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rdkit/Code/GraphMol/catch_chirality.cpp
Greg Landrum 4bbbc6611d Add a CXSMILES option to the MolHash (#5058) 
* Nonchiral atoms should be removed from StereoGroups

This fixes a bug where atoms which have no chirality were left in StereoGroups

In order to make this work, ROMol::setStereoGroups() needed to be made public.
That shouldn't be a problem since it doesn't change connectivity.

* support CXSmiles extensions in the hashes

* initial tests for that

* some cleanup

* copyright header cleanup

* minor refactoring

* call out the changes in the release notes

* extension and more testing

* add python wrappers
2022-03-03 16:00:38 +01:00

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//
// Copyright (C) 2020-2021 Greg Landrum and other RDKit contributors
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/StereoGroup.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolFileStereochem.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
using namespace RDKit;
TEST_CASE("bond StereoInfo", "[unittest]") {
SECTION("basics") {
{
auto mol = "CC=C(C#C)C=C"_smiles;
REQUIRE(mol);
auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 4);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
CHECK(sinfo.controllingAtoms[2] == 3);
CHECK(sinfo.controllingAtoms[3] == 5);
CHECK(sinfo.specified == Chirality::StereoSpecified::Unspecified);
CHECK(sinfo.descriptor == Chirality::StereoDescriptor::None);
}
{
auto mol = "CC=NC=N"_smiles;
REQUIRE(mol);
auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 4);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
CHECK(sinfo.controllingAtoms[2] == 3);
CHECK(sinfo.controllingAtoms[3] == Chirality::StereoInfo::NOATOM);
}
}
SECTION("stereo") {
{
auto mol = "C/C=C(/C#C)C"_smiles;
REQUIRE(mol);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms().size() == 2);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[0] == 0);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[1] == 3);
auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 4);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
CHECK(sinfo.controllingAtoms[2] == 3);
CHECK(sinfo.controllingAtoms[3] == 5);
CHECK(sinfo.specified == Chirality::StereoSpecified::Specified);
CHECK(sinfo.descriptor == Chirality::StereoDescriptor::Bond_Trans);
}
{ // check an example where one of the stereo atoms isn't the first
// neighbor
auto mol = "C/C=C(/C)C#C"_smiles;
REQUIRE(mol);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms().size() == 2);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[0] == 0);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[1] == 4);
auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 4);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
CHECK(sinfo.controllingAtoms[2] == 3);
CHECK(sinfo.controllingAtoms[3] == 4);
CHECK(sinfo.specified == Chirality::StereoSpecified::Specified);
CHECK(sinfo.descriptor == Chirality::StereoDescriptor::Bond_Trans);
}
{
auto mol = "C/C=C(\\C#C)C"_smiles;
REQUIRE(mol);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms().size() == 2);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[0] == 0);
CHECK(mol->getBondWithIdx(1)->getStereoAtoms()[1] == 3);
auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 4);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
CHECK(sinfo.controllingAtoms[2] == 3);
CHECK(sinfo.controllingAtoms[3] == 5);
CHECK(sinfo.specified == Chirality::StereoSpecified::Specified);
CHECK(sinfo.descriptor == Chirality::StereoDescriptor::Bond_Cis);
}
{ // any bonds
auto mol = "CC=C(C#C)C"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
auto sinfo = Chirality::detail::getStereoInfo(mol->getBondWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Bond_Double);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 4);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == Chirality::StereoInfo::NOATOM);
CHECK(sinfo.controllingAtoms[2] == 3);
CHECK(sinfo.controllingAtoms[3] == 5);
CHECK(sinfo.specified == Chirality::StereoSpecified::Unknown);
CHECK(sinfo.descriptor == Chirality::StereoDescriptor::None);
}
}
}
TEST_CASE("isBondPotentialStereoBond", "[unittest]") {
SECTION("basics") {
{
auto mol = "CC=C(C#C)C=C"_smiles;
REQUIRE(mol);
CHECK(
Chirality::detail::isBondPotentialStereoBond(mol->getBondWithIdx(1)));
CHECK(!Chirality::detail::isBondPotentialStereoBond(
mol->getBondWithIdx(5)));
CHECK(!Chirality::detail::isBondPotentialStereoBond(
mol->getBondWithIdx(3)));
CHECK(!Chirality::detail::isBondPotentialStereoBond(
mol->getBondWithIdx(4)));
}
{
auto mol = "CC=NC=N"_smiles;
REQUIRE(mol);
CHECK(
Chirality::detail::isBondPotentialStereoBond(mol->getBondWithIdx(1)));
CHECK(!Chirality::detail::isBondPotentialStereoBond(
mol->getBondWithIdx(3)));
}
{
SmilesParserParams ps;
ps.removeHs = false;
std::unique_ptr<ROMol> mol{SmilesToMol("[H]C=CC=C([H])[H]", ps)};
REQUIRE(mol);
CHECK(!Chirality::detail::isBondPotentialStereoBond(
mol->getBondWithIdx(1)));
CHECK(!Chirality::detail::isBondPotentialStereoBond(
mol->getBondWithIdx(3)));
}
}
SECTION("ring size") {
{
auto m = "C1=CCCCC1"_smiles;
REQUIRE(m);
CHECK(
!Chirality::detail::isBondPotentialStereoBond(m->getBondWithIdx(0)));
}
{
auto m = "C1=CCCCCC1"_smiles;
REQUIRE(m);
CHECK(
!Chirality::detail::isBondPotentialStereoBond(m->getBondWithIdx(0)));
}
{
auto m = "C12=C(CCCC2)CCCCCC1"_smiles;
REQUIRE(m);
CHECK(
!Chirality::detail::isBondPotentialStereoBond(m->getBondWithIdx(0)));
}
}
}
TEST_CASE("atom StereoInfo", "[unittest]") {
SECTION("basics") {
{
auto mol = "CC(F)(Cl)CNC(C)C"_smiles;
REQUIRE(mol);
auto sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 4);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == 2);
CHECK(sinfo.controllingAtoms[2] == 3);
CHECK(sinfo.controllingAtoms[3] == 4);
CHECK(sinfo.specified == Chirality::StereoSpecified::Unspecified);
CHECK(sinfo.descriptor == Chirality::StereoDescriptor::None);
sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(6));
CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(sinfo.centeredOn == 6);
REQUIRE(sinfo.controllingAtoms.size() == 3);
CHECK(sinfo.controllingAtoms[0] == 5);
CHECK(sinfo.controllingAtoms[1] == 7);
CHECK(sinfo.controllingAtoms[2] == 8);
CHECK(sinfo.specified == Chirality::StereoSpecified::Unspecified);
CHECK(sinfo.descriptor == Chirality::StereoDescriptor::None);
}
{
auto mol = "C[C@](F)(Cl)CNC(C)C"_smiles;
REQUIRE(mol);
auto sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 4);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == 2);
CHECK(sinfo.controllingAtoms[2] == 3);
CHECK(sinfo.controllingAtoms[3] == 4);
CHECK(sinfo.specified == Chirality::StereoSpecified::Specified);
CHECK(sinfo.descriptor == Chirality::StereoDescriptor::Tet_CCW);
}
{
auto mol = "CN1CC1N(F)C"_smiles;
REQUIRE(mol);
auto sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 3);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == 2);
CHECK(sinfo.controllingAtoms[2] == 3);
}
{
auto mol = "O[As](F)C[As]C[As]"_smiles;
REQUIRE(mol);
auto sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(1));
CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(sinfo.centeredOn == 1);
REQUIRE(sinfo.controllingAtoms.size() == 3);
CHECK(sinfo.controllingAtoms[0] == 0);
CHECK(sinfo.controllingAtoms[1] == 2);
CHECK(sinfo.controllingAtoms[2] == 3);
sinfo = Chirality::detail::getStereoInfo(mol->getAtomWithIdx(4));
CHECK(sinfo.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(sinfo.centeredOn == 4);
REQUIRE(sinfo.controllingAtoms.size() == 2);
CHECK(sinfo.controllingAtoms[0] == 3);
CHECK(sinfo.controllingAtoms[1] == 5);
}
}
}
TEST_CASE("isAtomPotentialTetrahedralCenter", "[unittest]") {
SECTION("basics") {
{
auto mol = "CC(F)(Cl)CNC(C)(C)C"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(1)));
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(0)));
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(4)));
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(6)));
}
{
auto mol = "CN1CC1N(F)C"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(1)));
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(4)));
}
{
auto mol = "O=S(F)CC[S+]([O-])CS=O"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(1)));
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(5)));
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(8)));
}
{
auto mol = "O=[Se](F)CC[Se+]([O-])C[Se]=O"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(1)));
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(5)));
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(8)));
}
{
auto mol = "OP(F)CPCP"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(1)));
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(4)));
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(6)));
}
{
auto mol = "O[As](F)C[As]C[As]"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(1)));
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(4)));
CHECK(!Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(6)));
}
{
auto mol = "O[P]([O-])(=O)OC"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(
mol->getAtomWithIdx(1)));
}
}
}
TEST_CASE("isAtomPotentialStereoAtom", "[unittest]") {
SECTION("basics") {
{
auto mol = "CC(F)(Cl)CNC(C)(C)C"_smiles;
REQUIRE(mol);
for (const auto atom : mol->atoms()) {
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(atom) ==
Chirality::detail::isAtomPotentialStereoAtom(atom));
}
}
{
auto mol = "CN1CC1N(F)C"_smiles;
REQUIRE(mol);
for (const auto atom : mol->atoms()) {
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(atom) ==
Chirality::detail::isAtomPotentialStereoAtom(atom));
}
}
{
auto mol = "O=S(F)CC[S+]([O-])CS=O"_smiles;
REQUIRE(mol);
for (const auto atom : mol->atoms()) {
CHECK(Chirality::detail::isAtomPotentialTetrahedralCenter(atom) ==
Chirality::detail::isAtomPotentialStereoAtom(atom));
}
}
}
}
TEST_CASE("possible stereochemistry on atoms", "[chirality]") {
SECTION("specified") {
{
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::Specified);
CHECK(stereoInfo[0].centeredOn == 4);
std::vector<unsigned> catoms = {1, 5, 6, 7};
CHECK(stereoInfo[0].controllingAtoms == catoms);
}
{
auto mol = "C[C@@H](O)[C@H](C)[C@H](C)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 == 1);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
CHECK(stereoInfo[1].centeredOn == 3);
CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[2].specified == Chirality::StereoSpecified::Specified);
CHECK(stereoInfo[2].centeredOn == 5);
}
{
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 = {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());
}
}
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);
}
}
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 = pickBondsToWedge(*mol);
REQUIRE(wedgedBonds.size() == 1);
auto head = wedgedBonds.begin();
CHECK(head->first == 3);
CHECK(head->second == 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 = pickBondsToWedge(*mol);
REQUIRE(wedgedBonds.size() == 1);
auto head = wedgedBonds.begin();
CHECK(head->first == 3);
CHECK(head->second == 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 = pickBondsToWedge(*mol);
REQUIRE(wedgedBonds.size() == 1);
auto head = wedgedBonds.begin();
CHECK(head->first == 6);
CHECK(head->second == 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
SmilesParserParams ps;
ps.useLegacyStereo = false;
SECTION("original failing example") {
std::unique_ptr<RWMol> m{
SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2", ps)};
REQUIRE(m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
SECTION("original passing example") {
std::unique_ptr<RWMol> m{SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)CC2", ps)};
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", ps)};
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", ps)};
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", ps)};
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));
}
}
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