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//
// Copyright (C) 2025 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 <string>
#include "RDGeneral/test.h"
#include <catch2/catch_all.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/test_fixtures.h>
using namespace RDKit;
TEST_CASE("explicit tests") {
// making some of the other atropisomer tests explicitly test what we expect
std::string rdbase = getenv("RDBASE");
REQUIRE(rdbase != "");
SECTION("basics") {
std::string file =
rdbase +
"/Code/GraphMol/FileParsers/test_data/atropisomers/AtropManyChirals.sdf";
auto mol = v2::FileParsers::MolFromMolFile(file);
REQUIRE(mol);
CHECK(mol->getBondWithIdx(7)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW);
}
SECTION("macrocycle") {
std::string file =
rdbase +
"/Code/GraphMol/FileParsers/test_data/atropisomers/macrocycle-5-meta-Cl-ortho-hash.sdf";
auto mol = v2::FileParsers::MolFromMolFile(file);
REQUIRE(mol);
CHECK(mol->getBondWithIdx(15)->getStereo() ==
Bond::BondStereo::STEREOATROPCW);
}
SECTION("with stereo groups and other chiral centers") {
REQUIRE(rdbase != "");
std::string file =
rdbase +
"/Code/GraphMol/FileParsers/test_data/atropisomers/AtropManyChiralsEnhanced.sdf";
auto mol = v2::FileParsers::MolFromMolFile(file);
REQUIRE(mol);
CHECK(mol->getBondWithIdx(7)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW);
CHECK(mol->getAtomWithIdx(6)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
CHECK(mol->getAtomWithIdx(9)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
CHECK(mol->getAtomWithIdx(13)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
CHECK(mol->getAtomWithIdx(16)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
CHECK(mol->getAtomWithIdx(10)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
REQUIRE(mol->getStereoGroups().size() == 2);
{
const auto &sg = mol->getStereoGroups()[0];
CHECK(sg.getAtoms().size() == 2);
CHECK(sg.getBonds().size() == 1);
}
{
const auto &sg = mol->getStereoGroups()[1];
CHECK(sg.getAtoms().size() == 2);
CHECK(sg.getBonds().size() == 0);
}
}
}
TEST_CASE("atropisomerism and dependent chirality") {
SECTION("chirality allows stereoisomers") {
{
auto m = "C=C(C)C1=CC([C@H](C)O)=CC([C@@H](C)O)=C1 |wD:3.14|"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(2)->getStereo() ==
Bond::BondStereo::STEREOATROPCW);
}
#if 0
// FIX: this test does not work, this is Github #8340
{
// the two stereocenters are identical, we should not have atropisomerism
auto m = "C=C(C)C1=CC([C@H](C)O)=CC([C@H](C)O)=C1 |wD:3.14|"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(2)->getStereo() == Bond::BondStereo::STEREONONE);
}
#endif
}
SECTION("atropisomers allow chirality") {
#if 0
// FIX: this test does not work
{
// here the atropisomeric bonds have opposite stereochemistry, so the
// central atom should be chiral, this is Github #8341
auto m =
"C=C(C1C=C(C)C=CC=1)[C@H](C)C(=C)C1C=C(C)C=CC=1 |wD:2.2,wD:13.14|"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW);
CHECK(m->getBondWithIdx(12)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW);
CHECK(m->getAtomWithIdx(9)->getChiralTag() !=
Atom::ChiralType::CHI_UNSPECIFIED);
}
#endif
{
// here the atropisomeric bonds have the same stereochemistry, so the
// central atom should not be chiral
auto m =
"C=C(C1C=C(C)C=CC=1)[C@H](C)C(=C)C1C=C(C)C=CC=1 |wD:2.2,wU:13.14|"_smiles;
REQUIRE(m);
CHECK(m->getBondWithIdx(1)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW);
CHECK(m->getBondWithIdx(12)->getStereo() ==
Bond::BondStereo::STEREOATROPCW);
CHECK(m->getAtomWithIdx(9)->getChiralTag() ==
Atom::ChiralType::CHI_UNSPECIFIED);
}
}
}
TEST_CASE("Github #8602: atropisomer with slight z coordinates") {
std::string rdbase = getenv("RDBASE");
rdbase += "/Code/GraphMol/FileParsers/test_data/atropisomers/";
SECTION("as reported") {
auto m = v2::FileParsers::MolFromMolFile(rdbase + "atropWith3d_8602.mol");
REQUIRE(m);
for (auto bond : m->bonds()) {
// we read in the molecule, but the bonds should be co-planar
// in the current implementation, where 2D mol in 3D does not
// fall back to a 2D bond explicit annotation check
CHECK(bond->getStereo() != Bond::BondStereo::STEREOATROPCW);
CHECK(bond->getStereo() != Bond::BondStereo::STEREOATROPCCW);
}
}
SECTION("x axis is Z axis") {
auto m =
v2::FileParsers::MolFromMolFile(rdbase + "atropWith3d_8602_allZ.mol");
REQUIRE(m);
for (auto bond : m->bonds()) {
// we read in the molecule, but the bonds should be co-planar
// in the current implementation, where 2D mol in 3D does not
// fall back to a 2D bond explicit annotation check
CHECK(bond->getStereo() != Bond::BondStereo::STEREOATROPCW);
CHECK(bond->getStereo() != Bond::BondStereo::STEREOATROPCCW);
}
}
}
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