 0 0 0 0
|
|
8 10 2 0 0 0 0
|
|
9 11 2 0 0 0 0
|
|
11 13 1 0 0 0 0
|
|
M STY 4 1 SUP 2 SUP 3 SUP 4 SUP
|
|
M SAL 1 1 12
|
|
M SBL 1 1 11
|
|
M SMT 1 R3a
|
|
M SAP 1 1 12 6 1
|
|
M SCL 1 CXN
|
|
M SAL 2 1 13
|
|
M SBL 2 1 15
|
|
M SMT 2 R3b
|
|
M SAP 2 1 13 11 1
|
|
M SCL 2 CXN
|
|
M SAL 3 1 14
|
|
M SBL 3 1 6
|
|
M SMT 3 R1
|
|
M SAP 3 1 14 3 1
|
|
M SCL 3 CXN
|
|
M SAL 4 1 15
|
|
M SBL 4 1 7
|
|
M SMT 4 R2
|
|
M SAP 4 1 15 4 1
|
|
M SCL 4 CXN
|
|
M END
|
|
> <Compound Name>
|
|
VM-0021367
|
|
|
|
> <CDD Number>
|
|
CDD-3832787
|
|
|
|
$$$$
|
|
)";
|
|
|
|
TEST_CASE("ValidateStereo", "[accurateCIP]") {
|
|
SECTION("validateStereoUniqOldCanon1") {
|
|
testStereoValidationFromMol(validateStereoUniq1,
|
|
"*/C=C/C(=O)C1=C(*)N(*)C(=O)NC1* |,,,|", true,
|
|
true);
|
|
}
|
|
|
|
SECTION("validateStereoUniqNewCanon1") {
|
|
testStereoValidationFromMol(validateStereoUniq1,
|
|
"*/C=C/C(=O)C1=C(*)N(*)C(=O)NC1* |,,,|", false,
|
|
true);
|
|
}
|
|
|
|
SECTION("validateStereoUniqNewNoCanon1") {
|
|
testStereoValidationFromMol(validateStereoUniq1,
|
|
"N1C(=O)N(*)C(*)=C(C(/C=C/*)=O)C1* |,,,|",
|
|
false, false);
|
|
}
|
|
|
|
SECTION("SprioChiralLostOldNoCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockSpiro,
|
|
"C1C[C@H](Cl)CCC12CC[C@@H](C)CC2", true, false);
|
|
}
|
|
|
|
SECTION("SprioChiralLostOldCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockSpiro,
|
|
"C[C@H]1CCC2(CC1)CC[C@H](Cl)CC2", true, true);
|
|
}
|
|
|
|
SECTION("SprioChiralNotLostNewNoCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockSpiro,
|
|
"C1C[C@H](Cl)CC[C@]12CC[C@@H](C)CC2", false,
|
|
false);
|
|
}
|
|
|
|
SECTION("SprioChiralNotLostNewCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockSpiro,
|
|
"C[C@H]1CC[C@@]2(CC1)CC[C@H](Cl)CC2", false,
|
|
true);
|
|
}
|
|
|
|
SECTION("DoubleBondMarkedStereoOldNoCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockDoubleBondNoStereo,
|
|
"C1(=CC)COC(C)OC1", true, false);
|
|
}
|
|
SECTION("DoubleBondMarkedStereoNewNoCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockDoubleBondNoStereo,
|
|
"C1(=CC)COC(C)OC1", false, false);
|
|
}
|
|
|
|
SECTION("DoubleBondMarkedStereoOldCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockDoubleBondNoStereo,
|
|
"CC=C1COC(C)OC1", true, true);
|
|
}
|
|
|
|
SECTION("DoubleBondMarkedStereoNewCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockDoubleBondNoStereo,
|
|
"CC=C1COC(C)OC1", false, true);
|
|
}
|
|
|
|
SECTION("DoubleBondStereo2OldCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockDoubleBondNoStereo2,
|
|
"CC(/C=N/NC(=O)c1c(Br)cnn1C)=C\\c1ccccc1", true,
|
|
true);
|
|
}
|
|
SECTION("DoubleBondStereo2NewCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockDoubleBondNoStereo2,
|
|
"CC(=C\\c1ccccc1)/C=N/NC(=O)c1c(Br)cnn1C",
|
|
false, true);
|
|
}
|
|
|
|
SECTION("DoubleBondStereo2NewNoCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockDoubleBondNoStereo2,
|
|
"c1(C(=O)N/N=C/C(C)=C/c2ccccc2)c(Br)cnn1C",
|
|
false, false);
|
|
}
|
|
SECTION("DoubleBondStereo2OldNoCanon") {
|
|
testStereoValidationFromMol(validateStereoMolBlockDoubleBondNoStereo2,
|
|
"c1(C(=O)N/N=C/C(C)=C/c2ccccc2)c(Br)cnn1C",
|
|
true, false);
|
|
}
|
|
|
|
SECTION("ValidateStereoError1OldCanon") {
|
|
testStereoValidationFromMol(
|
|
validateStereoError1,
|
|
"COc1cccc(/C=C(\\C#N)c2nnc(N3CCOCC3)n2-c2ccccc2)c1", true, true);
|
|
}
|
|
SECTION("ValidateStereoError1NewCanon") {
|
|
testStereoValidationFromMol(
|
|
validateStereoError1,
|
|
"COc1cccc(/C=C(\\C#N)c2nnc(N3CCOCC3)n2-c2ccccc2)c1", false, true);
|
|
}
|
|
SECTION("ValidateStereoError1OldNoCanon") {
|
|
testStereoValidationFromMol(
|
|
validateStereoError1,
|
|
"COc1cccc(/C=C(\\C#N)c2nnc(N3CCOCC3)n2-c2ccccc2)c1", true, false);
|
|
}
|
|
SECTION("ValidateStereoError1NewNoCanon") {
|
|
testStereoValidationFromMol(
|
|
validateStereoError1,
|
|
"COc1cccc(/C=C(\\C#N)c2nnc(N3CCOCC3)n2-c2ccccc2)c1", false, false);
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"assignStereochemistry should clear crossed double bonds that can't have stereo") {
|
|
SECTION("basics") {
|
|
auto m = "CC=C(C)C"_smiles;
|
|
REQUIRE(m);
|
|
m->getBondWithIdx(1)->setBondDir(Bond::BondDir::EITHERDOUBLE);
|
|
bool clean = true;
|
|
bool flag = true;
|
|
bool force = true;
|
|
{
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
auto cp(*m);
|
|
RDKit::MolOps::assignStereochemistry(cp, clean, force, flag);
|
|
CHECK(cp.getBondWithIdx(1)->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
{
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(true);
|
|
auto cp(*m);
|
|
RDKit::MolOps::assignStereochemistry(cp, clean, force, flag);
|
|
CHECK(cp.getBondWithIdx(1)->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
}
|
|
SECTION("make sure we don't mess with actual potential stereosystems") {
|
|
auto m = "CC=C(C)[13CH3]"_smiles;
|
|
REQUIRE(m);
|
|
m->getBondWithIdx(1)->setBondDir(Bond::BondDir::EITHERDOUBLE);
|
|
bool clean = true;
|
|
bool flag = true;
|
|
bool force = true;
|
|
{
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
auto cp(*m);
|
|
RDKit::MolOps::assignStereochemistry(cp, clean, force, flag);
|
|
// the crossed bond dir has been translated to unknown stereo:
|
|
CHECK(cp.getBondWithIdx(1)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOANY);
|
|
}
|
|
{
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(true);
|
|
auto cp(*m);
|
|
RDKit::MolOps::assignStereochemistry(cp, clean, force, flag);
|
|
// the crossed bond dir has been translated to unknown stereo:
|
|
CHECK(cp.getBondWithIdx(1)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOANY);
|
|
}
|
|
}
|
|
SECTION("make sure stereoatoms are also cleared") {
|
|
auto m = "CC=C(C)C"_smiles;
|
|
REQUIRE(m);
|
|
m->getBondWithIdx(1)->setBondDir(Bond::BondDir::EITHERDOUBLE);
|
|
m->getBondWithIdx(1)->setStereoAtoms(0, 3);
|
|
bool clean = true;
|
|
bool flag = true;
|
|
bool force = true;
|
|
{
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
auto cp(*m);
|
|
RDKit::MolOps::assignStereochemistry(cp, clean, force, flag);
|
|
CHECK(cp.getBondWithIdx(1)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondWithIdx(1)->getStereoAtoms().empty());
|
|
}
|
|
{
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(true);
|
|
auto cp(*m);
|
|
RDKit::MolOps::assignStereochemistry(cp, clean, force, flag);
|
|
CHECK(cp.getBondWithIdx(1)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondWithIdx(1)->getStereoAtoms().empty());
|
|
}
|
|
}
|
|
SECTION("ensure we can enumerate stereo on either double bonds") {
|
|
auto mol = R"CTAB(
|
|
Mrv2004 11072316002D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 8 0 0 1
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 1.859 2.7821 0 0
|
|
M V30 2 C 3.2818 2.1928 0 0
|
|
M V30 3 C 3.8711 0.77 0 0
|
|
M V30 4 C 3.2818 -0.6528 0 0
|
|
M V30 5 C 1.859 -1.2421 0 0
|
|
M V30 6 C 0.4362 -0.6528 0 0
|
|
M V30 7 C -0.1533 0.77 0 0
|
|
M V30 8 C 0.4362 2.1928 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 4 3 CFG=2
|
|
M V30 4 2 4 5
|
|
M V30 5 1 5 6
|
|
M V30 6 1 6 7
|
|
M V30 7 1 7 8
|
|
M V30 8 1 1 8
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END)CTAB"_ctab;
|
|
// mol->debugMol(std::cerr);
|
|
std::string smi = MolToCXSmiles(*mol, SmilesWriteParams());
|
|
std::unique_ptr<ROMol> f(SmilesToMol(smi));
|
|
mol->getBondWithIdx(3)->setStereo(Bond::BondStereo::STEREOCIS);
|
|
f->getBondWithIdx(0)->setStereo(Bond::BondStereo::STEREOCIS);
|
|
CHECK(MolToSmiles(*mol) == "C1=C\\CCCCCC/1");
|
|
CHECK(MolToSmiles(*f) == "C1=C\\CCCCCC/1");
|
|
mol->getBondWithIdx(3)->setStereo(Bond::BondStereo::STEREOTRANS);
|
|
f->getBondWithIdx(0)->setStereo(Bond::BondStereo::STEREOTRANS);
|
|
CHECK(MolToSmiles(*mol) == "C1=C/CCCCCC/1");
|
|
CHECK(MolToSmiles(*f) == "C1=C/CCCCCC/1");
|
|
}
|
|
}
|
|
TEST_CASE("adding two wedges to chiral centers") {
|
|
SECTION("basics") {
|
|
auto mol = R"CTAB(
|
|
Mrv2219 02112315062D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 5 4 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 O -3.6667 2.5 0 0
|
|
M V30 2 C -2.333 3.27 0 0 CFG=1
|
|
M V30 3 F -0.9993 2.5 0 0
|
|
M V30 4 C -3.103 4.6037 0 0
|
|
M V30 5 N -1.3955 4.4918 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 2 4
|
|
M V30 4 1 2 5 CFG=1
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(mol);
|
|
CHECK(mol->getNumAtoms() == 5);
|
|
|
|
Chirality::BondWedgingParameters ps;
|
|
ps.wedgeTwoBondsIfPossible = true;
|
|
|
|
{
|
|
RWMol cp(*mol);
|
|
Chirality::wedgeMolBonds(cp);
|
|
CHECK(cp.getBondBetweenAtoms(1, 3)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 4)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 0)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 2)->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
{
|
|
RWMol cp(*mol);
|
|
Chirality::wedgeMolBonds(cp, nullptr, &ps);
|
|
CHECK(cp.getBondBetweenAtoms(1, 3)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 4)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 4)->getBondDir() !=
|
|
cp.getBondBetweenAtoms(1, 3)->getBondDir());
|
|
CHECK(cp.getBondBetweenAtoms(1, 0)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 2)->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
{
|
|
// Wedge a second bond after we already wedged a first one
|
|
|
|
RWMol cp(*mol);
|
|
Chirality::wedgeMolBonds(cp);
|
|
CHECK(cp.getBondBetweenAtoms(1, 3)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 4)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 0)->getBondDir() == Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 2)->getBondDir() == Bond::BondDir::NONE);
|
|
|
|
Chirality::wedgeMolBonds(cp, nullptr, &ps);
|
|
|
|
REQUIRE(count_wedged_bonds(cp) == 2);
|
|
|
|
CHECK(cp.getBondBetweenAtoms(1, 3)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 4)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(cp.getBondBetweenAtoms(1, 4)->getBondDir() !=
|
|
cp.getBondBetweenAtoms(1, 3)->getBondDir());
|
|
}
|
|
{
|
|
// What if the first wedged bond is not our preferred one?
|
|
|
|
for (auto wedgedAtomIdx : {0, 2, 4}) {
|
|
INFO("wedgedAtomIdx: " << wedgedAtomIdx);
|
|
|
|
RWMol cp(*mol);
|
|
REQUIRE(count_wedged_bonds(cp) == 0);
|
|
|
|
auto bond = cp.getBondBetweenAtoms(1, wedgedAtomIdx);
|
|
if (bond->getEndAtomIdx() == 1) {
|
|
// One of the bonds in the input is reversed, make sure the chiral
|
|
// atom is always at the start so that the wedge is valid!
|
|
auto tmp = bond->getBeginAtomIdx();
|
|
bond->setBeginAtomIdx(bond->getEndAtomIdx());
|
|
bond->setEndAtomIdx(tmp);
|
|
}
|
|
|
|
// This probably disagrees with the chirality in some of the test cases,
|
|
// but that's not relevant for this test
|
|
bond->setBondDir(Bond::BondDir::BEGINWEDGE);
|
|
|
|
Chirality::wedgeMolBonds(cp, nullptr, &ps);
|
|
|
|
CHECK(count_wedged_bonds(cp) == 2);
|
|
}
|
|
}
|
|
}
|
|
SECTION(
|
|
"more complex 1, this should only have one wedge for each of the two chiral centers") {
|
|
std::string smi =
|
|
"[H][C@@]12CC(=O)N1[C@@H](C(=O)O)C(C)(C)S2(=O)=O |(-2.78382,0.183015,;-1.38222,-0.351313,;-2.12923,-1.65207,;-0.828466,-2.39908,;-0.436905,-3.84707,;-0.0814577,-1.09832,;1.03095,-0.0920638,;2.49888,-0.400554,;2.96569,-1.82607,;3.50001,0.71647,;0.41769,1.27685,;1.8432,1.74365,;0.102447,2.74335,;-1.07373,1.11662,;-1.07718,2.61662,;-2.56587,1.26998,)|";
|
|
SmilesParserParams spps;
|
|
spps.removeHs = false;
|
|
std::unique_ptr<RWMol> m{SmilesToMol(smi, spps)};
|
|
REQUIRE(m);
|
|
Chirality::BondWedgingParameters bwps;
|
|
bwps.wedgeTwoBondsIfPossible = true;
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer(), &bwps);
|
|
unsigned nWedged = 0;
|
|
for (const auto bond : m->bonds()) {
|
|
if (bond->getBondDir() != Bond::BondDir::NONE) {
|
|
++nWedged;
|
|
}
|
|
}
|
|
CHECK(nWedged == 2);
|
|
}
|
|
SECTION("more complex 2, have two wedges around the chiral center") {
|
|
std::string smi =
|
|
"[H][C@@]12CCCN1C(=O)CN1C(=O)[C@](C)(N)O[C@]12O |(-0.888297,0.626611,;-1.19852,-0.840959,;-1.94707,-2.14084,;-3.41464,-1.83061,;-3.5731,-0.339006,;-2.20347,0.272634,;-1.74154,1.69974,;-2.74648,2.81333,;-0.274666,2.01325,;0.730277,0.899655,;2.23028,0.901335,;3.11059,2.11585,;2.6954,-0.52473,;3.44685,-1.82293,;4.06503,0.0869091,;1.48286,-1.40777,;0.26835,-0.527448,;-0.0418744,-1.99502,)|";
|
|
SmilesParserParams spps;
|
|
spps.removeHs = false;
|
|
std::unique_ptr<RWMol> m{SmilesToMol(smi, spps)};
|
|
REQUIRE(m);
|
|
Chirality::BondWedgingParameters bwps;
|
|
bwps.wedgeTwoBondsIfPossible = true;
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer(), &bwps);
|
|
CHECK(m->getBondWithIdx(12)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(m->getBondWithIdx(13)->getBondDir() != Bond::BondDir::NONE);
|
|
}
|
|
SECTION("another one") {
|
|
auto m =
|
|
"CC[C@@]1(O)C(=O)OCc2c1cc1-c3nc4ccccc4cc3Cn1c2=O |(-2.67178,3.55256,;-2.43493,2.07138,;-3.59925,1.12567,;-4.32841,2.43652,;-5.01681,0.635215,;-6.15033,1.61763,;-5.30084,-0.837648,;-4.16731,-1.82006,;-2.74976,-1.3296,;-2.46573,0.143259,;-1.04818,0.633713,;0.085343,-0.348697,;1.57389,-0.163687,;2.43243,1.06631,;3.92692,0.937796,;4.78546,2.1678,;6.27994,2.03928,;6.91588,0.680758,;6.05734,-0.549244,;4.56286,-0.420725,;3.70432,-1.65073,;2.20983,-1.52221,;1.11432,-2.54683,;-0.198688,-1.82156,;-1.61624,-2.31201,;-1.90027,-3.78488,)|"_smiles;
|
|
REQUIRE(m);
|
|
Chirality::BondWedgingParameters bwps;
|
|
bwps.wedgeTwoBondsIfPossible = true;
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer(), &bwps);
|
|
CHECK(m->getBondWithIdx(1)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(m->getBondWithIdx(1)->getBeginAtomIdx() == 2);
|
|
CHECK(m->getBondWithIdx(2)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(m->getBondWithIdx(2)->getBeginAtomIdx() == 2);
|
|
}
|
|
SECTION("favor degree 1") {
|
|
auto m =
|
|
"[H][C@@]12CC[C@@](C)(O)[C@H](CC[C@@](C)(O)C=C)[C@@]1(C)CCCC2(C)C |(3.59567,-1.0058,;2.33379,-0.194852,;2.4456,-1.69068,;1.20608,-2.53542,;-0.145252,-1.88434,;-1.63777,-1.73471,;-0.551787,-3.3282,;-0.257063,-0.388514,;-1.60839,0.262569,;-2.84791,-0.582176,;-4.19924,0.068907,;-5.55057,0.71999,;-4.85032,-1.28242,;-3.54816,1.42024,;-4.3929,2.65976,;0.982456,0.456231,;-0.368873,1.10731,;0.870645,1.95206,;2.11016,2.7968,;3.46149,2.14572,;3.5733,0.649893,;5.02699,1.01975,;4.35205,-0.632117,)|"_smiles;
|
|
REQUIRE(m);
|
|
Chirality::BondWedgingParameters bwps;
|
|
bwps.wedgeTwoBondsIfPossible = true;
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer(), &bwps);
|
|
CHECK(m->getBondWithIdx(9)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(m->getBondWithIdx(10)->getBondDir() != Bond::BondDir::NONE);
|
|
CHECK(m->getBondWithIdx(11)->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"RDKit Issue #6217: Atoms may get flagged with non-tetrahedral stereo even when it is not allowed",
|
|
"[bug][stereo][non-tetrahedral]") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
|
|
AllowNontetrahedralChiralityFixture reset_non_tetrahedral_allowed;
|
|
Chirality::setAllowNontetrahedralChirality(false);
|
|
|
|
auto m = "CS(=O)(=O)O"_smiles;
|
|
REQUIRE(m);
|
|
REQUIRE(m->getNumAtoms() == 5);
|
|
|
|
auto stereoInfo = Chirality::findPotentialStereo(*m);
|
|
CHECK(stereoInfo.size() == 0);
|
|
|
|
auto at = m->getAtomWithIdx(1);
|
|
|
|
auto sinfo = Chirality::detail::getStereoInfo(at);
|
|
CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
|
|
REQUIRE(at->getAtomicNum() == 16);
|
|
CHECK(!at->hasProp(common_properties::_ChiralityPossible));
|
|
}
|
|
|
|
TEST_CASE(
|
|
"RDKit Issue #6239: Tri-coordinate atom with implicit + neighbor H atom is found potentially chiral",
|
|
"[bug][stereo]") {
|
|
// Parametrize test to run under legacy and new stereo perception
|
|
const auto legacy_stereo = GENERATE(true, false);
|
|
INFO("Legacy stereo perception == " << legacy_stereo);
|
|
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(legacy_stereo);
|
|
|
|
auto p = SmilesParserParams();
|
|
p.removeHs = false;
|
|
|
|
std::unique_ptr<RWMol> m{SmilesToMol("[H]C(C)CC", p)};
|
|
|
|
REQUIRE(m);
|
|
REQUIRE(m->getNumAtoms() == 5);
|
|
|
|
auto at = m->getAtomWithIdx(1);
|
|
REQUIRE(at->getAtomicNum() == 6);
|
|
REQUIRE(at->getDegree() == 3);
|
|
|
|
CHECK(!at->hasProp(common_properties::_ChiralityPossible));
|
|
|
|
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(at));
|
|
|
|
auto stereoInfo = Chirality::findPotentialStereo(*m);
|
|
CHECK(stereoInfo.size() == 0);
|
|
|
|
auto sinfo = Chirality::detail::getStereoInfo(at);
|
|
CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
|
|
}
|
|
|
|
TEST_CASE("double bonded N with H should be stereogenic", "[bug][stereo]") {
|
|
SECTION("assign stereo") {
|
|
// Parametrize test to run under legacy and new stereo perception
|
|
const auto legacy_stereo = GENERATE(true, false);
|
|
INFO("Legacy stereo perception == " << legacy_stereo);
|
|
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(legacy_stereo);
|
|
auto m = "[H]/N=C/F"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(1)->getStereo() != Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("find potential stereo") {
|
|
auto m = "[H]/N=C/F"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(Chirality::detail::isBondPotentialStereoBond(m->getBondWithIdx(1)));
|
|
bool cleanIt = false;
|
|
bool flagPossible = true;
|
|
auto si = Chirality::findPotentialStereo(*m, cleanIt, flagPossible);
|
|
CHECK(si.size() == 1);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Issue in GitHub #6473", "[bug][stereo]") {
|
|
constexpr const char *mb = R"CTAB(
|
|
RDKit 2D
|
|
|
|
6 5 0 0 0 0 0 0 0 0999 V2000
|
|
2.0443 0.2759 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7038 2.5963 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.3828 2.5961 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.0444 1.8228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6359 1.8229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.3827 -0.4985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 4 1 0
|
|
4 2 1 0
|
|
4 3 2 0
|
|
2 5 1 0
|
|
6 1 1 0
|
|
M END)CTAB";
|
|
|
|
auto use_legacy_stereo = GENERATE(true, false);
|
|
CAPTURE(use_legacy_stereo);
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(use_legacy_stereo);
|
|
|
|
std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
|
|
REQUIRE(mol);
|
|
|
|
// Removal of the stereogenic H will cause loss of stereo information
|
|
// on the imine double bond, and although the bond is still detected as
|
|
// potentially stereo, it will be reverted to "unspecified"
|
|
auto bond = mol->getBondWithIdx(2);
|
|
REQUIRE(bond->getBondType() == Bond::BondType::DOUBLE);
|
|
CHECK(Chirality::detail::isBondPotentialStereoBond(bond));
|
|
CHECK(bond->getStereo() == Bond::BondStereo::STEREONONE);
|
|
|
|
if (!use_legacy_stereo) {
|
|
auto sinfo = Chirality::detail::getStereoInfo(bond);
|
|
REQUIRE(sinfo.type == Chirality::StereoType::Bond_Double);
|
|
CHECK(sinfo.specified == Chirality::StereoSpecified::Unspecified);
|
|
REQUIRE(sinfo.controllingAtoms.size() == 4);
|
|
CHECK(sinfo.controllingAtoms[0] == 0);
|
|
CHECK(sinfo.controllingAtoms[1] == 1);
|
|
CHECK(sinfo.controllingAtoms[2] == Chirality::StereoInfo::NOATOM);
|
|
CHECK(sinfo.controllingAtoms[3] == Chirality::StereoInfo::NOATOM);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("GitHub Issue #6640", "[bug][stereo]") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
|
|
auto p = SmilesParserParams();
|
|
p.sanitize = false;
|
|
p.removeHs = false;
|
|
std::string smiles{"NC1=NC(=N)N=C(N)C1C"};
|
|
std::unique_ptr<RWMol> mol(SmilesToMol(smiles, p));
|
|
REQUIRE(mol);
|
|
|
|
MolOps::removeHs(*mol);
|
|
|
|
auto cleanIt = true;
|
|
auto force = true;
|
|
auto flagPossibleStereoCenters = true;
|
|
MolOps::assignStereochemistry(*mol, cleanIt, force,
|
|
flagPossibleStereoCenters);
|
|
}
|
|
|
|
TEST_CASE("zero bond-length chirality cases") {
|
|
SECTION("basics") {
|
|
{
|
|
auto m = R"CTAB(derived from CHEMBL3183068
|
|
Mrv2211 07202306222D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 10 10 0 0 1
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N 3.231 0 0 0
|
|
M V30 2 C 4.0137 -1.3378 0 0
|
|
M V30 3 C 2.6757 -2.1004 0 0
|
|
M V30 4 C 2.6757 -3.6389 0 0
|
|
M V30 5 C 1.3378 -1.3378 0 0
|
|
M V30 6 C 5.4672 -0.99 0 0
|
|
M V30 7 C 1.3378 -4.4216 0 0
|
|
M V30 8 C 0 -2.1205 0 0
|
|
M V30 9 C 0 -3.659 0 0
|
|
M V30 10 F 4.0137 -1.3378 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1 CFG=3
|
|
M V30 2 1 2 3
|
|
M V30 3 1 2 6
|
|
M V30 4 1 2 10
|
|
M V30 5 2 3 4
|
|
M V30 6 1 3 5
|
|
M V30 7 1 4 7
|
|
M V30 8 2 5 8
|
|
M V30 9 2 7 9
|
|
M V30 10 1 8 9
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
{
|
|
auto m = R"CTAB(derived from CHEMBL3183068
|
|
Mrv2211 07202306222D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 10 10 0 0 1
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N 3.231 0 0 0
|
|
M V30 2 C 4.0137 -1.3378 0 0
|
|
M V30 3 C 2.6757 -2.1004 0 0
|
|
M V30 4 C 2.6757 -3.6389 0 0
|
|
M V30 5 C 1.3378 -1.3378 0 0
|
|
M V30 6 C 4.0137 -1.3378 0 0
|
|
M V30 7 C 1.3378 -4.4216 0 0
|
|
M V30 8 C 0 -2.1205 0 0
|
|
M V30 9 C 0 -3.659 0 0
|
|
M V30 10 F 4.5135 -2.6451 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1 CFG=3
|
|
M V30 2 1 2 3
|
|
M V30 3 1 2 6
|
|
M V30 4 1 2 10
|
|
M V30 5 2 3 4
|
|
M V30 6 1 3 5
|
|
M V30 7 1 4 7
|
|
M V30 8 2 5 8
|
|
M V30 9 2 7 9
|
|
M V30 10 1 8 9
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("t-shaped chirality cases") {
|
|
SECTION("ChEMBL example") {
|
|
{
|
|
auto m = R"CTAB(CHEMBL3183068
|
|
RDKit 2D
|
|
|
|
11 11 0 0 1 0 0 0 0 0999 V2000
|
|
1.7309 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.1502 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4334 -1.1252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4334 -1.9494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7167 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.8669 -0.2974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7167 -2.3687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -1.1360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -1.9602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.5836 -0.7060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.5694 -1.4334 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 6
|
|
2 3 1 0
|
|
2 6 1 0
|
|
2 11 1 0
|
|
3 4 2 0
|
|
3 5 1 0
|
|
4 7 1 0
|
|
5 8 2 0
|
|
6 10 1 0
|
|
7 9 2 0
|
|
8 9 1 0
|
|
M END
|
|
> <chembl_id>
|
|
CHEMBL3183068
|
|
|
|
> <chembl_pref_name>
|
|
None
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
{
|
|
auto m = R"CTAB(CHEMBL3183068 (with an H removed)
|
|
RDKit 2D
|
|
|
|
10 10 0 0 1 0 0 0 0 0999 V2000
|
|
1.7309 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.1502 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4334 -1.1252 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4334 -1.9494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7167 -0.7167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.8669 -0.2974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7167 -2.3687 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -1.1360 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -1.9602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.5836 -0.7060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 6
|
|
2 3 1 0
|
|
2 6 1 0
|
|
3 4 2 0
|
|
3 5 1 0
|
|
4 7 1 0
|
|
5 8 2 0
|
|
6 10 1 0
|
|
7 9 2 0
|
|
8 9 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
}
|
|
|
|
SECTION("four-coordinate") {
|
|
{
|
|
auto m = R"CTAB(
|
|
Mrv2211 07202306492D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 5 4 0 0 1
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N -3.3332 0.9919 0 0
|
|
M V30 2 C -2.5555 -0.3373 0 0
|
|
M V30 3 O -3.885 -1.095 0 0
|
|
M V30 4 C -1.2263 0.4404 0 0
|
|
M V30 5 F -1.7854 -1.6709 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1 CFG=3
|
|
M V30 2 1 2 3
|
|
M V30 3 1 2 4
|
|
M V30 4 1 2 5
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
{
|
|
auto m = R"CTAB(
|
|
Mrv2211 07202306492D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 5 4 0 0 1
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N -3.3332 0.9919 0 0
|
|
M V30 2 C -2.5555 -0.3373 0 0
|
|
M V30 3 O -3.885 -1.095 0 0
|
|
M V30 4 C -1.2263 0.4404 0 0
|
|
M V30 5 F -1.7854 -1.6709 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1
|
|
M V30 2 1 2 3
|
|
M V30 3 1 2 4
|
|
M V30 4 1 2 5 CFG=3
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
{
|
|
auto m = R"CTAB(
|
|
Mrv2211 07202306492D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 5 4 0 0 1
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N -3.3332 0.9919 0 0
|
|
M V30 2 C -2.5555 -0.3373 0 0
|
|
M V30 3 O -3.885 -1.095 0 0
|
|
M V30 4 C -1.2263 0.4404 0 0
|
|
M V30 5 F -1.7854 -1.6709 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1
|
|
M V30 2 1 2 3 CFG=1
|
|
M V30 3 1 2 4
|
|
M V30 4 1 2 5
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("almost linear, degree 4") {
|
|
SECTION("from chembl 1") {
|
|
auto m = R"CTAB(CHEMBL3680147
|
|
RDKit 2D
|
|
|
|
15 16 0 0 1 0 0 0 0 0999 V2000
|
|
3.8912 -4.9570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.8933 -3.7570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.5951 -3.0039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.5973 -1.5031 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.2073 -4.4014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
6.2131 -3.2886 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.4656 -1.9881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.9978 -2.2972 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
5.9557 -0.8928 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 1
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
5 6 2 0
|
|
6 7 1 0
|
|
7 8 2 0
|
|
8 9 1 0
|
|
9 10 2 0
|
|
10 5 1 0
|
|
2 11 1 0
|
|
11 12 1 0
|
|
12 13 1 0
|
|
13 14 2 0
|
|
14 2 1 0
|
|
13 15 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
SECTION("from chembl 2") {
|
|
auto m = R"CTAB(CHEMBL76346
|
|
RDKit 2D
|
|
|
|
16 17 0 0 1 0 0 0 0 0999 V2000
|
|
3.4292 -0.4250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.7167 -0.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.7167 0.8125 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.4292 -1.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.1500 -0.0125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.7667 -1.7292 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.1500 0.8208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.4292 1.2333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.0250 -2.5167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.8500 -2.5167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.0042 -0.4250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
4.1042 -1.7292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.4250 2.0583 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2250 -2.7292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.2375 -3.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.0042 -3.5250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
3 2 1 0
|
|
4 1 1 0
|
|
5 1 1 0
|
|
6 4 1 0
|
|
7 5 2 0
|
|
8 7 1 0
|
|
9 6 1 0
|
|
10 12 1 0
|
|
11 2 2 0
|
|
12 4 1 0
|
|
13 8 1 0
|
|
9 14 1 6
|
|
15 9 1 0
|
|
16 14 1 0
|
|
3 8 2 0
|
|
10 9 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(8)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
SECTION("from chembl 3") {
|
|
auto m = R"CTAB(CHEMBL3577363
|
|
RDKit 2D
|
|
|
|
15 16 0 0 0 0 0 0 0 0999 V2000
|
|
-2.5989 1.5003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.3863 2.3198 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.8514 3.7459 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.3514 3.7442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.8133 2.3171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 2.7000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.3383 -1.3500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.6369 0.8981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.1471 4.7175 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
5 1 1 0
|
|
6 7 2 0
|
|
7 8 1 0
|
|
8 9 2 0
|
|
9 10 1 0
|
|
10 11 2 0
|
|
11 6 1 0
|
|
8 12 1 0
|
|
9 1 1 0
|
|
6 13 1 0
|
|
1 14 1 6
|
|
3 15 2 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(0)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
SECTION("from chembl 4") {
|
|
auto m =
|
|
R"CTAB(derived from CHEMBL2373651. This was wrong in the RDKit implementation
|
|
Mrv2211 07212313282D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 7 7 0 0 1
|
|
M V30 BEGIN ATOM
|
|
M V30 1 O -7.4486 0.4751 0 0
|
|
M V30 2 C -6.1148 -0.2949 0 0
|
|
M V30 3 C -6.1148 1.2451 0 0
|
|
M V30 4 C -4.7811 -1.0649 0 0
|
|
M V30 5 C -4.7811 2.0151 0 0
|
|
M V30 6 H -6.1148 1.2451 0 0
|
|
M V30 7 H -6.1148 -0.2949 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1
|
|
M V30 2 1 3 1
|
|
M V30 3 1 2 3
|
|
M V30 4 1 2 4
|
|
M V30 5 1 3 5
|
|
M V30 6 1 3 6 CFG=1
|
|
M V30 7 1 2 7 CFG=3
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
CHECK(m->getAtomWithIdx(2)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
}
|
|
SECTION("cut from CHEMBL4578507") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 9 8 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 10.694361 -35.424753 0.000000 0
|
|
M V30 2 C 9.463880 -34.700253 0.000000 0
|
|
M V30 3 C 8.217865 -35.405903 0.000000 0
|
|
M V30 4 C 8.207044 -36.840940 0.000000 0
|
|
M V30 5 N 9.449393 -37.570327 0.000000 0
|
|
M V30 6 C 6.965044 -36.121153 0.000000 0
|
|
M V30 7 O 8.215247 -33.985178 0.000000 0
|
|
M V30 8 H 6.885805 -37.382701 0.000000 0
|
|
M V30 9 H 9.169786 -33.305883 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 4 3
|
|
M V30 4 1 4 5
|
|
M V30 5 1 4 6
|
|
M V30 6 1 2 7
|
|
M V30 7 1 4 8 CFG=3
|
|
M V30 8 1 2 9 CFG=3
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
$$$$)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(3)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
|
|
SECTION("derived from CHEMBL4578507") {
|
|
auto m = R"CTAB(CHEMBL4578507
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 17 19 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 6.828300 -21.526500 0.000000 0
|
|
M V30 2 C 7.542200 -21.113800 0.000000 0
|
|
M V30 3 C 7.537900 -20.291100 0.000000 0
|
|
M V30 4 C 6.829700 -19.884700 0.000000 0
|
|
M V30 5 C 6.121000 -21.114600 0.000000 0
|
|
M V30 6 C 6.127300 -20.296500 0.000000 0
|
|
M V30 7 C 5.422300 -19.881400 0.000000 0
|
|
M V30 8 C 4.708400 -20.285700 0.000000 0
|
|
M V30 9 C 4.702200 -21.107900 0.000000 0
|
|
M V30 10 N 5.414000 -21.525800 0.000000 0
|
|
M V30 11 C 3.990600 -20.695500 0.000000 0
|
|
M V30 12 O 4.706900 -19.471700 0.000000 0
|
|
M V30 13 C 3.988500 -19.876800 0.000000 0
|
|
M V30 14 O 3.284900 -21.104500 0.000000 0
|
|
M V30 15 F 8.242300 -19.879800 0.000000 0
|
|
M V30 16 H 3.945200 -21.418300 0.000000 0 MASS=2
|
|
M V30 17 H 5.253800 -19.082500 0.000000 0 MASS=2
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 5 1
|
|
M V30 2 1 1 2
|
|
M V30 3 2 2 3
|
|
M V30 4 1 3 4
|
|
M V30 5 2 4 6
|
|
M V30 6 1 5 6
|
|
M V30 7 1 5 10
|
|
M V30 8 1 6 7
|
|
M V30 9 1 7 8
|
|
M V30 10 1 9 8
|
|
M V30 11 1 9 10
|
|
M V30 12 1 9 11
|
|
M V30 13 1 7 12
|
|
M V30 14 1 11 13
|
|
M V30 15 1 13 12
|
|
M V30 16 1 11 14 CFG=3
|
|
M V30 17 1 3 15
|
|
M V30 18 1 9 16 CFG=3
|
|
M V30 19 1 7 17 CFG=3
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(6)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(8)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(10)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
|
|
SECTION("derived from CHEMBL123021") {
|
|
auto m = R"CTAB(CHEMBL123021
|
|
RDKit 2D
|
|
|
|
16 17 0 0 1 0 0 0 0 0999 V2000
|
|
-2.8208 -0.5792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.8208 0.2458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.5375 -0.1542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.4083 -0.5792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1125 -0.9917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.4000 0.2458 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1125 0.6583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6833 0.6583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1083 -1.8167 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.1125 1.4833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6833 1.4833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6958 -0.9917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0250 -0.5875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0375 1.8958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.3161 1.1145 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.3141 0.2829 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
1 3 1 0
|
|
4 5 1 0
|
|
5 1 1 0
|
|
6 4 2 0
|
|
7 2 1 0
|
|
8 6 1 0
|
|
9 5 2 0
|
|
10 7 2 0
|
|
11 8 2 0
|
|
12 4 1 0
|
|
13 12 1 0
|
|
14 11 1 0
|
|
2 3 1 0
|
|
7 6 1 0
|
|
2 15 1 6
|
|
1 16 1 6
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(0)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
|
|
SECTION("derived from CHEMBL85809") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 9 9 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N 7.185783 -5.677981 0.000000 0
|
|
M V30 2 C 7.207427 -7.106480 0.000000 0
|
|
M V30 3 O 9.032790 -6.219079 0.000000 0
|
|
M V30 4 O 10.172645 -8.527707 0.000000 0
|
|
M V30 5 C 10.886895 -7.106480 0.000000 0
|
|
M V30 6 C 7.900033 -8.527707 0.000000 0
|
|
M V30 7 C 10.865251 -5.677981 0.000000 0
|
|
M V30 8 H 7.185783 -8.534979 0.000000 0 MASS=2
|
|
M V30 9 H 10.865251 -8.534979 0.000000 0 MASS=2
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1 CFG=1
|
|
M V30 2 1 3 2
|
|
M V30 3 1 4 6
|
|
M V30 4 1 5 3
|
|
M V30 5 1 6 2
|
|
M V30 6 1 5 7 CFG=1
|
|
M V30 7 1 2 8 CFG=3
|
|
M V30 8 1 5 9 CFG=3
|
|
M V30 9 1 4 5
|
|
M V30 END BOND
|
|
M V30 BEGIN COLLECTION
|
|
M V30 MDLV30/STEABS ATOMS=(2 2 5)
|
|
M V30 END COLLECTION
|
|
M V30 END CTAB
|
|
M END
|
|
$$$$
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
CHECK(m->getAtomWithIdx(4)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
}
|
|
|
|
SECTION("derived from CHEMBL2333552") {
|
|
auto m = R"CTAB(blah
|
|
RDKit 2D
|
|
|
|
18 20 0 0 0 0 0 0 0 0999 V2000
|
|
35.6738 -9.2984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
34.9598 -8.8850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
34.9588 -9.7100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
32.1164 -7.2274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
32.1164 -8.0541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
32.8299 -8.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
32.8299 -6.8099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
33.5434 -7.2274 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
33.5399 -8.0541 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
34.9720 -7.2335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
34.2572 -6.8149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
31.3992 -6.8162 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
32.8308 -9.2901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
33.5319 -8.8767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
34.9684 -8.0602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
34.2507 -8.4688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
35.7656 -8.2712 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
34.2458 -7.6408 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
3 2 1 0
|
|
4 5 1 0
|
|
4 7 1 0
|
|
5 6 1 0
|
|
6 9 1 0
|
|
8 7 2 0
|
|
8 9 1 0
|
|
8 11 1 0
|
|
9 16 1 0
|
|
15 10 1 0
|
|
10 11 1 0
|
|
4 12 2 0
|
|
6 13 1 6
|
|
9 14 1 6
|
|
16 15 1 0
|
|
2 16 1 0
|
|
15 2 1 0
|
|
15 17 1 6
|
|
16 18 1 6
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(5)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(m->getAtomWithIdx(8)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
CHECK(m->getAtomWithIdx(14)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(m->getAtomWithIdx(15)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
}
|
|
SECTION("CHEMBL94022") {
|
|
auto m = R"CTAB(CHEMBL94022
|
|
RDKit 2D
|
|
|
|
16 18 0 0 1 0 0 0 0 0999 V2000
|
|
2.0917 -2.6875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2667 -2.7042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.6917 -3.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.6750 -3.2667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.4792 -4.0667 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.5000 -3.2042 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.5500 -2.2917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.1792 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.8125 -3.9667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.1708 -2.7042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.5500 -1.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8833 -2.2917 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.1708 -1.0542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8833 -1.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6792 -3.2917 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.7917 -2.2542 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2 1 1 0
|
|
3 1 1 0
|
|
1 4 1 1
|
|
5 4 2 0
|
|
6 4 1 0
|
|
7 2 1 0
|
|
8 5 1 0
|
|
9 6 1 0
|
|
10 7 2 0
|
|
11 7 1 0
|
|
12 10 1 0
|
|
13 11 2 0
|
|
14 13 1 0
|
|
2 15 1 1
|
|
1 16 1 6
|
|
3 2 1 0
|
|
8 9 1 0
|
|
14 12 2 0
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(0)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
}
|
|
SECTION("overlapping neighbors") {
|
|
auto m = R"CTAB(derived from CHEMBL3752539
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 14 15 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -1.237143 -0.714286 0.000000 0
|
|
M V30 2 C -1.237143 0.714286 0.000000 0
|
|
M V30 3 C -2.474381 1.428571 0.000000 0
|
|
M V30 4 C -3.711524 0.714286 0.000000 0
|
|
M V30 5 C -2.474381 -1.428571 0.000000 0
|
|
M V30 6 C -3.711524 -0.714286 0.000000 0
|
|
M V30 7 O -2.474381 -2.857143 0.000000 0
|
|
M V30 8 H -4.536286 -0.238095 0.000000 0
|
|
M V30 9 H -1.649524 -1.904762 0.000000 0
|
|
M V30 10 C -4.948762 -1.428571 0.000000 0
|
|
M V30 11 C -2.474381 -1.428571 0.000000 0
|
|
M V30 12 C -3.711524 0.714286 0.000000 0
|
|
M V30 13 O -3.711524 -0.714286 0.000000 0
|
|
M V30 14 H -2.474381 2.380952 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 1 5
|
|
M V30 3 1 2 3
|
|
M V30 4 1 3 4
|
|
M V30 5 1 4 6
|
|
M V30 6 1 5 6
|
|
M V30 7 1 5 7
|
|
M V30 8 1 6 10
|
|
M V30 9 1 6 8 CFG=1
|
|
M V30 10 1 5 9 CFG=3
|
|
M V30 11 1 1 11 CFG=3
|
|
M V30 12 1 3 12
|
|
M V30 13 1 12 13
|
|
M V30 14 1 11 13
|
|
M V30 15 1 3 14 CFG=1
|
|
M V30 END BOND
|
|
M V30 BEGIN COLLECTION
|
|
M V30 MDLV30/STEABS ATOMS=(1 6)
|
|
M V30 MDLV30/STERAC1 ATOMS=(3 1 3 5)
|
|
M V30 END COLLECTION
|
|
M V30 END CTAB
|
|
M END
|
|
$$$$
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(2)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(0)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
SECTION("bond atoms overlapping central atom at the end of wedge bonds") {
|
|
auto m = R"CTAB(CHEMBL3612237
|
|
RDKit 2D
|
|
|
|
14 15 0 0 0 0 0 0 0 0999 V2000
|
|
-0.6828 -1.6239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6828 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6090 0.5905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.9007 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.9007 -1.6239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6090 -2.3805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.9007 1.3471 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6828 1.3471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6090 2.0668 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6319 1.4849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.5072 2.6784 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7280 0.9964 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.6828 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.9007 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
1 6 1 0
|
|
2 3 1 0
|
|
3 4 1 0
|
|
4 5 1 0
|
|
5 6 1 0
|
|
4 7 1 0
|
|
2 8 1 0
|
|
8 9 1 0
|
|
7 9 1 0
|
|
3 10 1 1
|
|
10 11 1 0
|
|
10 12 2 0
|
|
2 13 1 1
|
|
4 14 1 1
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
// if the bond is wedged, then we should have chirality even if the bonded
|
|
// atom overlaps the central atom
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(3)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getAtomWithIdx(2)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("github #6931: atom maps influencing chirality perception") {
|
|
SECTION("basics") {
|
|
auto m = "[CH3:1]C([CH3:2])(O)F"_smiles;
|
|
REQUIRE(m);
|
|
bool cleanIt = true;
|
|
bool force = true;
|
|
bool flagPossibleStereoCenters = true;
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
MolOps::assignStereochemistry(*m, cleanIt, force,
|
|
flagPossibleStereoCenters);
|
|
CHECK(
|
|
!m->getAtomWithIdx(1)->hasProp(common_properties::_ChiralityPossible));
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github Issue #6981: Parsing a Mol leaks the \"_needsDetectBondStereo\" property",
|
|
"[bug][stereo]") {
|
|
// Parametrize test to run under legacy and new stereo perception
|
|
const auto legacy_stereo = GENERATE(true, false);
|
|
INFO("Legacy stereo perception == " << legacy_stereo);
|
|
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(legacy_stereo);
|
|
|
|
auto m = R"CTAB(
|
|
Mrv2311 12122315472D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -9.2083 1.8333 0 0
|
|
M V30 2 C -8.0639 0.8029 0 0
|
|
M V30 3 C -6.5239 0.8029 0 0
|
|
M V30 4 C -5.7539 -0.5308 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 2 1 CFG=2
|
|
M V30 2 2 2 3
|
|
M V30 3 1 3 4
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
|
|
REQUIRE(m);
|
|
REQUIRE(m->getNumAtoms() == 4);
|
|
|
|
CHECK(m->hasProp("_needsDetectBondStereo") == false);
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github Issue #7076: new stereo code not properly handling crossed double bonds") {
|
|
// Parametrize test to run under legacy and new stereo perception
|
|
SECTION("second part") {
|
|
const auto legacy_stereo = GENERATE(true, false);
|
|
INFO("Legacy stereo perception == " << legacy_stereo);
|
|
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(legacy_stereo);
|
|
|
|
auto m = R"CTAB(
|
|
Mrv2211 01252410552D
|
|
|
|
10 9 0 0 0 0 999 V2000
|
|
0.0000 -1.4364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7108 -3.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -3.8988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8208 -1.4364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -2.2572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.7108 -2.6676 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4217 -2.2572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -4.7196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.2439 -5.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7108 -5.1300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 4 1 0 0 0 0
|
|
1 5 2 0 0 0 0
|
|
2 3 1 0 0 0 0
|
|
2 6 2 3 0 0 0
|
|
3 8 2 0 0 0 0
|
|
5 6 1 0 0 0 0
|
|
6 7 1 0 0 0 0
|
|
8 9 1 0 0 0 0
|
|
8 10 1 0 0 0 0
|
|
M END)CTAB"_ctab;
|
|
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(3)->getStereo() == Bond::BondStereo::STEREOANY);
|
|
}
|
|
SECTION("original") {
|
|
std::string ctab = R"CTAB(7630532
|
|
RDKit 2D
|
|
|
|
37 41 0 0 0 0 0 0 0 0999 V2000
|
|
0.0000 -1.7500 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.8660 -4.2500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -4.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7500 -1.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.0000 -1.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -2.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8675 0.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2475 -0.8825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.4975 -2.6175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.8675 0.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.2475 -2.6175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.4975 -0.8825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.8660 -3.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8675 1.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.2527 -0.8825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.5027 -2.6175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.8675 1.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.2527 -2.6175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.5027 -0.8825 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.0000 2.0104 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.7604 -1.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-3.0104 -1.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.7321 -2.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.0000 -5.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.5155 -6.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8660 -6.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.3801 -6.1225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.8631 -7.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.5126 -7.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7306 -5.7475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.2507 -6.6251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-1.7337 -7.7526 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
2.3832 -8.1276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.6012 -6.2501 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3.2566 -7.6302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-2.6071 -7.2552 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 4 1 0
|
|
1 5 1 0
|
|
1 6 1 0
|
|
1 7 2 0
|
|
2 3 1 0
|
|
2 14 2 3
|
|
3 25 2 0
|
|
4 8 2 0
|
|
4 11 1 0
|
|
5 9 2 0
|
|
5 12 1 0
|
|
6 10 2 0
|
|
6 13 1 0
|
|
7 14 1 0
|
|
8 15 1 0
|
|
9 16 1 0
|
|
10 17 1 0
|
|
11 18 2 0
|
|
12 19 2 0
|
|
13 20 2 0
|
|
14 24 1 0
|
|
15 21 2 0
|
|
16 22 2 0
|
|
17 23 2 0
|
|
18 21 1 0
|
|
19 22 1 0
|
|
20 23 1 0
|
|
25 26 1 0
|
|
25 27 1 0
|
|
26 28 2 0
|
|
26 30 1 0
|
|
27 29 2 0
|
|
27 31 1 0
|
|
28 32 1 0
|
|
29 33 1 0
|
|
30 34 2 0
|
|
31 35 2 0
|
|
32 36 2 0
|
|
33 37 2 0
|
|
34 36 1 0
|
|
35 37 1 0
|
|
M END)CTAB";
|
|
const auto legacy_stereo = GENERATE(true, false);
|
|
INFO("Legacy stereo perception == " << legacy_stereo);
|
|
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(legacy_stereo);
|
|
{
|
|
// normal file parsing
|
|
auto m = std::unique_ptr<RWMol>(MolBlockToMol(ctab));
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(5)->getStereo() == Bond::BondStereo::STEREOANY);
|
|
CHECK(m->getBondWithIdx(6)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
{
|
|
// no sanitization during parsing
|
|
bool sanitize = false;
|
|
bool removeHs = false;
|
|
auto m = std::unique_ptr<RWMol>(MolBlockToMol(ctab, sanitize, removeHs));
|
|
REQUIRE(m);
|
|
MolOps::sanitizeMol(*m);
|
|
bool cleanIt = true;
|
|
bool force = true;
|
|
MolOps::assignStereochemistry(*m, cleanIt, force);
|
|
CHECK(m->getBondWithIdx(5)->getStereo() == Bond::BondStereo::STEREOANY);
|
|
CHECK(m->getBondWithIdx(6)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"github #3369: support new CIP code and StereoGroups in addStereoAnnotations()") {
|
|
auto m1 =
|
|
"C[C@@H]1N[C@H](C)[C@@H]([C@H](C)[C@@H]1C)C1[C@@H](C)O[C@@H](C)[C@@H](C)[C@H]1C/C=C/C |a:5,o1:1,8,o2:14,16,&1:18,&2:3,6,r|"_smiles;
|
|
REQUIRE(m1);
|
|
SECTION("defaults") {
|
|
ROMol m2(*m1);
|
|
Chirality::addStereoAnnotations(m2);
|
|
|
|
std::string txt;
|
|
CHECK(m2.getAtomWithIdx(5)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "abs (S)");
|
|
CHECK(m2.getAtomWithIdx(3)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "and2");
|
|
}
|
|
SECTION("double bonds") {
|
|
ROMol m2(*m1);
|
|
REQUIRE(m2.getBondBetweenAtoms(20, 21));
|
|
m2.getBondBetweenAtoms(20, 21)->setStereo(Bond::BondStereo::STEREOTRANS);
|
|
// initially no label is assigned since we have TRANS
|
|
Chirality::addStereoAnnotations(m2);
|
|
CHECK(
|
|
!m2.getBondBetweenAtoms(20, 21)->hasProp(common_properties::bondNote));
|
|
|
|
CIPLabeler::assignCIPLabels(m2);
|
|
std::string txt;
|
|
CHECK(m2.getBondBetweenAtoms(20, 21)->getPropIfPresent(
|
|
common_properties::_CIPCode, txt));
|
|
CHECK(txt == "E");
|
|
Chirality::addStereoAnnotations(m2);
|
|
CHECK(m2.getBondBetweenAtoms(20, 21)->getPropIfPresent(
|
|
common_properties::bondNote, txt));
|
|
CHECK(txt == "(E)");
|
|
}
|
|
|
|
SECTION("custom labels") {
|
|
ROMol m2(*m1);
|
|
CIPLabeler::assignCIPLabels(m2);
|
|
|
|
std::string absLabel = "abs [{cip}]";
|
|
std::string orLabel = "o{id} ({cip})";
|
|
std::string andLabel = "&{id} ({cip})";
|
|
std::string cipLabel = "[{cip}]";
|
|
std::string bondLabel = "[{cip}]";
|
|
Chirality::addStereoAnnotations(m2, absLabel, orLabel, andLabel, cipLabel,
|
|
bondLabel);
|
|
|
|
std::string txt;
|
|
|
|
CHECK(m2.getAtomWithIdx(5)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "abs [S]");
|
|
|
|
CHECK(m2.getAtomWithIdx(3)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "&2 (R)");
|
|
|
|
CHECK(m2.getAtomWithIdx(1)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "o1 (S)");
|
|
|
|
CHECK(m2.getAtomWithIdx(11)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "[R]");
|
|
|
|
CHECK(m2.getBondBetweenAtoms(20, 21)->getPropIfPresent(
|
|
common_properties::bondNote, txt));
|
|
CHECK(txt == "[E]");
|
|
}
|
|
|
|
SECTION("empty labels") {
|
|
ROMol m2(*m1);
|
|
CIPLabeler::assignCIPLabels(m2);
|
|
|
|
std::string absLabel = "";
|
|
std::string orLabel = "o{id} ({cip})";
|
|
std::string andLabel = "&{id} ({cip})";
|
|
std::string cipLabel = "[{cip}]";
|
|
std::string bondLabel = "";
|
|
Chirality::addStereoAnnotations(m2, absLabel, orLabel, andLabel, cipLabel,
|
|
bondLabel);
|
|
|
|
std::string txt;
|
|
|
|
CHECK(!m2.getAtomWithIdx(5)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
|
|
CHECK(m2.getAtomWithIdx(3)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "&2 (R)");
|
|
|
|
CHECK(m2.getAtomWithIdx(1)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "o1 (S)");
|
|
|
|
CHECK(m2.getAtomWithIdx(11)->getPropIfPresent(common_properties::atomNote,
|
|
txt));
|
|
CHECK(txt == "[R]");
|
|
|
|
CHECK(!m2.getBondBetweenAtoms(20, 21)->getPropIfPresent(
|
|
common_properties::bondNote, txt));
|
|
}
|
|
}
|
|
|
|
TEST_CASE("do not wedge bonds to attachment points") {
|
|
SECTION("basics") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 4 3 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 0.000000 0.000000 0.000000 0 ATTCHPT=1
|
|
M V30 2 F -1.299038 0.750000 0.000000 0
|
|
M V30 3 Cl -0.000000 -1.500000 0.000000 0
|
|
M V30 4 O 1.299038 0.750000 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 CFG=1
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getNumAtoms() == 4);
|
|
MolOps::expandAttachmentPoints(*m);
|
|
CHECK(m->getNumAtoms() == 5);
|
|
CHECK(m->getAtomWithIdx(4)->getTotalValence() == 1);
|
|
Chirality::wedgeMolBonds(*m);
|
|
CHECK(m->getBondBetweenAtoms(0, 4)->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
SECTION("cage") {
|
|
auto m = R"CTAB(
|
|
Mrv2305 03052406362D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 8 9 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -3.125 2.5817 0 0 CFG=1
|
|
M V30 2 C -4.4587 1.8117 0 0
|
|
M V30 3 C -4.4587 0.2716 0 0
|
|
M V30 4 C -3.125 -0.4984 0 0
|
|
M V30 5 C -1.7913 0.2716 0 0
|
|
M V30 6 N -1.7913 1.8117 0 0
|
|
M V30 7 O -2.5357 1.1589 0 0
|
|
M V30 8 * -3.125 4.1217 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 1 4 5
|
|
M V30 5 1 5 6
|
|
M V30 6 1 1 7
|
|
M V30 7 1 7 4
|
|
M V30 8 1 1 8
|
|
M V30 9 1 1 6 CFG=1
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
m->getAtomWithIdx(7)->setProp(common_properties::_fromAttachPoint, 1);
|
|
Chirality::wedgeMolBonds(*m);
|
|
CHECK(m->getBondBetweenAtoms(0, 7)->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"github #7203: Remove invalid stereo groups on MolOps::assignStereochemistry") {
|
|
SECTION("single-atom groups") {
|
|
for (auto use_legacy : {false, true}) {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(use_legacy);
|
|
INFO(use_legacy);
|
|
auto m = "C[C@H](N)[C@@H](C)C |o1:1,o2:3|"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(m->getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getStereoGroups().size() == 1);
|
|
}
|
|
}
|
|
SECTION("two-atom groups") {
|
|
for (auto use_legacy : {false, true}) {
|
|
Chirality::setUseLegacyStereoPerception(use_legacy);
|
|
INFO(use_legacy);
|
|
{ // no removal necessary
|
|
auto m = "C[C@H](N)[C@@H](F)C |o1:1,3|"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(m->getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
CHECK(m->getStereoGroups().size() == 1);
|
|
CHECK(m->getStereoGroups()[0].getAtoms().size() == 2);
|
|
}
|
|
{ // removal
|
|
auto m = "C[C@H](N)[C@@H](C)C |o1:1,3|"_smiles;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(m->getAtomWithIdx(3)->getChiralTag() ==
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getStereoGroups().size() == 1);
|
|
CHECK(m->getStereoGroups()[0].getAtoms().size() == 1);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"GitHub Issue #7346: Trigonal Pyramid Carbon may or not have a parity depending on atom ordering",
|
|
"[bug]") {
|
|
// First atom not in the same plane as the rest
|
|
const auto m0 = R"CTAB(
|
|
3D
|
|
|
|
5 4 0 0 1 0 999 V2000
|
|
-0.2052 0.0804 -0.7454 F 0 0 0 0 0 0
|
|
-0.5696 0.2231 -2.0688 C 0 0 0 0 0 0
|
|
-2.2748 -0.0294 -1.1593 Br 0 0 0 0 0 0
|
|
0.2659 -1.3655 -2.0764 Cl 0 0 0 0 0 0
|
|
-0.1867 1.1526 -2.4961 D 0 0 0 0 0 0
|
|
1 2 1 0 0 0
|
|
2 3 1 0 0 0
|
|
2 4 1 0 0 0
|
|
2 5 1 0 0 0
|
|
M END)CTAB"_ctab;
|
|
|
|
// All atoms in the same plane except the rest
|
|
const auto m1 = R"CTAB(
|
|
3D
|
|
|
|
5 4 0 0 1 0 999 V2000
|
|
-0.1867 1.1526 -2.4961 D 0 0 0 0 0 0
|
|
-0.5696 0.2231 -2.0688 C 0 0 0 0 0 0
|
|
-2.2748 -0.0294 -1.1593 Br 0 0 0 0 0 0
|
|
0.2659 -1.3655 -2.0764 Cl 0 0 0 0 0 0
|
|
-0.2052 0.0804 -0.7454 F 0 0 0 0 0 0
|
|
1 2 1 0 0 0
|
|
2 3 1 0 0 0
|
|
2 4 1 0 0 0
|
|
2 5 1 0 0 0
|
|
M END)CTAB"_ctab;
|
|
|
|
REQUIRE(m0);
|
|
REQUIRE(m1);
|
|
|
|
const auto cAt0 = m0->getAtomWithIdx(1);
|
|
const auto cAt1 = m1->getAtomWithIdx(1);
|
|
REQUIRE(cAt0->getAtomicNum() == 6);
|
|
REQUIRE(cAt1->getAtomicNum() == 6);
|
|
|
|
// Two atoms changes positions in the molblocks, but their coordinates
|
|
// didn't change, so they must have opposite parities in order to
|
|
// preserve the absolute chirality
|
|
CHECK(cAt0->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
|
|
CHECK(cAt1->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
|
|
CIPLabeler::assignCIPLabels(*m0);
|
|
CIPLabeler::assignCIPLabels(*m1);
|
|
|
|
CHECK(cAt0->getProp<std::string>(common_properties::_CIPCode) ==
|
|
cAt1->getProp<std::string>(common_properties::_CIPCode));
|
|
}
|
|
|
|
TEST_CASE(
|
|
"Github #7300: incorrect chiral carbon perception for some phosphates") {
|
|
SECTION("basics") {
|
|
auto m = "NC(CP(=O)(O)O)CP(=O)(O)O"_smiles;
|
|
REQUIRE(m);
|
|
auto sis = Chirality::findPotentialStereo(*m);
|
|
CHECK(sis.empty());
|
|
}
|
|
SECTION("make sure Ps can still yield chiral centers") {
|
|
auto m = "NC(CP(=O)(O)[O-])CP(=O)(O)[O-]"_smiles;
|
|
REQUIRE(m);
|
|
auto sis = Chirality::findPotentialStereo(*m);
|
|
CHECK(sis.size() == 3);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("github 7371") {
|
|
SECTION("basics") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 20 21 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N -0.024300 -1.051200 0.000000 0
|
|
M V30 2 C 0.690200 -1.463700 0.000000 0
|
|
M V30 3 O 0.690200 -2.288700 0.000000 0
|
|
M V30 4 N 1.404500 -1.051200 0.000000 0
|
|
M V30 5 C 2.119100 -1.463700 0.000000 0
|
|
M V30 6 C 2.119100 -2.288700 0.000000 0
|
|
M V30 7 C 1.404500 -2.701200 0.000000 0
|
|
M V30 8 C 2.833500 -2.701200 0.000000 0
|
|
M V30 9 C 3.547900 -2.288700 0.000000 0
|
|
M V30 10 N 3.547900 -1.463700 0.000000 0
|
|
M V30 11 C 2.833600 -1.051200 0.000000 0
|
|
M V30 12 C 3.363800 -0.419100 0.000000 0
|
|
M V30 13 C 4.176300 -0.562300 0.000000 0
|
|
M V30 14 C 3.081600 0.356100 0.000000 0
|
|
M V30 15 C 1.404500 -0.226000 0.000000 0
|
|
M V30 16 N 2.155300 0.191900 0.000000 0
|
|
M V30 17 C 2.161900 1.051300 0.000000 0
|
|
M V30 18 C 1.417800 1.480900 0.000000 0
|
|
M V30 19 C 0.676800 1.045500 0.000000 0
|
|
M V30 20 C 0.690200 0.186400 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 2 2 3
|
|
M V30 3 1 4 2
|
|
M V30 4 1 4 5
|
|
M V30 5 2 5 6
|
|
M V30 6 1 6 7
|
|
M V30 7 1 6 8
|
|
M V30 8 2 8 9
|
|
M V30 9 1 9 10
|
|
M V30 10 2 10 11
|
|
M V30 11 1 11 12
|
|
M V30 12 1 12 13
|
|
M V30 13 1 12 14
|
|
M V30 14 1 4 15
|
|
M V30 15 2 15 16
|
|
M V30 16 1 16 17
|
|
M V30 17 2 17 18
|
|
M V30 18 1 18 19
|
|
M V30 19 2 19 20
|
|
M V30 20 1 5 11 CFG=1
|
|
M V30 21 1 20 15
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(3)->getStereo() == Bond::BondStereo::STEREOATROPCW);
|
|
// after reading in, there's no bond wedging:
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer());
|
|
// now there is:
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
if (bnd->getIdx() != 19) {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
} else {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::BEGINWEDGE);
|
|
}
|
|
}
|
|
}
|
|
SECTION("3d") {
|
|
auto m = R"CTAB(
|
|
RDKit 3D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 20 21 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 N 0.382755 -0.645531 -2.970173 0
|
|
M V30 2 C 1.191902 -0.080895 -1.951313 0
|
|
M V30 3 O 2.258061 0.469395 -2.326427 0
|
|
M V30 4 N 0.799020 -0.142115 -0.557889 0
|
|
M V30 5 C -0.412487 -0.780398 -0.245786 0
|
|
M V30 6 C -0.494802 -2.127175 0.018641 0
|
|
M V30 7 C 0.666160 -3.010952 -0.001627 0
|
|
M V30 8 C -1.739073 -2.694470 0.315567 0
|
|
M V30 9 C -2.888797 -1.963937 0.355103 0
|
|
M V30 10 N -2.786157 -0.648937 0.093334 0
|
|
M V30 11 C -1.586505 -0.059517 -0.200695 0
|
|
M V30 12 C -1.679580 1.394735 -0.453406 0
|
|
M V30 13 C -1.637015 2.096392 0.888082 0
|
|
M V30 14 C -3.022840 1.757751 -1.085608 0
|
|
M V30 15 C 1.696224 0.471157 0.348870 0
|
|
M V30 16 N 1.608949 1.758263 0.730152 0
|
|
M V30 17 C 2.457188 2.346328 1.581612 0
|
|
M V30 18 C 3.501956 1.626784 2.127981 0
|
|
M V30 19 C 3.644663 0.298166 1.774403 0
|
|
M V30 20 C 2.724579 -0.259689 0.878536 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 2 2 3
|
|
M V30 3 1 4 2
|
|
M V30 4 1 4 5
|
|
M V30 5 2 5 6
|
|
M V30 6 1 6 7
|
|
M V30 7 1 6 8
|
|
M V30 8 2 8 9
|
|
M V30 9 1 9 10
|
|
M V30 10 2 10 11
|
|
M V30 11 1 11 12
|
|
M V30 12 1 12 13
|
|
M V30 13 1 12 14
|
|
M V30 14 1 4 15
|
|
M V30 15 2 15 16
|
|
M V30 16 1 16 17
|
|
M V30 17 2 17 18
|
|
M V30 18 1 18 19
|
|
M V30 19 2 19 20
|
|
M V30 20 1 5 11 CFG=1
|
|
M V30 21 1 20 15
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(3)->getStereo() == Bond::BondStereo::STEREOATROPCW);
|
|
// after reading in, there's no bond wedging:
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer());
|
|
// now there is:
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
if (bnd->getIdx() != 4) {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
} else {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::BEGINWEDGE);
|
|
}
|
|
}
|
|
}
|
|
SECTION("favor larger rings") {
|
|
auto m = R"CTAB(
|
|
Mrv2401 04262410272D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 13 14 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 2.5796 -3.2152 0 0
|
|
M V30 2 N 2.1037 -4.6798 0 0
|
|
M V30 3 N 0.5637 -4.6798 0 0
|
|
M V30 4 C 0.0878 -3.2152 0 0
|
|
M V30 5 C -1.3768 -2.7393 0 0
|
|
M V30 6 C 1.3337 -2.31 0 0
|
|
M V30 7 C 1.3337 -0.77 0 0
|
|
M V30 8 C 0 0 0 0
|
|
M V30 9 Cl -1.3337 -0.77 0 0
|
|
M V30 10 C 0 1.54 0 0
|
|
M V30 11 C 1.3337 2.31 0 0
|
|
M V30 12 C 2.6674 1.54 0 0
|
|
M V30 13 C 2.6674 -0 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 2 3 4
|
|
M V30 4 1 4 5
|
|
M V30 5 1 6 4 CFG=1
|
|
M V30 6 2 1 6
|
|
M V30 7 1 6 7
|
|
M V30 8 2 7 8
|
|
M V30 9 1 8 9
|
|
M V30 10 1 8 10
|
|
M V30 11 2 10 11
|
|
M V30 12 1 11 12
|
|
M V30 13 2 12 13
|
|
M V30 14 1 7 13
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondBetweenAtoms(5, 6)->getStereo() ==
|
|
Bond::BondStereo::STEREOATROPCW);
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer());
|
|
// now there is:
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
if (bnd->getIdx() != 13) {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
} else {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::BEGINWEDGE);
|
|
}
|
|
}
|
|
}
|
|
SECTION("favor larger rings 3D") {
|
|
auto m = R"CTAB(
|
|
RDKit 3D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 13 14 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 1.472629 -1.845227 -0.264711 0
|
|
M V30 2 N 2.829375 -1.724790 -0.334942 0
|
|
M V30 3 N 3.127980 -0.437811 -0.267564 0
|
|
M V30 4 C 1.973684 0.284699 -0.153598 0
|
|
M V30 5 C 1.905135 1.771086 -0.051971 0
|
|
M V30 6 C 0.912735 -0.591792 -0.150090 0
|
|
M V30 7 C -0.495016 -0.243797 -0.046092 0
|
|
M V30 8 C -1.102614 -0.154763 1.189160 0
|
|
M V30 9 Cl -0.084572 -0.483042 2.603743 0
|
|
M V30 10 C -2.434893 0.170808 1.361855 0
|
|
M V30 11 C -3.202022 0.420663 0.247454 0
|
|
M V30 12 C -2.626093 0.340227 -1.000486 0
|
|
M V30 13 C -1.279199 0.010190 -1.157641 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 2 3 4
|
|
M V30 4 1 4 5
|
|
M V30 5 1 6 4 CFG=3
|
|
M V30 6 2 1 6
|
|
M V30 7 1 6 7
|
|
M V30 8 2 7 8
|
|
M V30 9 1 8 9
|
|
M V30 10 1 8 10
|
|
M V30 11 2 10 11
|
|
M V30 12 1 11 12
|
|
M V30 13 2 12 13
|
|
M V30 14 1 7 13
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getBondBetweenAtoms(5, 6)->getStereo() ==
|
|
Bond::BondStereo::STEREOATROPCW);
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
}
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer());
|
|
// now there is:
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
if (bnd->getIdx() != 7) {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
} else {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::BEGINWEDGE);
|
|
}
|
|
}
|
|
}
|
|
|
|
SECTION("avoid macrocycles") {
|
|
auto m =
|
|
"C1=C(C2=CCCCCCCCCCC2)CCC1 |(-1.71835,-1.22732,;-1.61655,-0.232318,;-0.751953,0.270082,;-0.754753,1.27008,;0.109847,1.77248,;0.977247,1.27488,;1.84185,1.77728,;2.70925,1.27968,;2.71205,0.279682,;1.84745,-0.222718,;1.85025,-1.22272,;0.985647,-1.72512,;0.118247,-1.22752,;0.115447,-0.227518,;-2.53135,0.171882,;-3.19835,-0.573118,;-2.69595,-1.43772,)|"_smiles;
|
|
REQUIRE(m);
|
|
m->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOATROPCW);
|
|
Chirality::wedgeMolBonds(*m, &m->getConformer());
|
|
// now there is:
|
|
for (const auto bnd : m->bonds()) {
|
|
INFO(bnd->getIdx());
|
|
if (bnd->getIdx() != 13) {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::NONE);
|
|
} else {
|
|
CHECK(bnd->getBondDir() == Bond::BondDir::BEGINWEDGE);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"github #7434: planar amide nitrogen incorrectly flagged as _ChiralityPossible") {
|
|
SECTION("as reported") {
|
|
auto m1 = "O=C1CCCCC[C@@H]2CN1CCO2"_smiles;
|
|
REQUIRE(m1);
|
|
// new stereo
|
|
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
|
|
m1->getAtomWithIdx(7)));
|
|
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
|
|
m1->getAtomWithIdx(9)));
|
|
|
|
// force old stereo
|
|
UseLegacyStereoPerceptionFixture resetStereoPerception{true};
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
auto si = Chirality::findPotentialStereo(*m1, cleanIt, flagPossible);
|
|
CHECK(si.size() == 1);
|
|
}
|
|
SECTION("details") {
|
|
auto m1 = "C1CCCCC[C@@H]2CN1CCO2"_smiles;
|
|
REQUIRE(m1);
|
|
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
|
|
m1->getAtomWithIdx(6)));
|
|
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
|
|
m1->getAtomWithIdx(8)));
|
|
|
|
// force old stereo
|
|
UseLegacyStereoPerceptionFixture resetStereoPerception{true};
|
|
bool cleanIt = true;
|
|
bool flagPossible = true;
|
|
{
|
|
auto si = Chirality::findPotentialStereo(*m1, cleanIt, flagPossible);
|
|
CHECK(si.size() == 2);
|
|
}
|
|
m1->getAtomWithIdx(8)->setHybridization(Atom::HybridizationType::SP2);
|
|
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
|
|
m1->getAtomWithIdx(8)));
|
|
{
|
|
auto si = Chirality::findPotentialStereo(*m1, cleanIt, flagPossible);
|
|
CHECK(si.size() == 1);
|
|
}
|
|
m1->getAtomWithIdx(8)->setHybridization(Atom::HybridizationType::SP3);
|
|
m1->getBondBetweenAtoms(0, 8)->setIsConjugated(true);
|
|
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
|
|
m1->getAtomWithIdx(8)));
|
|
{
|
|
auto si = Chirality::findPotentialStereo(*m1, cleanIt, flagPossible);
|
|
CHECK(si.size() == 1);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("github #7438: expose code for simplified stereo labels") {
|
|
SECTION("basics") {
|
|
{
|
|
auto m = "C[C@H](N)[C@@H](C)F |o1:1,3|"_smiles;
|
|
REQUIRE(m);
|
|
{
|
|
ROMol m2(*m);
|
|
Chirality::simplifyEnhancedStereo(m2);
|
|
std::string note;
|
|
CHECK(m2.getPropIfPresent(common_properties::molNote, note));
|
|
CHECK(note == "OR enantiomer");
|
|
CHECK(m2.getStereoGroups().empty());
|
|
}
|
|
{
|
|
ROMol m2(*m);
|
|
bool removeAffectedStereoGroups = false;
|
|
Chirality::simplifyEnhancedStereo(m2, removeAffectedStereoGroups);
|
|
std::string note;
|
|
CHECK(m2.getPropIfPresent(common_properties::molNote, note));
|
|
CHECK(note == "OR enantiomer");
|
|
CHECK(m2.getStereoGroups().size() == 1);
|
|
}
|
|
}
|
|
{
|
|
auto m = "C[C@H](N)[C@@H](C)F |&1:1,3|"_smiles;
|
|
REQUIRE(m);
|
|
{
|
|
ROMol m2(*m);
|
|
Chirality::simplifyEnhancedStereo(m2);
|
|
std::string note;
|
|
CHECK(m2.getPropIfPresent(common_properties::molNote, note));
|
|
CHECK(note == "AND enantiomer");
|
|
CHECK(m2.getStereoGroups().empty());
|
|
}
|
|
{
|
|
ROMol m2(*m);
|
|
bool removeAffectedStereoGroups = false;
|
|
Chirality::simplifyEnhancedStereo(m2, removeAffectedStereoGroups);
|
|
std::string note;
|
|
CHECK(m2.getPropIfPresent(common_properties::molNote, note));
|
|
CHECK(note == "AND enantiomer");
|
|
CHECK(m2.getStereoGroups().size() == 1);
|
|
}
|
|
}
|
|
}
|
|
|
|
SECTION("incomplete") {
|
|
auto m = "C[C@H](N)[C@@H](C)F |o1:1|"_smiles;
|
|
REQUIRE(m);
|
|
{
|
|
ROMol m2(*m);
|
|
Chirality::simplifyEnhancedStereo(m2);
|
|
CHECK(!m2.hasProp(common_properties::molNote));
|
|
CHECK(m2.getStereoGroups().size() == 1);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("CipLabelAtropsOnRing", "[basic]") {
|
|
SECTION("atropisomers1") {
|
|
std::string molBlock = R"(
|
|
Mrv2304 04172300142D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 24 26 0 0 1
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -0.0002 1.5403 0 0
|
|
M V30 2 N -0.0002 3.0805 0 0 CFG=1
|
|
M V30 3 C -1.334 3.8508 0 0
|
|
M V30 4 C -2.6678 3.0807 0 0
|
|
M V30 5 C -1.334 5.391 0 0
|
|
M V30 6 C 1.3338 5.391 0 0
|
|
M V30 7 C 1.3338 3.8508 0 0
|
|
M V30 8 Br 2.6676 3.0807 0 0
|
|
M V30 9 C -1.3338 0.7702 0 0
|
|
M V30 10 C -2.6678 1.5403 0 0
|
|
M V30 11 C -1.3338 -0.7702 0 0
|
|
M V30 12 C -2.6678 -1.5401 0 0
|
|
M V30 13 C -0.0002 -1.5403 0 0
|
|
M V30 14 N -0.0002 -3.0805 0 0 CFG=1
|
|
M V30 15 C 1.3338 -3.8508 0 0
|
|
M V30 16 C 2.6676 -3.0805 0 0
|
|
M V30 17 C 1.3338 -5.391 0 0
|
|
M V30 18 C -1.334 -5.391 0 0
|
|
M V30 19 C -1.334 -3.8508 0 0
|
|
M V30 20 Br -2.6678 -3.0805 0 0
|
|
M V30 21 C 1.3338 -0.7702 0 0
|
|
M V30 22 C 2.6678 -1.5403 0 0
|
|
M V30 23 C 1.3338 0.7702 0 0
|
|
M V30 24 C 2.6678 1.5404 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 1 3 4
|
|
M V30 4 2 3 5
|
|
M V30 5 1 5 6
|
|
M V30 6 2 6 7
|
|
M V30 7 1 2 7 CFG=1
|
|
M V30 8 1 7 8
|
|
M V30 9 2 1 9
|
|
M V30 10 1 9 10
|
|
M V30 11 1 9 11
|
|
M V30 12 1 11 12
|
|
M V30 13 2 11 13
|
|
M V30 14 1 13 14
|
|
M V30 15 1 14 15 CFG=1
|
|
M V30 16 1 15 16
|
|
M V30 17 2 15 17
|
|
M V30 18 1 17 18
|
|
M V30 19 2 18 19
|
|
M V30 20 1 14 19
|
|
M V30 21 1 19 20
|
|
M V30 22 1 13 21
|
|
M V30 23 1 21 22
|
|
M V30 24 2 21 23
|
|
M V30 25 1 1 23
|
|
M V30 26 1 23 24
|
|
M V30 END BOND
|
|
M V30 END CTAB
|
|
M END
|
|
)";
|
|
|
|
UseLegacyStereoPerceptionFixture useLegacy(false);
|
|
|
|
std::unique_ptr<RWMol> mol(MolBlockToMol(molBlock, true, false));
|
|
|
|
REQUIRE(mol);
|
|
|
|
CHECK(mol->getBondWithIdx(0)->getStereo() ==
|
|
Bond::BondStereo::STEREOATROPCCW);
|
|
CHECK(mol->getBondWithIdx(13)->getStereo() ==
|
|
Bond::BondStereo::STEREOATROPCCW);
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"GitHub #7509: atomChiralTypeFromBondDirPseudo3D fails for poorly scaled molecular coordinates") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
5 4 0 0 0 0 0 0 0 0999 V2000
|
|
-2.0785 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7794 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.5196 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.8187 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.5196 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 2 1 0
|
|
2 3 1 0
|
|
3 4 1 1
|
|
3 5 1 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
|
|
auto at = m->getAtomWithIdx(2);
|
|
REQUIRE(at->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
|
|
auto &pos = m->getConformer().getPositions();
|
|
std::for_each(pos.begin(), pos.end(),
|
|
[](RDGeom::Point3D &pos) { pos *= 6.0; });
|
|
|
|
// Reset chirality and the original bond direction
|
|
// (it was stripped after parsing m for the first time)
|
|
at->setChiralTag(Atom::ChiralType::CHI_UNSPECIFIED);
|
|
m->getBondBetweenAtoms(2, 3)->setBondDir(Bond::BondDir::BEGINWEDGE);
|
|
|
|
MolOps::assignChiralTypesFromBondDirs(*m);
|
|
|
|
CHECK(at->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL_CW);
|
|
}
|
|
|
|
TEST_CASE("findMesoCenters") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(false);
|
|
|
|
SECTION("basics") {
|
|
std::vector<std::pair<std::string,
|
|
std::vector<std::pair<unsigned int, unsigned int>>>>
|
|
cases{
|
|
{"C[C@@H](Cl)C[C@H](C)Cl", {{1, 4}}},
|
|
{"C[C@@H](Cl)C[C@@H](Cl)C", {{1, 4}}},
|
|
{"C[C@H](Cl)C[C@H](C)Cl", {}},
|
|
{"OC(F)C([C@H](F)O)[C@@H](F)O", {{4, 7}}},
|
|
{"N[C@H]1CC[C@@H](O)CC1", {{1, 4}}},
|
|
{"N[C@H]1CC[C@H](O)CC1", {{1, 4}}},
|
|
{"N[C@H]1CC[C@@H](N)CC1", {{1, 4}}},
|
|
{"N[C@H]1CC[C@H](N)CC1", {{1, 4}}},
|
|
{"N[C@H]1C[C@@H](N)C1", {{1, 3}}},
|
|
{"N[C@H]1C[C@H](N)C1", {{1, 3}}},
|
|
{"C1CC[C@H]2CCCC[C@H]2C1", {{3, 8}}},
|
|
// multiple groups
|
|
{"C[C@@H](Cl)C([C@H](C)Cl)C([C@H](F)O)[C@@H](F)O",
|
|
{{1, 4}, {8, 11}}},
|
|
{"C1[C@H](F)C[C@H]1C[C@H]1C[C@H](N)C1", {{1, 4}, {6, 8}}},
|
|
// not sure if this next one is right:
|
|
{"N[C@H]1[C@H](F)[C@@H](N)[C@@H]1F", {{1, 4}, {2, 6}}},
|
|
};
|
|
for (auto &[smi, expected] : cases) {
|
|
INFO(smi);
|
|
auto m = v2::SmilesParse::MolFromSmiles(smi);
|
|
REQUIRE(m);
|
|
auto res = Chirality::findMesoCenters(*m);
|
|
REQUIRE(res.size() == expected.size());
|
|
CHECK(res == expected);
|
|
for (auto [a1, a2] : res) {
|
|
unsigned int oa = m->getNumAtoms() + 1;
|
|
CHECK(m->getAtomWithIdx(a1)->getPropIfPresent(
|
|
common_properties::_mesoOtherAtom, oa));
|
|
CHECK(oa == a2);
|
|
CHECK(m->getAtomWithIdx(a2)->getPropIfPresent(
|
|
common_properties::_mesoOtherAtom, oa));
|
|
CHECK(oa == a1);
|
|
}
|
|
}
|
|
}
|
|
SECTION("with enhanced stereo") {
|
|
std::vector<std::pair<std::string,
|
|
std::vector<std::pair<unsigned int, unsigned int>>>>
|
|
cases{{"N[C@H]1CC[C@@H](O)CC1 |o1:1,4|", {{1, 4}}}};
|
|
for (auto &[smi, expected] : cases) {
|
|
INFO(smi);
|
|
auto m = v2::SmilesParse::MolFromSmiles(smi);
|
|
REQUIRE(m);
|
|
auto res = Chirality::findMesoCenters(*m);
|
|
REQUIRE(res.size() == expected.size());
|
|
CHECK(res == expected);
|
|
}
|
|
}
|
|
SECTION("options") {
|
|
{
|
|
auto m = "[13CH3][C@@H](C)C[C@@H](C)[13CH3]"_smiles;
|
|
REQUIRE(m);
|
|
auto res = Chirality::findMesoCenters(*m);
|
|
REQUIRE(res.size() == 1);
|
|
CHECK(res == std::vector<std::pair<unsigned int, unsigned int>>{{1, 4}});
|
|
bool includeIsotopes = false;
|
|
res = Chirality::findMesoCenters(*m, includeIsotopes);
|
|
REQUIRE(res.empty());
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"github #7598: FindPotentialStereo() missing some results if cleanIt is False") {
|
|
SECTION("as reported") {
|
|
std::vector<std::string> smileses = {"C[C@H](F)C(C)[C@H](F)C",
|
|
"CC([C@H](C)F)[C@@H](C)F",
|
|
"CC([C@H](C)F)[C@H](F)C"};
|
|
for (const auto &smi : smileses) {
|
|
auto m = v2::SmilesParse::MolFromSmiles(smi);
|
|
REQUIRE(m);
|
|
bool flagPossible = true;
|
|
for (bool cleanIt : {true, false}) {
|
|
auto si = Chirality::findPotentialStereo(*m, cleanIt, flagPossible);
|
|
INFO(smi + " " + std::to_string(cleanIt));
|
|
CHECK(si.size() == 3);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"GitHub Issue #7929: AssignStereochemistry(cleanIt=True) does not clean _CIPCode property on bonds") {
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(true);
|
|
|
|
auto m = "CC"_smiles;
|
|
REQUIRE(m);
|
|
|
|
m->getAtomWithIdx(0)->setProp(common_properties::_CIPCode, "X");
|
|
m->getBondWithIdx(0)->setProp(common_properties::_CIPCode, "X");
|
|
|
|
bool clean = true;
|
|
bool flag = true;
|
|
bool force = true;
|
|
|
|
SECTION("legacy stereo perception") {
|
|
Chirality::setUseLegacyStereoPerception(true);
|
|
|
|
RDKit::MolOps::assignStereochemistry(*m, clean, force, flag);
|
|
|
|
CHECK(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode) == false);
|
|
CHECK(m->getBondWithIdx(0)->hasProp(common_properties::_CIPCode) == false);
|
|
}
|
|
SECTION("new stereo perception") {
|
|
Chirality::setUseLegacyStereoPerception(false);
|
|
|
|
RDKit::MolOps::assignStereochemistry(*m, clean, force, flag);
|
|
|
|
CHECK(m->getAtomWithIdx(0)->hasProp(common_properties::_CIPCode) == false);
|
|
CHECK(m->getBondWithIdx(0)->hasProp(common_properties::_CIPCode) == false);
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Github issue #7983: stereogroup lost on chiral sulfoxide") {
|
|
SECTION("basics") {
|
|
auto m = R"CTAB(
|
|
Mrv2317 02032512242D
|
|
|
|
0 0 0 0 0 999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 21 22 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C -4.001 -2.31 0 0
|
|
M V30 2 C -2.6674 -3.08 0 0
|
|
M V30 3 C -1.3337 -2.31 0 0
|
|
M V30 4 C 0 -3.08 0 0
|
|
M V30 5 C 0 -4.6198 0 0
|
|
M V30 6 N 1.3337 -5.3898 0 0
|
|
M V30 7 C 2.6674 -4.6198 0 0
|
|
M V30 8 O 2.6674 -3.08 0 0
|
|
M V30 9 O 4.001 -5.3898 0 0
|
|
M V30 10 C 5.3345 -4.6198 0 0
|
|
M V30 11 C 6.6682 -5.3898 0 0
|
|
M V30 12 C 8.0019 -4.6198 0 0
|
|
M V30 13 C 9.3356 -5.3898 0 0
|
|
M V30 14 C 9.3356 -6.9298 0 0
|
|
M V30 15 C 8.0019 -7.6998 0 0
|
|
M V30 16 C 6.6682 -6.9298 0 0
|
|
M V30 17 S 5.3345 -7.6998 0 0 CFG=2
|
|
M V30 18 C 4.001 -6.9298 0 0
|
|
M V30 19 O 5.3345 -9.2398 0 0
|
|
M V30 20 C -1.3337 -5.3898 0 0
|
|
M V30 21 C -2.6674 -4.6198 0 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 1 1 2
|
|
M V30 2 4 2 3
|
|
M V30 3 4 3 4
|
|
M V30 4 4 4 5
|
|
M V30 5 1 5 6
|
|
M V30 6 1 6 7
|
|
M V30 7 2 7 8
|
|
M V30 8 1 7 9
|
|
M V30 9 1 9 10
|
|
M V30 10 1 10 11
|
|
M V30 11 4 11 12
|
|
M V30 12 4 12 13
|
|
M V30 13 4 13 14
|
|
M V30 14 4 14 15
|
|
M V30 15 4 15 16
|
|
M V30 16 4 11 16
|
|
M V30 17 1 17 16
|
|
M V30 18 2 17 19
|
|
M V30 19 4 5 20
|
|
M V30 20 4 20 21
|
|
M V30 21 4 2 21
|
|
M V30 22 1 17 18 CFG=1
|
|
M V30 END BOND
|
|
M V30 BEGIN COLLECTION
|
|
M V30 MDLV30/STEABS ATOMS=(1 17)
|
|
M V30 END COLLECTION
|
|
M V30 END CTAB
|
|
M END)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
auto &sgs = m->getStereoGroups();
|
|
REQUIRE(sgs.size() == 1);
|
|
CHECK(sgs[0].getGroupType() == StereoGroupType::STEREO_ABSOLUTE);
|
|
CHECK(sgs[0].getAtoms().size() == 1);
|
|
CHECK(sgs[0].getAtoms().at(0)->getIdx() == 16);
|
|
}
|
|
SECTION("making sure sulfoxides do not trigger atropisomerism") {
|
|
auto m = R"CTAB(
|
|
RDKit 2D
|
|
|
|
0 0 0 0 0 0 0 0 0 0999 V3000
|
|
M V30 BEGIN CTAB
|
|
M V30 COUNTS 10 10 0 0 0
|
|
M V30 BEGIN ATOM
|
|
M V30 1 C 1.892852 4.651432 0.000000 0
|
|
M V30 2 C 3.199931 3.915535 0.000000 0
|
|
M V30 3 C 3.216171 2.415622 0.000000 0
|
|
M V30 4 C 1.925330 1.651602 0.000000 0
|
|
M V30 5 C 0.618251 2.387492 0.000000 0
|
|
M V30 6 C 0.602011 3.887408 0.000000 0
|
|
M V30 7 S -0.705072 4.623298 0.000000 0
|
|
M V30 8 C -0.672591 1.623472 0.000000 0
|
|
M V30 9 O -0.721314 6.123210 0.000000 0
|
|
M V30 10 C -1.995913 3.859276 0.000000 0
|
|
M V30 END ATOM
|
|
M V30 BEGIN BOND
|
|
M V30 1 2 1 2
|
|
M V30 2 1 2 3
|
|
M V30 3 2 3 4
|
|
M V30 4 1 4 5
|
|
M V30 5 2 5 6
|
|
M V30 6 1 6 1 CFG=1
|
|
M V30 7 1 6 7
|
|
M V30 8 1 5 8
|
|
M V30 9 2 7 9
|
|
M V30 10 1 7 10 CFG=1
|
|
M V30 END BOND
|
|
M V30 BEGIN COLLECTION
|
|
M V30 MDLV30/STEABS ATOMS=(1 7)
|
|
M V30 END COLLECTION
|
|
M V30 END CTAB
|
|
M END
|
|
$$$$
|
|
)CTAB"_ctab;
|
|
REQUIRE(m);
|
|
CHECK(m->getAtomWithIdx(6)->getChiralTag() !=
|
|
Atom::ChiralType::CHI_UNSPECIFIED);
|
|
CHECK(m->getBondBetweenAtoms(5, 6)->getStereo() ==
|
|
Bond::BondStereo::STEREONONE);
|
|
}
|
|
SECTION("examples from #8323") {
|
|
std::string pathName = getenv("RDBASE");
|
|
pathName += "/Code/GraphMol/test_data/Github8323.sdf";
|
|
SDMolSupplier suppl(pathName);
|
|
while (!suppl.atEnd()) {
|
|
auto mol = suppl.next();
|
|
REQUIRE(mol);
|
|
auto &sgs = mol->getStereoGroups();
|
|
REQUIRE(sgs.size() == 1);
|
|
REQUIRE(mol->hasProp("StereoGroupOnAtom"));
|
|
auto aid = std::stoul(mol->getProp<std::string>("StereoGroupOnAtom"));
|
|
CHECK(sgs[0].getAtoms().size() == 1);
|
|
CHECK(sgs[0].getAtoms().at(0)->getIdx() == aid);
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE("Github #8420: imines and crossed bonds") {
|
|
bool useLegacy = GENERATE(true, false);
|
|
CAPTURE(useLegacy);
|
|
UseLegacyStereoPerceptionFixture reset_stereo_perception(useLegacy);
|
|
SECTION("as reported") {
|
|
std::string ctab = R"CTAB(
|
|
MJ250100
|
|
|
|
7 7 0 0 1 0 0 0 0 0999 V2000
|
|
0.6961 0.4995 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.0196 1.7395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.7332 0.4968 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4118 0.9090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1.4118 1.7395 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
0.6961 2.1583 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
-0.0196 0.9101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
3 7 2 3 0 0 0
|
|
4 5 1 0 0 0 0
|
|
5 6 1 0 0 0 0
|
|
2 6 1 0 0 0 0
|
|
2 7 1 0 0 0 0
|
|
1 4 1 0 0 0 0
|
|
1 7 1 0 0 0 0
|
|
M END)CTAB";
|
|
auto m = v2::FileParsers::MolFromMolBlock(ctab);
|
|
REQUIRE(m);
|
|
CHECK(m->getBondWithIdx(0)->getStereo() == Bond::BondStereo::STEREONONE);
|
|
}
|
|
} |