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rdkit/Code/GraphMol/catch_chirality.cpp
Greg Landrum 867c2976f9 Fix bad interaction between the useLegacyStereo options in the SMILES parser (#5576) 
* partial fix

* prepare testing code for the deprecation

* more detail in the release notes
2022-10-07 16:53:59 +02:00

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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 <cstdlib>
#include "catch.hpp"
#include <boost/noncopyable.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/FileParsers/MolSupplier.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
using namespace RDKit;
class TestFixtureTemplate : public boost::noncopyable {
public:
TestFixtureTemplate() = delete;
TestFixtureTemplate(std::string var, bool (*getter_func)(),
void (*setter_func)(bool))
: m_var{std::move(var)},
m_getter_func{getter_func},
m_setter_func{setter_func} {
auto evar = std::getenv(m_var.c_str());
m_env_var_set = evar == nullptr;
m_flag_state = (*m_getter_func)();
}
~TestFixtureTemplate() {
if (m_env_var_set) {
(*m_setter_func)(m_flag_state);
} else {
#if _MSC_VER
_putenv_s(m_var.c_str(), "");
#else
unsetenv(m_var.c_str());
#endif
}
}
private:
std::string m_var;
bool (*m_getter_func)();
void (*m_setter_func)(bool);
bool m_flag_state;
bool m_env_var_set;
};
class UseLegacyStereoPerceptionFixture : private TestFixtureTemplate {
public:
UseLegacyStereoPerceptionFixture()
: TestFixtureTemplate(RDKit::Chirality::useLegacyStereoEnvVar,
&RDKit::Chirality::getUseLegacyStereoPerception,
&RDKit::Chirality::setUseLegacyStereoPerception) {}
};
class AllowNontetrahedralChiralityFixture : private TestFixtureTemplate {
public:
AllowNontetrahedralChiralityFixture()
: TestFixtureTemplate(
RDKit::Chirality::nonTetrahedralStereoEnvVar,
&RDKit::Chirality::getAllowNontetrahedralChirality,
&RDKit::Chirality::setAllowNontetrahedralChirality) {}
};
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 = {2, 0, 4, 5};
CHECK(stereoInfo[0].controllingAtoms == catoms);
}
{
auto mol = "CC=C(Cl)C"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[0].centeredOn == 1);
std::vector<unsigned> catoms = {0, Chirality::StereoInfo::NOATOM, 3, 4};
CHECK(stereoInfo[0].controllingAtoms == catoms);
}
}
SECTION("bond with unknown set, real") {
auto mol = "CC=C(C)F"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
}
SECTION("bond with unknown set, not real") {
auto mol = "CC=C(C)C"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOANY);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
CHECK(stereoInfo.size() == 0);
}
}
TEST_CASE("para-stereocenters and assignStereochemistry", "[chirality]") {
SECTION("simplest") {
auto mol = "CC(F)C(C)C(C)F"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 3);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].controllingAtoms.size() == 3);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 3);
CHECK(stereoInfo[1].controllingAtoms.size() == 3);
CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[2].centeredOn == 5);
CHECK(stereoInfo[2].controllingAtoms.size() == 3);
}
SECTION("including bonds") {
// thanks to Salome Rieder for this nasty example
auto mol = "CC=CC(C=CC)C(C)C(C=CC)C=CC"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
CHECK(stereoInfo.size() == 7);
std::sort(stereoInfo.begin(), stereoInfo.end(),
[](const Chirality::StereoInfo &a,
const Chirality::StereoInfo &b) -> bool {
return (a.type < b.type) && (a.centeredOn < b.centeredOn) &&
(a.specified < b.specified) &&
(a.descriptor < b.descriptor) &&
(a.controllingAtoms < b.controllingAtoms);
});
REQUIRE(stereoInfo.size() == 7);
CHECK(stereoInfo[6].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[6].centeredOn == 13);
CHECK(stereoInfo[5].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[5].centeredOn == 10);
CHECK(stereoInfo[4].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[4].centeredOn == 4);
CHECK(stereoInfo[3].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[3].centeredOn == 1);
CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[2].centeredOn == 9);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 7);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 3);
}
SECTION("sugar fun") {
auto mol = "C1(O)C(O)C(O)C(O)C(O)C1O"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 6);
for (const auto &si : stereoInfo) {
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(si.centeredOn % 2 == 0);
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
}
}
}
TEST_CASE("ring stereochemistry", "[chirality]") {
SECTION("partially specified") {
SmilesParserParams ps;
ps.sanitize = false;
std::unique_ptr<RWMol> mol{SmilesToMol("C[C@H]1CCC(C)CC1", ps)};
REQUIRE(mol);
// std::cerr << "------------ 3 -------------" << std::endl;
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 4);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
}
SECTION("specified") {
auto mol = "C[C@H]1CC[C@@H](C)CC1"_smiles;
REQUIRE(mol);
// std::cerr << "------------ 1 -------------" << std::endl;
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 4);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
}
SECTION("unspecified") {
auto mol = "CC1CCC(C)CC1"_smiles;
REQUIRE(mol);
// std::cerr << "------------ 2 -------------" << std::endl;
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 4);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
}
SECTION("four ring") {
auto mol = "C[C@H]1C[C@@H](C)C1"_smiles;
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 3);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
}
SECTION("four ring unspecified") {
auto mol = "CC1CC(C)C1"_smiles;
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 3);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
}
}
TEST_CASE("tricky recursive example from Dan Nealschneider", "[chirality]") {
SECTION("adapted") {
auto mol = "CC=C1CCC(O)CC1"_smiles;
REQUIRE(mol);
mol->updatePropertyCache();
MolOps::setBondStereoFromDirections(*mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 5);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[1].centeredOn == 1);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
}
SECTION("simplified") {
// can't sanitize this because the current (2020.03) assignStereochemistry
// code doesn't recognize the stereo here and removes it
SmilesParserParams ps;
ps.sanitize = false;
ps.removeHs = false;
std::unique_ptr<ROMol> mol(SmilesToMol("C/C=C1/C[C@H](O)C1", ps));
REQUIRE(mol);
mol->updatePropertyCache();
MolOps::setBondStereoFromDirections(*mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 4);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[1].centeredOn == 1);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
}
// FIX this still isn't working
SECTION("unspecified") {
auto mol = "CC=C1C[CH](O)C1"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 4);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[1].centeredOn == 1);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
}
}
TEST_CASE("unknown stereo", "[chirality]") {
SECTION("atoms") {
auto mol = "CC(O)C[C@@H](O)F"_smiles;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(0, 1));
mol->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BondDir::UNKNOWN);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 4);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
}
SECTION("atoms2") {
// artificial situation: "squiggly bond" overrides the specified atomic
// stereo
auto mol = "C[C@H](O)C[C@@H](O)F"_smiles;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(0, 1));
mol->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BondDir::UNKNOWN);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 4);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
}
SECTION("bonds") {
{
auto mol = "CC=CC"_smiles;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(1, 2));
mol->getBondBetweenAtoms(1, 2)->setBondDir(Bond::BondDir::EITHERDOUBLE);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
}
{
auto mol = "CC=CC=C"_smiles;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(1, 2));
mol->getBondBetweenAtoms(1, 2)->setBondDir(Bond::BondDir::EITHERDOUBLE);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
}
}
SECTION("bonds with squiggle bonds") {
{ // to begin atom
auto mol = "CC=CC"_smiles;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(0, 1));
mol->getBondBetweenAtoms(0, 1)->setBondDir(Bond::BondDir::UNKNOWN);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
}
{ // to end atom
auto mol = "CC=CC"_smiles;
REQUIRE(mol);
REQUIRE(mol->getBondBetweenAtoms(2, 3));
mol->getBondBetweenAtoms(2, 3)->setBondDir(Bond::BondDir::UNKNOWN);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unknown);
}
}
}
TEST_CASE("cleaning chirality", "[chirality]") {
SECTION("atoms") {
auto mol = "CC(O)C"_smiles;
REQUIRE(mol);
mol->getAtomWithIdx(1)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CW);
{
// by default we don't clean up, so the chiral center survives even though
// we don't get any results:
auto stereoInfo = Chirality::findPotentialStereo(*mol);
CHECK(stereoInfo.size() == 0);
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
}
{
bool cleanIt = true;
auto stereoInfo = Chirality::findPotentialStereo(*mol, cleanIt);
CHECK(stereoInfo.size() == 0);
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
SECTION("bonds") {
auto mol = "CC=C(C)C"_smiles;
REQUIRE(mol);
mol->getBondWithIdx(1)->setStereoAtoms(0, 3);
mol->getBondWithIdx(1)->setStereo(Bond::BondStereo::STEREOCIS);
{
// by default we don't clean up, so the stereo bond survives even though
// we don't get any results:
auto stereoInfo = Chirality::findPotentialStereo(*mol);
CHECK(stereoInfo.size() == 0);
CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOCIS);
}
{
bool cleanIt = true;
auto stereoInfo = Chirality::findPotentialStereo(*mol, cleanIt);
CHECK(stereoInfo.size() == 0);
CHECK(mol->getBondWithIdx(1)->getStereo() ==
Bond::BondStereo::STEREONONE);
}
}
}
TEST_CASE("flagPossible", "[chirality]") {
SECTION("atoms") {
auto mol = "CC(O)[C@H](F)O"_smiles;
REQUIRE(mol);
{
// by default we do use flagPossible:
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 3);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
}
{
bool cleanIt = false;
bool flagPossible = false;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 3);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
}
}
SECTION("bonds") {
auto mol = "CC=C/C=C/C"_smiles;
REQUIRE(mol);
{
// by default we do use flagPossible
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[1].centeredOn == 3);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Specified);
}
{
bool cleanIt = true;
bool flagPossible = false;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].type == Chirality::StereoType::Bond_Double);
CHECK(stereoInfo[0].centeredOn == 3);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Specified);
}
}
}
TEST_CASE("cleanup after removing possible centers", "[chirality]") {
SECTION("atoms1") {
auto mol = "FC(Cl)(F)C(C(Cl)(F)F)I"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
CHECK(stereoInfo.empty());
}
SECTION("bonds1") {
auto mol = "FC(Cl)(F)C(C(Cl)(F)F)=CF"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
CHECK(stereoInfo.empty());
}
SECTION("atoms2") {
auto mol = "ClC(F)(F)C(=CC(F)C=C(C(F)(F)Cl)C(F)(F)Cl)C(Cl)(F)F"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
CHECK(stereoInfo.empty());
}
}
TEST_CASE("findPotentialStereo problems related to #3490", "[chirality][bug]") {
SECTION("example 1") {
auto mol = "CC1CC(O)C1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 3);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
}
SECTION("example 2a") {
auto mol = "C(C(C)C1)C12CCN2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("example 2b") {
auto mol = "CC(C1)CC12CCN2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("example 2c") {
auto mol = "C([C@H](C)C1)[C@]12CCN2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("example 2d") {
auto mol = "C[C@H](C1)C[C@]12CCN2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("example 3") {
auto mol = "C(C(C)C1)C12CN(C3)CCCCC23"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 4); // [1, 4, 6, 12]
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 4);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[2].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[2].centeredOn == 6);
CHECK(stereoInfo[2].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[3].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[3].centeredOn == 12);
CHECK(stereoInfo[3].specified == Chirality::StereoSpecified::Unspecified);
}
}
TEST_CASE("ring stereo finding is overly aggressive", "[chirality][bug]") {
SECTION("Finding too much 1a") {
auto mol = "CC1CCCCC1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 0);
}
SECTION("Finding too much 1b") {
auto mol = "CC1CCC(C)CC1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("Finding too much 1c") {
auto mol = "C[C@H]1CCC(C)CC1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("Finding too much 1d") {
auto mol = "CC1(C)CCCCC1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 0);
}
SECTION("Finding too much 1e") {
auto mol = "CC1(C)CCC(C)CC1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 0);
}
SECTION("Finding too much 1f") {
auto mol = "C2CC2C1(C2CC2)CCCCC1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 0);
}
SECTION("Finding too much 1g") {
auto mol = "CC1CC2(CCC2)C1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 0);
}
SECTION("Finding too much 1h") {
auto mol = "CC1CC2(CC(C)C2)C1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 3);
}
SECTION("Finding too much 2a") {
auto mol = "CC1CCNCC1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 0);
}
SECTION("Finding too much 2b") {
auto mol = "CC1CCN(C)CC1"_smiles; // 3-coordinate N is not stereogenic
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 0);
}
SECTION("Finding too much 3a") {
auto mol = "CC1CCC1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 0);
}
SECTION("Finding too much 3b") {
auto mol = "CC1CC(C)C1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("fused rings 1") {
auto mol = "C1CCC2CCCCC2C1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("fused rings 2") {
auto mol = "C1CC2CCCC2C1"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
SECTION("cages 1") {
auto mol = "CC1CN2CCC1CC2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 3);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[1].centeredOn == 3);
CHECK(stereoInfo[2].centeredOn == 6);
}
SECTION("cages 1b") {
auto mol = "O1CN2CCC1CC2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
CHECK(stereoInfo[0].centeredOn == 2);
CHECK(stereoInfo[1].centeredOn == 5);
}
SECTION("cages 2") {
auto mol = "C1CC2(O)CCC1(C)CC2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
CHECK(stereoInfo[0].centeredOn == 2);
CHECK(stereoInfo[1].centeredOn == 6);
}
SECTION("cages 3") {
auto mol = "C1CC2(O)CCC1CC2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
CHECK(stereoInfo[0].centeredOn == 2);
CHECK(stereoInfo[1].centeredOn == 6);
}
SECTION("adamantyl") {
auto mol = "CC12CC3CC(CC(C3)C1)C2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 4);
}
SECTION("bug 1a") {
// example that came up during testing
auto mol = "C(=O)C(C(C)N2C=C2)C(=O)"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].centeredOn == 3);
}
SECTION("bug 1b") {
// example that came up during testing
auto mol = "C(=O)C(C(CC)c2ccc(Cl)cc2)C(=O)"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].centeredOn == 3);
}
SECTION("bug 1c") {
// example that came up during testing
auto mol = "O=CC(C=O)C(C)n2cccc2"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].centeredOn == 5);
}
SECTION("bug 1c") {
// example that came up during testing
auto mol = "C(=O)C(C(C)n2cccc2)C(=O)"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].centeredOn == 3);
}
SECTION("bug 1d") {
// example that came up during testing
auto mol = "C(O)C(C(C)n2cccc2)C(O)"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
REQUIRE(stereoInfo.size() == 1);
CHECK(stereoInfo[0].centeredOn == 3);
}
SECTION("just a bug") {
// example that came up during testing
auto mol = "CC1=CN(C2OC(CNC(=O)C3c4ccccc4Sc4ccccc43)CC2)C(=O)NC1=O"_smiles;
REQUIRE(mol);
bool cleanIt = true;
bool flagPossible = true;
auto stereoInfo =
Chirality::findPotentialStereo(*mol, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 2);
}
}
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
UseLegacyStereoPerceptionFixture reset_stereo_perception;
Chirality::setUseLegacyStereoPerception(false);
SECTION("original failing example") {
auto m = "C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2"_smiles;
REQUIRE(m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
SECTION("original failing example, findPossible") {
UseLegacyStereoPerceptionFixture inner_reset_stereo_perception;
Chirality::setUseLegacyStereoPerception(true);
SmilesParserParams ps2;
ps2.sanitize = false;
std::unique_ptr<RWMol> m{
SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2", ps2)};
REQUIRE(m);
MolOps::sanitizeMol(*m);
auto stereoInfo = Chirality::findPotentialStereo(*m, true, true);
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(4)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(11)->getChiralTag() == Atom::CHI_UNSPECIFIED);
REQUIRE(stereoInfo.size() == 4);
for (const auto &si : stereoInfo) {
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
if (si.centeredOn != 9) {
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
} else {
CHECK(si.specified == Chirality::StereoSpecified::Specified);
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
}
}
}
SECTION("original passing example") {
auto m = "C[C@H]1CCC2(CC1)CC[C@H](C)CC2"_smiles;
REQUIRE(m);
// if the middle is unspecified, the two ends can't be specified
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(9)->getChiralTag() == Atom::CHI_UNSPECIFIED);
{
bool cleanIt = true;
bool flagPossible = true;
RWMol m2(*m);
auto stereoInfo =
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 3);
for (const auto &si : stereoInfo) {
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
}
}
{
bool cleanIt = true;
bool flagPossible = false;
RWMol m2(*m);
auto stereoInfo =
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
CHECK(stereoInfo.empty());
}
}
SECTION("specified chirality on spiro atom") {
auto m = "C[C@H]1CC[C@@]2(CC[C@H](C)CC2)CC1"_smiles;
REQUIRE(m);
// now the middle is specified, so the two ends are as well
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(7)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(4)->getChiralTag() != Atom::CHI_UNSPECIFIED);
{
bool cleanIt = true;
bool flagPossible = true;
RWMol m2(*m);
auto stereoInfo =
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 3);
for (const auto &si : stereoInfo) {
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(si.specified == Chirality::StereoSpecified::Specified);
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
}
}
{
bool cleanIt = true;
bool flagPossible = false;
RWMol m2(*m);
auto stereoInfo =
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 3);
for (const auto &si : stereoInfo) {
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(si.specified == Chirality::StereoSpecified::Specified);
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
}
}
}
SECTION("three spiro rings, unspecified spiro links") {
auto m = "C[C@H]1CCC2(CC1)CCC1(CC[C@H](C)CC1)CC2"_smiles;
REQUIRE(m);
{
bool cleanIt = true;
bool flagPossible = true;
RWMol m2(*m);
auto stereoInfo =
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 4);
for (const auto &si : stereoInfo) {
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
}
}
}
SECTION("three spiro rings, specified spiro links") {
auto m = "C[C@H]1CC[C@@]2(CC1)CC[C@]1(CC[C@H](C)CC1)CC2"_smiles;
REQUIRE(m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(4)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(12)->getChiralTag() != Atom::CHI_UNSPECIFIED);
{
bool cleanIt = true;
bool flagPossible = true;
RWMol m2(*m);
auto stereoInfo =
Chirality::findPotentialStereo(m2, cleanIt, flagPossible);
CHECK(stereoInfo.size() == 4);
for (const auto &si : stereoInfo) {
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(si.specified == Chirality::StereoSpecified::Specified);
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
}
}
}
}
TEST_CASE(
"Github #4215: Ring stereo being discarded in spiro systems, using deprecated useLegacyStereo option") {
// Note: this bug is still there when using the legacy stereochemistry
// assignment. It's "non-trivial" to fix there and we've opted not to
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 failing example, findPossible") {
SmilesParserParams ps2;
ps2.sanitize = false;
std::unique_ptr<RWMol> m{
SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2", ps2)};
REQUIRE(m);
MolOps::sanitizeMol(*m);
auto stereoInfo = Chirality::findPotentialStereo(*m, true, true);
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(4)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(11)->getChiralTag() == Atom::CHI_UNSPECIFIED);
REQUIRE(stereoInfo.size() == 4);
for (const auto &si : stereoInfo) {
CHECK(si.type == Chirality::StereoType::Atom_Tetrahedral);
if (si.centeredOn != 9) {
CHECK(si.specified == Chirality::StereoSpecified::Unspecified);
CHECK(si.descriptor == Chirality::StereoDescriptor::None);
} else {
CHECK(si.specified == Chirality::StereoSpecified::Specified);
CHECK(si.descriptor != Chirality::StereoDescriptor::None);
}
}
}
SECTION("original passing example") {
std::unique_ptr<RWMol> m{SmilesToMol("C[C@H]1CCC2(CC1)CC[C@H](C)CC2", 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));
}
}
TEST_CASE(
"Github #5200: FindPotentialStereo does not clean stereoflags from atoms "
"which cannot be stereocenters") {
auto m = "CCF"_smiles;
REQUIRE(m);
m->getAtomWithIdx(1)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
bool cleanIt = true;
auto sinfo = Chirality::findPotentialStereo(*m, cleanIt);
CHECK(sinfo.empty());
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
TEST_CASE(
"Github #5196: Zero & coordinate bonds are being taken into account for "
"chirality") {
RDLog::LogStateSetter setter; // disable irritating warning messages
auto mol = R"CTAB(
RDKit 3D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 15 18 0 0 0
M V30 BEGIN ATOM
M V30 1 C -0.136359 0.025241 -0.986870 0
M V30 2 C 0.211183 -0.810922 0.138318 0
M V30 3 C -0.446638 -0.713741 1.305561 0
M V30 4 C -1.141107 0.914647 -0.916429 0
M V30 5 R -1.628248 -0.983190 -0.411960 0
M V30 6 H 0.392055 -0.106505 -1.920607 0
M V30 7 H 0.974038 -1.568492 0.017171 0
M V30 8 H -0.209921 -1.406535 2.084966 0
M V30 9 H -1.378909 1.482059 -1.807349 0
M V30 10 C -1.544607 0.306162 1.588191 0
M V30 11 C -1.946856 1.186683 0.358271 0
M V30 12 H -1.207983 0.944410 2.407927 0
M V30 13 H -2.419549 -0.225146 1.965589 0
M V30 14 H -3.006492 1.040978 0.144313 0
M V30 15 H -1.830875 2.240146 0.620809 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 2 1
M V30 2 2 3 2
M V30 3 2 4 1
M V30 4 0 1 5
M V30 5 0 2 5
M V30 6 0 3 5
M V30 7 0 4 5
M V30 8 1 1 6
M V30 9 1 2 7
M V30 10 1 3 8
M V30 11 1 4 9
M V30 12 1 10 3
M V30 13 1 11 4
M V30 14 1 11 10
M V30 15 1 12 10
M V30 16 1 13 10
M V30 17 1 14 11
M V30 18 1 15 11
M V30 END BOND
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(mol);
SECTION("as reported") {
MolOps::assignStereochemistryFrom3D(*mol);
for (auto aidx : {0, 1, 2, 3}) {
CHECK(mol->getAtomWithIdx(aidx)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
SECTION("as reported - ZOBs") {
for (auto bidx : {3, 4, 5, 6}) {
mol->getBondWithIdx(bidx)->setBondType(Bond::BondType::ZERO);
}
MolOps::assignStereochemistryFrom3D(*mol);
for (auto idx : {0, 1, 2, 3}) {
CHECK(mol->getAtomWithIdx(idx)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
SECTION("as reported - datives") {
for (auto bidx : {3, 4, 5, 6}) {
mol->getBondWithIdx(bidx)->setBondType(Bond::BondType::DATIVE);
}
MolOps::assignStereochemistryFrom3D(*mol);
for (auto idx : {0, 1, 2, 3}) {
CHECK(mol->getAtomWithIdx(idx)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
SECTION("as reported - reversed datives") {
// structure is bogus, but we want to test
for (auto bidx : {3, 4, 5, 6}) {
auto bond = mol->getBondWithIdx(bidx);
bond->setEndAtomIdx(bond->getBeginAtomIdx());
bond->setBeginAtomIdx(4);
bond->setBondType(Bond::BondType::DATIVE);
}
MolOps::assignStereochemistryFrom3D(*mol);
for (auto idx : {0, 1, 2, 3}) {
CHECK(mol->getAtomWithIdx(idx)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
SECTION("as reported - singles") {
// structure is bogus, but we want to test
for (auto bidx : {3, 4, 5, 6}) {
mol->getBondWithIdx(bidx)->setBondType(Bond::BondType::SINGLE);
}
MolOps::assignStereochemistryFrom3D(*mol);
for (auto idx : {0, 1, 2, 3}) {
CHECK(mol->getAtomWithIdx(idx)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
SECTION("assignStereochemistry") {
auto mol = "[Fe]C(=C)O |C:1.0|"_smiles;
REQUIRE(mol);
for (auto bt : {Bond::BondType::DATIVE, Bond::BondType::ZERO,
Bond::BondType::UNSPECIFIED}) {
mol->getAtomWithIdx(1)->setChiralTag(
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
mol->getBondWithIdx(0)->setBondType(bt);
bool cleanit = true;
bool force = true;
MolOps::assignStereochemistry(*mol, cleanit, force);
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
SECTION("isAtomPotentialTetrahedralCenter() and getStereoInfo()") {
auto mol = "[Fe]C(=C)O |C:1.0|"_smiles;
REQUIRE(mol);
for (auto bt : {Bond::BondType::DATIVE, Bond::BondType::ZERO,
Bond::BondType::UNSPECIFIED}) {
mol->getAtomWithIdx(1)->setChiralTag(
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
mol->getBondWithIdx(0)->setBondType(bt);
CHECK(!Chirality::detail::isAtomPotentialStereoAtom(
mol->getAtomWithIdx(1)));
bool cleanit = true;
auto sinfo = Chirality::findPotentialStereo(*mol, cleanit);
CHECK(sinfo.empty());
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
}
TEST_CASE(
"Github #5239: Precondition violation on chiral Atoms with zero order "
"bonds") {
RDLog::LogStateSetter setter; // disable irritating warning messages
auto molblock = R"CTAB(
RDKit 3D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 0 0 0
M V30 BEGIN ATOM
M V30 1 C -0.446600 -0.713700 1.305600 0
M V30 2 Fe -1.628200 -0.983200 -0.412000 0
M V30 3 Cl -0.049300 -1.876700 2.613900 0
M V30 4 C -1.544600 0.306200 1.588200 0
M V30 5 F 0.673700 0.029200 0.993700 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 3
M V30 2 1 1 4 CFG=1
M V30 3 1 1 5
M V30 4 0 2 1
M V30 END BOND
M V30 END CTAB
M END)CTAB";
bool sanitize = false;
std::unique_ptr<ROMol> mol(MolBlockToMol(molblock, sanitize));
REQUIRE(mol);
MolOps::assignStereochemistryFrom3D(*mol);
CHECK(mol->getAtomWithIdx(0)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
}
TEST_CASE("nontetrahedral stereo from 3D", "[nontetrahedral]") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/nontetrahedral_3d.sdf";
SECTION("basics") {
SDMolSupplier suppl(pathName);
while (!suppl.atEnd()) {
std::unique_ptr<ROMol> m{suppl.next()};
REQUIRE(m);
MolOps::assignChiralTypesFrom3D(*m);
auto ct = m->getProp<std::string>("ChiralType");
auto cp = m->getProp<unsigned>("ChiralPermutation");
auto atom = m->getAtomWithIdx(0);
if (ct == "SP") {
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_SQUAREPLANAR);
} else if (ct == "TB") {
CHECK(atom->getChiralTag() ==
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
} else if (ct == "TH") {
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL);
} else if (ct == "OH") {
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_OCTAHEDRAL);
}
CHECK(atom->getProp<unsigned>(common_properties::_chiralPermutation) ==
cp);
}
}
SECTION("disable nontetrahedral stereo") {
AllowNontetrahedralChiralityFixture reset_non_tetrahedral_allowed;
Chirality::setAllowNontetrahedralChirality(false);
SDMolSupplier suppl(pathName);
while (!suppl.atEnd()) {
std::unique_ptr<ROMol> m{suppl.next()};
REQUIRE(m);
MolOps::assignChiralTypesFrom3D(*m);
auto ct = m->getProp<std::string>("ChiralType");
auto atom = m->getAtomWithIdx(0);
if (ct == "TH") {
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_TETRAHEDRAL);
} else {
CHECK(atom->getChiralTag() == Atom::ChiralType::CHI_UNSPECIFIED);
}
}
}
}
TEST_CASE("assignStereochemistry shouldn't remove nontetrahedral stereo",
"[nontetrahedral]") {
SECTION("basics") {
SmilesParserParams parseps;
parseps.sanitize = false;
parseps.removeHs = false;
std::unique_ptr<RWMol> m{SmilesToMol("F[Pt@TB1](O)(Br)(N)Cl", parseps)};
REQUIRE(m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
bool cleanIt = true;
bool force = true;
MolOps::assignStereochemistry(*m, cleanIt, force);
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
}
SECTION("standard SMILES parsing") {
std::unique_ptr<RWMol> m{SmilesToMol("F[Pt@TB1](O)(Br)(N)Cl")};
REQUIRE(m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
}
SECTION("SMILES parsing w/o sanitization") {
SmilesParserParams parseps;
// we need to skip stereo assignment
parseps.sanitize = false;
std::unique_ptr<RWMol> m{SmilesToMol("F[Pt@TB1](O)(Br)(N)Cl", parseps)};
REQUIRE(m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_TRIGONALBIPYRAMIDAL);
}
}
TEST_CASE("remove hs and non-tetrahedral stereo", "[nontetrahedral]") {
SmilesParserParams parseps;
parseps.sanitize = false;
parseps.removeHs = false;
std::vector<std::string> smiles = {"F[Pt@TB1]([H])(Br)(N)Cl",
"F[Pt@TB]([H])(Br)(N)Cl"};
for (const auto &smi : smiles) {
std::unique_ptr<RWMol> m{SmilesToMol(smi, parseps)};
REQUIRE(m);
CHECK(m->getNumAtoms(6));
{
// the default is to not remove Hs to non-tetrahedral stereocenters
RWMol molcp(*m);
MolOps::removeHs(molcp);
CHECK(molcp.getNumAtoms() == 6);
}
{
// but we can enable it
RWMol molcp(*m);
MolOps::RemoveHsParameters ps;
ps.removeNontetrahedralNeighbors = true;
MolOps::removeHs(molcp, ps);
CHECK(molcp.getNumAtoms() == 5);
}
{
// but we can enable it
RWMol molcp(*m);
MolOps::removeAllHs(molcp);
CHECK(molcp.getNumAtoms() == 5);
}
}
}
TEST_CASE("getIdealAngle", "[nontetrahedral]") {
SECTION("TB1") {
auto m = "S[As@TB1](F)(Cl)(Br)N"_smiles;
REQUIRE(m);
CHECK(Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(0)));
CHECK(Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(5)));
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(2)));
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(3)));
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(4)));
CHECK(Chirality::getTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1))
->getIdx() == 0);
CHECK(Chirality::getTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1), -1)
->getIdx() == 5);
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(4)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(2), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(120, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(5)),
Catch::Matchers::WithinAbs(180, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(5), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(5), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(5), m->getAtomWithIdx(4)),
Catch::Matchers::WithinAbs(90, 0.001));
}
SECTION("TB1 missing 1") {
auto m = "S[As@TB1](F)(Cl)Br"_smiles;
REQUIRE(m);
CHECK(Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(0)));
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(2)));
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(3)));
CHECK(!Chirality::isTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(4)));
CHECK(Chirality::getTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1))
->getIdx() == 0);
CHECK(Chirality::getTrigonalBipyramidalAxialAtom(m->getAtomWithIdx(1),
-1) == nullptr);
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(4)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(2), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(120, 0.001));
}
}
TEST_CASE("getChiralPermutation", "[nontetrahedral]") {
SECTION("TB1") {
// clang-format off
std::vector<std::pair<std::list<int>, unsigned int>> data = {
{{2, 3, 4, 5, 6}, 1},
{{2, 3, 5, 4, 6}, 2},
{{2, 3, 4, 6, 5}, 3},
{{2, 3, 5, 6, 4}, 4},
{{2, 3, 6, 4, 5}, 5},
{{2, 3, 6, 5, 4}, 6},
{{2, 6, 3, 4, 5}, 7},
{{2, 6, 3, 5, 4}, 8},
{{3, 2, 4, 5, 6}, 9},
{{3, 2, 5, 4, 6}, 11},
{{3, 2, 4, 6, 5}, 10},
{{3, 2, 5, 6, 4}, 12},
{{3, 2, 6, 4, 5}, 13},
{{3, 2, 6, 5, 4}, 14},
{{3, 4, 2, 5, 6}, 15},
{{3, 5, 2, 4, 6}, 20},
{{3, 4, 2, 6, 5}, 16},
{{3, 5, 2, 6, 4}, 19},
{{3, 4, 5, 2, 6}, 17},
{{3, 5, 4, 2, 6}, 18},
};
// clang-format on
auto m = "CCS[As@TB1](F)(Cl)(Br)N"_smiles;
REQUIRE(m);
const auto atm = m->getAtomWithIdx(3);
for (const auto &pr : data) {
// std::cerr << "---- " << pr.second << std::endl;
CHECK(Chirality::getChiralPermutation(atm, pr.first) == pr.second);
}
}
SECTION("SP1") {
// clang-format off
std::vector<std::pair<std::list<int>, unsigned int>> data = {
{{2, 3, 4, 5}, 1},
{{2, 4, 3, 5}, 2},
{{2, 3, 5, 4}, 3},
};
// clang-format on
auto m = "CCC[Pt@SP1](F)(Cl)N"_smiles;
REQUIRE(m);
const auto atm = m->getAtomWithIdx(3);
for (const auto &pr : data) {
// std::cerr << "---- " << pr.second << std::endl;
CHECK(Chirality::getChiralPermutation(atm, pr.first) == pr.second);
}
}
SECTION("OH1") {
// clang-format off
std::vector<std::pair<std::list<int>, unsigned int>> data = {
{{2, 3, 4, 5, 6, 7}, 1},
{{2, 3, 6, 5, 4, 7}, 2},
{{2, 3, 4, 5, 7, 6}, 3},
{{2, 3, 6, 5, 7, 4}, 16},
{{2, 3, 4, 7, 5, 6}, 6},
{{2, 3, 6, 7, 5, 4}, 18},
{{2, 3, 7, 4, 5, 6}, 19},
{{2, 3, 7, 6, 5, 4}, 24},
{{2, 7, 3, 4, 5, 6}, 25},
{{2, 7, 3, 6, 5, 4}, 30},
{{2, 3, 4, 6, 5, 7}, 4},
{{2, 3, 6, 4, 5, 7}, 14},
{{2, 3, 4, 6, 7, 5}, 5},
{{2, 3, 6, 4, 7, 5}, 15},
{{2, 3, 4, 7, 6, 5}, 7},
{{2, 3, 6, 7, 4, 5}, 17},
{{2, 3, 7, 4, 6, 5}, 20},
{{2, 3, 7, 6, 4, 5}, 23},
{{2, 7, 3, 4, 6, 5}, 26},
{{2, 7, 3, 6, 4, 5}, 29},
{{2, 3, 5, 6, 4, 7}, 10},
{{2, 3, 5, 4, 6, 7}, 8},
{{2, 3, 5, 6, 7, 4}, 11},
{{2, 3, 5, 4, 7, 6}, 9},
{{2, 3, 5, 7, 6, 4}, 13},
{{2, 3, 5, 7, 4, 6}, 12},
{{2, 3, 7, 5, 6, 4}, 22},
{{2, 3, 7, 5, 4, 6}, 21},
{{2, 7, 3, 5, 6, 4}, 28},
{{2, 7, 3, 5, 4, 6}, 27},
};
// clang-format on
auto m = "CCO[Co@OH1](Cl)(C)(N)(F)P"_smiles;
REQUIRE(m);
const auto atm = m->getAtomWithIdx(3);
for (const auto &pr : data) {
// std::cerr << "---- " << pr.second << std::endl;
CHECK(Chirality::getChiralPermutation(atm, pr.first) == pr.second);
}
}
}
TEST_CASE("isAtomPotentialNontetrahedralCenter", "[nontetrahedral]") {
SECTION("basics") {
{
auto mol = "C[S+](O)F"_smiles;
REQUIRE(mol);
CHECK(!Chirality::detail::isAtomPotentialNontetrahedralCenter(
mol->getAtomWithIdx(1)));
}
{
auto mol = "C[SH](O)F"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialNontetrahedralCenter(
mol->getAtomWithIdx(1)));
}
{
auto mol = "C[S@SP](O)F"_smiles;
REQUIRE(mol);
CHECK(Chirality::detail::isAtomPotentialNontetrahedralCenter(
mol->getAtomWithIdx(1)));
}
}
}
TEST_CASE("nontetrahedral StereoInfo", "[nontetrahedral]") {
SECTION("SP") {
auto m = "C[Pt@SP1](F)(Cl)O"_smiles;
REQUIRE(m);
auto sinfo = Chirality::findPotentialStereo(*m);
REQUIRE(sinfo.size() == 1);
CHECK(sinfo[0].centeredOn == 1);
CHECK(sinfo[0].type == Chirality::StereoType::Atom_SquarePlanar);
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
CHECK(sinfo[0].permutation == 1);
CHECK(sinfo[0].controllingAtoms == std::vector<unsigned int>{0, 2, 3, 4});
}
SECTION("TB") {
auto m = "C[Fe@TB4](F)(Cl)(O)N"_smiles;
REQUIRE(m);
auto sinfo = Chirality::findPotentialStereo(*m);
REQUIRE(sinfo.size() == 1);
CHECK(sinfo[0].centeredOn == 1);
CHECK(sinfo[0].type == Chirality::StereoType::Atom_TrigonalBipyramidal);
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
CHECK(sinfo[0].permutation == 4);
CHECK(sinfo[0].controllingAtoms ==
std::vector<unsigned int>{0, 2, 3, 4, 5});
}
SECTION("TB0") {
auto m = "C[Fe@TB](F)(Cl)(O)N"_smiles;
REQUIRE(m);
auto sinfo = Chirality::findPotentialStereo(*m);
REQUIRE(sinfo.size() == 1);
CHECK(sinfo[0].centeredOn == 1);
CHECK(sinfo[0].specified == Chirality::StereoSpecified::Unknown);
CHECK(sinfo[0].type == Chirality::StereoType::Atom_TrigonalBipyramidal);
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
CHECK(sinfo[0].permutation == 0);
CHECK(sinfo[0].controllingAtoms ==
std::vector<unsigned int>{0, 2, 3, 4, 5});
}
SECTION("perceived as possible") {
auto m = "C[Fe](F)(Cl)(O)N"_smiles;
REQUIRE(m);
auto sinfo = Chirality::findPotentialStereo(*m);
REQUIRE(sinfo.size() == 1);
CHECK(sinfo[0].centeredOn == 1);
CHECK(sinfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(sinfo[0].type == Chirality::StereoType::Atom_TrigonalBipyramidal);
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
CHECK(sinfo[0].permutation == 0);
CHECK(sinfo[0].controllingAtoms ==
std::vector<unsigned int>{0, 2, 3, 4, 5});
}
SECTION("OH") {
auto m = "C[Fe@OH9](F)(Cl)(O)(N)Br"_smiles;
REQUIRE(m);
auto sinfo = Chirality::findPotentialStereo(*m);
REQUIRE(sinfo.size() == 1);
CHECK(sinfo[0].centeredOn == 1);
CHECK(sinfo[0].type == Chirality::StereoType::Atom_Octahedral);
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
CHECK(sinfo[0].permutation == 9);
CHECK(sinfo[0].controllingAtoms ==
std::vector<unsigned int>{0, 2, 3, 4, 5, 6});
}
SECTION("OH missing ligand") {
auto m = "C[Fe@OH9](F)(Cl)(O)N"_smiles;
REQUIRE(m);
auto sinfo = Chirality::findPotentialStereo(*m);
REQUIRE(sinfo.size() == 1);
CHECK(sinfo[0].centeredOn == 1);
CHECK(sinfo[0].type == Chirality::StereoType::Atom_Octahedral);
CHECK(sinfo[0].descriptor == Chirality::StereoDescriptor::None);
CHECK(sinfo[0].permutation == 9);
CHECK(sinfo[0].controllingAtoms ==
std::vector<unsigned int>{0, 2, 3, 4, 5});
}
}
TEST_CASE("github #5328: assignChiralTypesFrom3D() ignores wiggly bonds") {
SECTION("basics") {
auto m = R"CTAB(
RDKit 3D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 0 0 0
M V30 BEGIN ATOM
M V30 1 C 0.900794 -0.086835 0.009340 0
M V30 2 C -0.552652 0.319534 0.077502 0
M V30 3 F -0.861497 0.413307 1.437370 0
M V30 4 Cl -0.784572 1.925710 -0.672698 0
M V30 5 O -1.402227 -0.583223 -0.509512 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 2 4 CFG=2
M V30 4 1 2 5
M V30 END BOND
M V30 END CTAB
M END)CTAB"_ctab;
REQUIRE(m);
MolOps::assignChiralTypesFrom3D(*m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
SECTION("non-tetrahedral") {
auto m = R"CTAB(
Mrv2108 05252216313D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 6 5 0 0 0
M V30 BEGIN ATOM
M V30 1 C -1.7191 0.2488 -3.5085 0
M V30 2 As -1.0558 1.9209 -2.6345 0
M V30 3 F -0.4636 3.422 -1.7567 0
M V30 4 O -2.808 2.4243 -2.1757 0
M V30 5 Cl -0.1145 2.6609 -4.5048 0
M V30 6 Br 0.2255 0.6458 -1.079 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 2 4
M V30 4 1 2 5 CFG=2
M V30 5 1 2 6
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
MolOps::assignChiralTypesFrom3D(*m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
TEST_CASE("useLegacyStereoPerception feature flag") {
UseLegacyStereoPerceptionFixture reset_stereo_perception;
SECTION("original failing example") {
Chirality::setUseLegacyStereoPerception(true);
auto m = "C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2"_smiles;
REQUIRE(m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
SECTION("use new code") {
Chirality::setUseLegacyStereoPerception(false);
auto m = "C[C@H]1CCC2(CC1)CC[C@H](C)C(C)C2"_smiles;
REQUIRE(m);
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(9)->getChiralTag() != Atom::CHI_UNSPECIFIED);
}
std::string molblock = R"CTAB(
Mrv2108 05202206352D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 15 0 0 0
M V30 BEGIN ATOM
M V30 1 C -4.5417 3.165 0 0
M V30 2 C -5.8753 2.395 0 0
M V30 3 C -5.8753 0.855 0 0
M V30 4 C -4.5417 0.085 0 0 CFG=1
M V30 5 C -3.208 0.855 0 0
M V30 6 C -3.208 2.395 0 0
M V30 7 C -4.5417 -1.455 0 0
M V30 8 C -1.8743 0.085 0 0
M V30 9 C -4.5417 6.2451 0 0 CFG=2
M V30 10 C -5.8753 5.4751 0 0
M V30 11 C -5.8753 3.9351 0 0
M V30 12 C -3.208 3.9351 0 0
M V30 13 C -3.208 5.4751 0 0
M V30 14 C -4.5417 7.7851 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 4 5
M V30 5 1 5 6
M V30 6 1 1 6
M V30 7 1 4 7 CFG=1
M V30 8 1 5 8
M V30 9 1 9 10
M V30 10 1 10 11
M V30 11 1 12 13
M V30 12 1 9 13
M V30 13 1 11 1
M V30 14 1 1 12
M V30 15 1 9 14 CFG=1
M V30 END BOND
M V30 END CTAB
M END
)CTAB";
SECTION("original example, from mol block") {
Chirality::setUseLegacyStereoPerception(true);
std::unique_ptr<RWMol> m{MolBlockToMol(molblock)};
CHECK(m->getAtomWithIdx(3)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(8)->getChiralTag() == Atom::CHI_UNSPECIFIED);
}
SECTION("original example, from mol block, new code") {
Chirality::setUseLegacyStereoPerception(false);
std::unique_ptr<RWMol> m{MolBlockToMol(molblock)};
CHECK(m->getAtomWithIdx(3)->getChiralTag() != Atom::CHI_UNSPECIFIED);
CHECK(m->getAtomWithIdx(8)->getChiralTag() == Atom::CHI_UNSPECIFIED);
}
}
TEST_CASE("wedgeMolBonds to aromatic rings") {
auto m = R"CTAB(
RDKit 2D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 10 11 0 0 0
M V30 BEGIN ATOM
M V30 1 C 2.948889 -2.986305 0.000000 0
M V30 2 C 2.560660 -4.435194 0.000000 0
M V30 3 N 1.111771 -4.046965 0.000000 0
M V30 4 C 1.500000 -2.598076 0.000000 0
M V30 5 C 0.750000 -1.299038 0.000000 0
M V30 6 C 1.500000 0.000000 0.000000 0
M V30 7 C 0.750000 1.299038 0.000000 0
M V30 8 C -0.750000 1.299038 0.000000 0
M V30 9 C -1.500000 0.000000 0.000000 0
M V30 10 C -0.750000 -1.299038 0.000000 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 2 3
M V30 3 1 3 4
M V30 4 1 4 5 CFG=1
M V30 5 2 5 6
M V30 6 1 6 7
M V30 7 2 7 8
M V30 8 1 8 9
M V30 9 2 9 10
M V30 10 1 4 1
M V30 11 1 10 5
M V30 END BOND
M V30 END CTAB
M END
)CTAB"_ctab;
REQUIRE(m);
CHECK(m->getAtomWithIdx(3)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
CHECK(m->getBondWithIdx(2)->getBondDir() == Bond::BondDir::NONE);
CHECK(m->getBondWithIdx(3)->getBondDir() == Bond::BondDir::NONE);
SECTION("generating mol blocks") {
auto mb = MolToV3KMolBlock(*m);
CHECK(mb.find("M V30 10 1 4 1 CFG=1") == std::string::npos);
CHECK(mb.find("M V30 4 1 4 5 CFG=1") != std::string::npos);
}
SECTION("details: pickBondsWedge()") {
// this is with aromatic bonds
auto bnds = pickBondsToWedge(*m);
CHECK(bnds.at(3) == 3);
RWMol cp(*m);
// now try kekulized:
MolOps::Kekulize(cp);
bnds = pickBondsToWedge(cp);
CHECK(bnds.at(3) == 3);
}
}
TEST_CASE("github 5307: AssignAtomChiralTagsFromStructure ignores Hydrogens") {
std::string mb = R"CTAB(
RDKit 3D
0 0 0 0 0 0 0 0 0 0999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 5 4 0 0 0
M V30 BEGIN ATOM
M V30 1 C -0.022097 0.003215 0.016520 0
M V30 2 H -0.669009 0.889360 -0.100909 0
M V30 3 H -0.377788 -0.857752 -0.588296 0
M V30 4 H 0.096421 -0.315125 1.063781 0
M V30 5 H 0.972473 0.280302 -0.391096 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 1 1 3
M V30 3 1 1 4
M V30 4 1 1 5
M V30 END BOND
M V30 END CTAB
M END
)CTAB";
bool sanitize = true;
bool removeHs = false;
std::unique_ptr<RWMol> m{MolBlockToMol(mb, sanitize, removeHs)};
REQUIRE(m);
MolOps::assignChiralTypesFrom3D(*m);
CHECK(m->getAtomWithIdx(0)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
// assignStereochemistryFrom3D() actually checks:
MolOps::assignStereochemistryFrom3D(*m);
CHECK(m->getAtomWithIdx(0)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
TEST_CASE(
"github 5403: Incorrect perception of pseudoasymmetric centers on "
"non-canonical molecules") {
SECTION("basics") {
auto mol1 = "N[C@@]12CC[C@@](CC1)(C2)C(F)F"_smiles;
REQUIRE(mol1);
bool clean = true;
auto stereoInfo1 = Chirality::findPotentialStereo(*mol1, clean);
REQUIRE(stereoInfo1.size() == 2);
REQUIRE(stereoInfo1[0].centeredOn == 1);
REQUIRE(stereoInfo1[1].centeredOn == 4);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
CHECK(mol1->getAtomWithIdx(4)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
auto mol2 = "C1C[C@]2(C(F)F)CC[C@@]1(N)C2"_smiles;
REQUIRE(mol2);
auto stereoInfo2 = Chirality::findPotentialStereo(*mol2, clean);
REQUIRE(stereoInfo2.size() == 2);
CHECK(stereoInfo2[0].centeredOn == 2);
CHECK(stereoInfo2[1].centeredOn == 8);
{
RWMol cp(*mol2);
Chirality::findPotentialStereo(cp, true, false);
CHECK(cp.getAtomWithIdx(2)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
CHECK(cp.getAtomWithIdx(8)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
SECTION("new stereo") {
UseLegacyStereoPerceptionFixture reset_stereo_perception;
Chirality::setUseLegacyStereoPerception(false);
auto mol1 = "N[C@@]12CC[C@@](CC1)(C2)C(F)F"_smiles;
REQUIRE(mol1);
CHECK(mol1->getAtomWithIdx(1)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
CHECK(mol1->getAtomWithIdx(4)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
TEST_CASE("assignStereochemistry sets bond stereo with new stereo perception") {
SECTION("basics") {
UseLegacyStereoPerceptionFixture reset_stereo_perception;
Chirality::setUseLegacyStereoPerception(false);
{
auto m = "C/C=C/C"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
}
{
auto m = "C/C=C\\C"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOCIS);
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
}
{
auto m = "C(/C)=C/C"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOCIS);
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{1, 3});
}
{
auto m = "FC(/C)=C/C"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(m->getBondWithIdx(2)->getStereoAtoms() == std::vector<int>{0, 4});
}
{
auto m = "FC(/C)=C(F)/C"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREOCIS);
CHECK(m->getBondWithIdx(2)->getStereoAtoms() == std::vector<int>{0, 4});
}
}
}
TEST_CASE("chiral duplicates") {
UseLegacyStereoPerceptionFixture reset_stereo_perception;
Chirality::setUseLegacyStereoPerception(false);
SECTION("atom basics") {
auto mol = "C[C@](F)([C@H](F)Cl)[C@H](F)Cl"_smiles;
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(3)->getChiralTag() ==
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
CHECK(mol->getAtomWithIdx(6)->getChiralTag() ==
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
CHECK(mol->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
SECTION("double bonds and atoms") {
auto mol = "C/C(O)=C([C@H](F)Cl)/[C@H](F)Cl"_smiles;
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(4)->getChiralTag() ==
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
CHECK(mol->getAtomWithIdx(7)->getChiralTag() ==
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREONONE);
}
SECTION("double bonds and atoms 2") {
auto mol = "C/C(O)=C([C@H](F)Cl)/[C@@H](F)Cl"_smiles;
REQUIRE(mol);
CHECK(mol->getAtomWithIdx(4)->getChiralTag() ==
Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
CHECK(mol->getAtomWithIdx(7)->getChiralTag() ==
Atom::ChiralType::CHI_TETRAHEDRAL_CW);
CHECK(mol->getBondWithIdx(2)->getStereo() != Bond::BondStereo::STEREONONE);
}
SECTION("double bonds and double bonds") {
auto mol = "C/C(O)=C(/C=C/C)/C=C/C"_smiles;
REQUIRE(mol);
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(mol->getBondWithIdx(7)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(mol->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREONONE);
}
SECTION("double bonds and double bonds 2") {
auto mol = "C/C(O)=C(/C=C/C)/C=C\\C"_smiles;
REQUIRE(mol);
CHECK(mol->getBondWithIdx(4)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(mol->getBondWithIdx(7)->getStereo() == Bond::BondStereo::STEREOCIS);
CHECK(mol->getBondWithIdx(2)->getStereo() != Bond::BondStereo::STEREONONE);
}
}
TEST_CASE("more findPotential") {
UseLegacyStereoPerceptionFixture reset_stereo_perception;
Chirality::setUseLegacyStereoPerception(false);
SECTION("basics") {
{
auto m = "O[C@H](C)CC(C)C[C@@H](C)O"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 2);
}
{
auto m = "O[C@H](C)CC(C)C[C@H](C)O"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
{
auto m = "O[CH](C)C[C@H](C)C[CH](C)O"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
{
auto m = "O[CH](C)C[CH](C)C[CH](C)O"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
}
SECTION("double bond impact on atoms") {
{
auto m = "C[CH](/C=C/C)/C=C\\C"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
{
auto m = "C[CH](/C=C/C)/C=C/C"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 2);
}
{
auto m = "C[CH](C=CC)C=CC"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
{
auto m = "C[CH](C=CC)C=CC"_smiles;
REQUIRE(m);
m->getBondWithIdx(2)->setStereo(Bond::BondStereo::STEREOANY);
m->getBondWithIdx(5)->setStereo(Bond::BondStereo::STEREOANY);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
}
SECTION("atom impact on double bonds") {
{
auto m = "CC=C([C@H](F)Cl)[C@@H](F)Cl"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
{
auto m = "CC=C([C@H](F)Cl)[C@H](F)Cl"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 2);
}
{
auto m = "CC=C([CH](F)Cl)[CH](F)Cl"_smiles;
REQUIRE(m);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
{
auto m = "CC=C([CH](F)Cl)[CH](F)Cl"_smiles;
REQUIRE(m);
m->getBondBetweenAtoms(2, 3)->setBondDir(Bond::UNKNOWN);
m->getBondBetweenAtoms(2, 6)->setBondDir(Bond::UNKNOWN);
auto si = Chirality::findPotentialStereo(*m, true, true);
CHECK(si.size() == 3);
}
}
}
TEST_CASE("more findPotential and ring stereo") {
UseLegacyStereoPerceptionFixture reset_stereo_perception;
Chirality::setUseLegacyStereoPerception(false);
SECTION("simple") {
{
auto m = "CC1CCC(C)CC1"_smiles;
REQUIRE(m);
auto stereoInfo = Chirality::findPotentialStereo(*m, true, true);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].centeredOn == 1);
CHECK(stereoInfo[0].specified == Chirality::StereoSpecified::Unspecified);
CHECK(stereoInfo[1].type == Chirality::StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[1].centeredOn == 4);
CHECK(stereoInfo[1].specified == Chirality::StereoSpecified::Unspecified);
}
}
}
TEST_CASE(
"github 2984: RDKit misplaces stereochemistry/chirality information for "
"small ring") {
using namespace RDKit::Chirality;
UseLegacyStereoPerceptionFixture reset_stereo_perception;
SECTION("The mol with the issue") {
for (auto use_legacy : {false, true}) {
Chirality::setUseLegacyStereoPerception(use_legacy);
// With Legacy stereo, parsing the SMILES string will discard the
// problematic stereo features, so findPotentialStereo (which uses
// the new algorithm) will still find them, but they will be unspecified.
// Parsing with the new algorithm will preserve the features, so they
// can be correctly resolved.
auto specified_status = use_legacy ? StereoSpecified::Unspecified
: StereoSpecified::Specified;
auto mol = R"SMI(CC/C=C1\C[C@H](O)C1)SMI"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].centeredOn == 5);
CHECK(stereoInfo[0].type == StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].specified == specified_status);
CHECK(stereoInfo[1].centeredOn == 2);
CHECK(stereoInfo[1].type == StereoType::Bond_Double);
CHECK(stereoInfo[1].specified == specified_status);
}
}
// The other sections should yield the same results independently
// of which stereo algoritm is used, new or legacy
SECTION("Unspecified, but still potentially stereo") {
for (auto use_legacy : {false, true}) {
Chirality::setUseLegacyStereoPerception(use_legacy);
auto mol = R"SMI(CCC=C1CC(O)C1)SMI"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].centeredOn == 5);
CHECK(stereoInfo[0].type == StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].specified == StereoSpecified::Unspecified);
CHECK(stereoInfo[1].centeredOn == 2);
CHECK(stereoInfo[1].type == StereoType::Bond_Double);
CHECK(stereoInfo[1].specified == StereoSpecified::Unspecified);
}
}
SECTION("Specified") {
for (auto use_legacy : {false, true}) {
Chirality::setUseLegacyStereoPerception(use_legacy);
auto mol = R"SMI(CC/C=C1\CC[C@H]1O)SMI"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
REQUIRE(stereoInfo.size() == 2);
CHECK(stereoInfo[0].centeredOn == 6);
CHECK(stereoInfo[0].type == StereoType::Atom_Tetrahedral);
CHECK(stereoInfo[0].specified == StereoSpecified::Specified);
CHECK(stereoInfo[1].centeredOn == 2);
CHECK(stereoInfo[1].type == StereoType::Bond_Double);
CHECK(stereoInfo[1].specified == StereoSpecified::Specified);
}
}
SECTION("Stereo not possible") {
for (auto use_legacy : {false, true}) {
Chirality::setUseLegacyStereoPerception(use_legacy);
auto mol = R"SMI(CCC=C1CC(O)(O)C1)SMI"_smiles;
REQUIRE(mol);
auto stereoInfo = Chirality::findPotentialStereo(*mol);
CHECK(stereoInfo.empty());
}
}
}
TEST_CASE("double bond stereo with new chirality perception") {
UseLegacyStereoPerceptionFixture reset_stereo_perception;
Chirality::setUseLegacyStereoPerception(false);
SECTION("chain bonds") {
{
auto m = "C/C=C/C"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
}
{
SmilesParserParams ps;
ps.useLegacyStereo = false;
std::unique_ptr<RWMol> m{SmilesToMol("C/C=C/C", ps)};
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
}
}
SECTION("ring bonds") {
{
auto m = "C1/C=C/CCCCCCC1"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
}
{
SmilesParserParams ps;
ps.useLegacyStereo = false;
std::unique_ptr<RWMol> m{SmilesToMol("C1/C=C/CCCCCCC1", ps)};
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOTRANS);
CHECK(m->getBondWithIdx(1)->getStereoAtoms() == std::vector<int>{0, 3});
}
}
}
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