mirror of
https://github.com/rdkit/rdkit.git
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19bdd21de1
* add new test (it fails, of course) * isAtomPotentialTetrahedralCenter() there and tested tests cases for molecular stereo written (but failing, of course) create new_chirality.cpp, we will probably want to change this at some point new StereoInfo structure * more infrastructure - isBondPotentialStereoBond() - two getStereoInfo() functions - associated unit tests * backup * oops * backup * switch to always using four atoms for bonds * backup * add new test (it fails, of course) * isAtomPotentialTetrahedralCenter() there and tested tests cases for molecular stereo written (but failing, of course) create new_chirality.cpp, we will probably want to change this at some point new StereoInfo structure * more infrastructure - isBondPotentialStereoBond() - two getStereoInfo() functions - associated unit tests * backup * oops * backup * switch to always using four atoms for bonds * backup * this now actually works * doc update * add a test to demo that ring stereo is not working * more testing * add a fun CIP test * add review note * debugging * remove extraneous debugging turn off tests for ring-double bond stereo * disable the ring-stereo fix... this breaks a few tests, but we will recover * works, needs cleanup, chirality code needs re-testing * nothing works * Fixes #3322 * Python and C++ tests now pass * clang-format * first pass at python wrappers * improve doctest * basic optimization... stop with the copying * rename * all tests passing again * optimization * fix the sort in the tests * looks like this might fix the windows-dll build problems * update tests * the fun never ends * comment cleanup * handle deliberately unspecified atoms/bonds * add cleanIt option * add flagPossible * add option to use the new code to the SMILES parser * additional testing * additional testing * a bit of additional testing never hurts * changes in response to review * fixes a bug with potential parastereo not being cleared other changes in response to review * update docs
850 lines
33 KiB
C++
850 lines
33 KiB
C++
//
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// Copyright (C) 2020 Greg Landrum and T5 Informatics GmbH
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "catch.hpp"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Chirality.h>
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#include <GraphMol/MolOps.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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using namespace RDKit;
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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(!Chirality::detail::isBondPotentialStereoBond(
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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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}
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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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}
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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;
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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 == 4);
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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 == 6);
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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 == 8);
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}
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}
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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);
|
|
CHECK(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);
|
|
}
|
|
}
|
|
|
|
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 = {0, 2, 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("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);
|
|
}
|
|
}
|
|
#if 0
|
|
// FIX: the double bond stereo in rings isn't working. This also fails with the canonicalizer, so it's not unique to this code
|
|
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);
|
|
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 == 5);
|
|
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);
|
|
}
|
|
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);
|
|
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 == 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);
|
|
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 == 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);
|
|
}
|
|
}
|
|
#endif
|
|
|
|
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());
|
|
}
|
|
} |