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00a9dc49f7de5e69199526d16ef242e5001e72c4
rdkit/Code/GraphMol/DistGeomHelpers/catch_tests.cpp
Greg Landrum 00a9dc49f7 Fixes #8559 (#8560) 
* Fixes #8559

Also includes some minor refactoring of set14Bounds()

* apply the same change to the cis/trans trackers

* cleanup

---------

Co-authored-by: = <=>
2025-06-06 15:30:07 +02:00

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//
// Copyright (C) 2021-2024 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 <RDGeneral/test.h>
#include <catch2/catch_all.hpp>
#include <RDGeneral/RDLog.h>
#include <GraphMol/test_fixtures.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Atropisomers.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h>
#include <GraphMol/MolAlign/AlignMolecules.h>
#include "Embedder.h"
#include "BoundsMatrixBuilder.h"
#include <tuple>
#include <boost/algorithm/string.hpp>
#include <boost/algorithm/string/trim.hpp>
#ifdef RDK_TEST_MULTITHREADED
#include <csignal>
#include <thread>
#include <chrono>
#endif
using namespace RDKit;
TEST_CASE("Torsions not found in fused macrocycles", "[macrocycles]") {
RDLog::InitLogs();
SECTION("reported") {
// this is 6VY8 from the PDB
auto mol1 =
"CC[C@H](C)[C@@H]1NC(=O)[C@@H]2CCCN2C(=O)[C@@H]2CCCN2C(=O)[C@H]([C@@H](C)CC)NC(=O)[C@H](CO)NC(=O)[C@H](CCCC[NH3+])NC(=O)[C@H]([C@@H](C)O)NC(O)[C@@H]2CN3NNC[C@H]3C[C@H](NC1=O)C(O)N[C@@H](Cc1ccccc1)C(=O)N1CCC[C@H]1C(=O)N[C@@H](CC(=O)O)C(=O)NCC(=O)N[C@@H](CCCNC(N)=[NH2+])C(=O)N2"_smiles;
REQUIRE(mol1);
MolOps::addHs(*mol1);
ForceFields::CrystalFF::CrystalFFDetails details;
bool useExpTorsions = true;
bool useSmallRingTorsions = false;
bool useMacrocycleTorsions = true;
bool useBasicKnowledge = true;
unsigned int version = 2;
bool verbose = true;
std::stringstream sstrm;
rdInfoLog->SetTee(sstrm);
ForceFields::CrystalFF::getExperimentalTorsions(
*mol1, details, useExpTorsions, useSmallRingTorsions,
useMacrocycleTorsions, useBasicKnowledge, version, verbose);
rdInfoLog->ClearTee();
auto txt = sstrm.str();
CHECK(txt.find("{9-}") != std::string::npos);
}
SECTION("edges") {
std::vector<std::tuple<std::string, bool, unsigned int>> tests{
{"O=C1CNC(=O)C2CCC(N1)NC(=O)CNC2=O", true, 15}, // 9-9
{"O=C1NC2CCC(C(=O)N1)C(=O)NCC(=O)N2", true, 4}, // 9-8
{"O=C1NC2CCC(C(=O)N1)C(=O)NC(=O)N2", false, 0}, // 8-8
{"O=C1CC(=O)NC2NC(=O)CC(=O)NC(N1)NC(=O)CC(=O)N2", true,
18}}; // 12-12-12
for (const auto &tpl : tests) {
std::unique_ptr<RWMol> m{SmilesToMol(std::get<0>(tpl))};
REQUIRE(m);
MolOps::addHs(*m);
ForceFields::CrystalFF::CrystalFFDetails details;
bool useExpTorsions = true;
bool useSmallRingTorsions = false;
bool useMacrocycleTorsions = true;
bool useBasicKnowledge = true;
unsigned int version = 2;
bool verbose = true;
std::stringstream sstrm;
rdInfoLog->SetTee(sstrm);
std::cerr << "-----------" << std::endl;
ForceFields::CrystalFF::getExperimentalTorsions(
*m, details, useExpTorsions, useSmallRingTorsions,
useMacrocycleTorsions, useBasicKnowledge, version, verbose);
rdInfoLog->ClearTee();
auto txt = sstrm.str();
if (std::get<1>(tpl)) {
CHECK(txt.find("{9-}") != std::string::npos);
} else {
CHECK(txt.find("{9-}") == std::string::npos);
}
CHECK(details.expTorsionAngles.size() == std::get<2>(tpl));
}
}
}
namespace {
void compareConfs(const ROMol *m, const ROMol *expected, int molConfId = -1,
int expectedConfId = -1) {
PRECONDITION(m, "bad pointer");
PRECONDITION(expected, "bad pointer");
TEST_ASSERT(m->getNumAtoms() == expected->getNumAtoms());
const Conformer &conf1 = m->getConformer(molConfId);
const Conformer &conf2 = expected->getConformer(expectedConfId);
for (unsigned int i = 0; i < m->getNumAtoms(); i++) {
TEST_ASSERT(m->getAtomWithIdx(i)->getAtomicNum() ==
expected->getAtomWithIdx(i)->getAtomicNum());
RDGeom::Point3D pt1i = conf1.getAtomPos(i);
RDGeom::Point3D pt2i = conf2.getAtomPos(i);
TEST_ASSERT((pt1i - pt2i).length() < 0.05);
}
}
} // namespace
TEST_CASE("update parameters from JSON") {
std::string rdbase = getenv("RDBASE");
SECTION("DG") {
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.dg.mol";
std::unique_ptr<RWMol> ref{MolFileToMol(fname, true, false)};
REQUIRE(ref);
std::unique_ptr<RWMol> mol{SmilesToMol("OCCC")};
REQUIRE(mol);
MolOps::addHs(*mol);
CHECK(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params;
std::string json = R"JSON({"randomSeed":42})JSON";
DGeomHelpers::updateEmbedParametersFromJSON(params, json);
CHECK(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
compareConfs(ref.get(), mol.get());
}
SECTION("ETKDG") {
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/simple_torsion.etkdg.mol";
std::unique_ptr<RWMol> ref{MolFileToMol(fname, true, false)};
REQUIRE(ref);
std::unique_ptr<RWMol> mol{SmilesToMol("OCCC")};
REQUIRE(mol);
MolOps::addHs(*mol);
CHECK(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params;
std::string json = R"JSON({"randomSeed":42,
"useExpTorsionAnglePrefs":true,
"useBasicKnowledge":true})JSON";
DGeomHelpers::updateEmbedParametersFromJSON(params, json);
CHECK(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
compareConfs(ref.get(), mol.get());
}
SECTION("ETKDGv2") {
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/torsion.etkdg.v2.mol";
std::unique_ptr<RWMol> ref{MolFileToMol(fname, true, false)};
REQUIRE(ref);
std::unique_ptr<RWMol> mol{SmilesToMol("n1cccc(C)c1ON")};
REQUIRE(mol);
MolOps::addHs(*mol);
CHECK(ref->getNumAtoms() == mol->getNumAtoms());
DGeomHelpers::EmbedParameters params;
std::string json = R"JSON({"randomSeed":42,
"useExpTorsionAnglePrefs":true,
"useBasicKnowledge":true,
"ETversion":2})JSON";
DGeomHelpers::updateEmbedParametersFromJSON(params, json);
CHECK(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
compareConfs(ref.get(), mol.get());
}
SECTION("setting atommap") {
std::unique_ptr<RWMol> mol{SmilesToMol("OCCC")};
REQUIRE(mol);
MolOps::addHs(*mol);
{
DGeomHelpers::EmbedParameters params;
std::string json = R"JSON({"randomSeed":42,
"coordMap":{"0":[0,0,0],"1":[0,0,1.5],"2":[0,1.5,1.5]}})JSON";
DGeomHelpers::updateEmbedParametersFromJSON(params, json);
CHECK(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
delete params.coordMap;
auto conf = mol->getConformer();
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(1);
auto v2 = conf.getAtomPos(2) - conf.getAtomPos(1);
CHECK(v1.angleTo(v2) == Catch::Approx(M_PI / 2).margin(0.15));
}
}
}
TEST_CASE(
"github #4346: Specified cis/trans stereo being ignored during "
"conformation generation in macrocycles") {
auto useLegacy = GENERATE(true, false);
UseLegacyStereoPerceptionFixture fx(useLegacy);
CAPTURE(useLegacy);
SECTION("basics 1") {
auto m1 = "C1C/C=C/CCCCCCCC1"_smiles;
REQUIRE(m1);
if (useLegacy) {
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
Bond::BondStereo::STEREOE);
} else {
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
Bond::BondStereo::STEREOTRANS);
}
MolOps::addHs(*m1);
DGeomHelpers::EmbedParameters params = DGeomHelpers::KDG;
params.randomSeed = 0xf00d;
CHECK(DGeomHelpers::EmbedMolecule(*m1, params) != -1);
MolOps::assignStereochemistryFrom3D(*m1);
if (useLegacy) {
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
Bond::BondStereo::STEREOE);
} else {
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
Bond::BondStereo::STEREOTRANS);
}
}
SECTION("basics 2") {
auto m1 = "C1C/C=C\\CCCCCCCC1"_smiles;
REQUIRE(m1);
if (useLegacy) {
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
Bond::BondStereo::STEREOZ);
} else {
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
Bond::BondStereo::STEREOCIS);
}
MolOps::addHs(*m1);
DGeomHelpers::EmbedParameters params = DGeomHelpers::KDG;
params.randomSeed = 0xf00d;
CHECK(DGeomHelpers::EmbedMolecule(*m1, params) != -1);
MolOps::assignStereochemistryFrom3D(*m1);
if (useLegacy) {
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
Bond::BondStereo::STEREOZ);
} else {
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
Bond::BondStereo::STEREOCIS);
}
}
}
TEST_CASE("nontetrahedral stereo", "[nontetrahedral]") {
SECTION("bounds matrix basics") {
{
auto m = "Cl[Pt@SP1]([35Cl])([36Cl])[37Cl]"_smiles;
REQUIRE(m);
CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(0))
->getIdx() == 3);
CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(2))
->getIdx() == 4);
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(180, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(90, 0.001));
DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(m->getNumAtoms())};
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*m, bm);
// std::cerr << *bm << std::endl;
CHECK(bm->getLowerBound(0, 3) - bm->getLowerBound(0, 2) > 1.0);
CHECK(bm->getUpperBound(0, 3) - bm->getUpperBound(0, 2) > 1.0);
}
{
// Cl[Pt@SP1]([35Cl])([36Cl])* => Cl[Pt@SP3](*)([35Cl])[36Cl]
auto m = "Cl[Pt@SP3]([35Cl])[36Cl]"_smiles;
REQUIRE(m);
CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(0))
->getIdx() == 3);
CHECK(!Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(2)));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(3)),
Catch::Matchers::WithinAbs(180, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(90, 0.001));
DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(m->getNumAtoms())};
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*m, bm);
// std::cerr << *bm << std::endl;
CHECK(bm->getLowerBound(0, 3) - bm->getLowerBound(0, 2) > 1.0);
CHECK(bm->getUpperBound(0, 3) - bm->getUpperBound(0, 2) > 1.0);
}
{
// note that things aren't quite as nice here since we don't actually have
// TBP UFF parameters
auto m = "Cl[Pt@TB1]([35Cl])([36Cl])([37Cl])[38Cl]"_smiles;
REQUIRE(m);
CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(0))
->getIdx() == 5);
CHECK(!Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(2)));
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(0), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(90, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(3), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(120, 0.001));
DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(m->getNumAtoms())};
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*m, bm);
CHECK(bm->getLowerBound(0, 5) - bm->getLowerBound(0, 2) > 0.5);
CHECK(bm->getUpperBound(0, 5) - bm->getUpperBound(0, 2) > 0.5);
CHECK(bm->getLowerBound(0, 5) - bm->getLowerBound(2, 3) > 0.5);
CHECK(bm->getUpperBound(0, 5) - bm->getUpperBound(2, 3) > 0.5);
CHECK(bm->getLowerBound(2, 3) - bm->getLowerBound(0, 2) > 0.5);
CHECK(bm->getUpperBound(2, 3) - bm->getUpperBound(0, 2) > 0.5);
}
{
auto m = "Cl[Th@OH1]([35Cl])([36Cl])([37Cl])([38Cl])[39Cl]"_smiles;
REQUIRE(m);
CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(0))
->getIdx() == 6);
CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(2))
->getIdx() == 4);
CHECK(Chirality::getChiralAcrossAtom(m->getAtomWithIdx(1),
m->getAtomWithIdx(3))
->getIdx() == 5);
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(0), m->getAtomWithIdx(6)),
Catch::Matchers::WithinAbs(180, 0.001));
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(4), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(180, 0.001));
CHECK_THAT(
Chirality::getIdealAngleBetweenLigands(
m->getAtomWithIdx(1), m->getAtomWithIdx(3), m->getAtomWithIdx(2)),
Catch::Matchers::WithinAbs(90, 0.001));
DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(m->getNumAtoms())};
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*m, bm);
CHECK(bm->getLowerBound(0, 6) - bm->getLowerBound(0, 2) > 0.5);
CHECK(bm->getUpperBound(0, 6) - bm->getUpperBound(0, 3) > 0.5);
CHECK(bm->getLowerBound(0, 6) - bm->getLowerBound(2, 3) > 0.5);
CHECK(bm->getUpperBound(0, 6) - bm->getUpperBound(2, 4) < 0.01);
CHECK(bm->getLowerBound(2, 4) - bm->getLowerBound(2, 3) > 0.5);
}
}
#if 1
SECTION("Embedding") {
{
auto m = "Cl[Pt@SP1](<-N)(<-N)[Cl]"_smiles;
REQUIRE(m);
m->setProp("_Name", "cis platin");
MolOps::addHs(*m);
CHECK(DGeomHelpers::EmbedMolecule(*m) == 0);
auto mb = MolToV3KMolBlock(*m);
// std::cerr << mb << std::endl;
std::unique_ptr<RWMol> m2(MolBlockToMol(mb));
MolOps::assignStereochemistryFrom3D(*m2);
CHECK(m2->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_SQUAREPLANAR);
unsigned int perm = 100;
CHECK(m2->getAtomWithIdx(1)->getPropIfPresent(
common_properties::_chiralPermutation, perm));
CHECK(perm == 1);
}
{
auto m = "Cl[Pt@SP3](<-N)(<-N)[Cl]"_smiles;
REQUIRE(m);
m->setProp("_Name", "trans platin");
MolOps::addHs(*m);
CHECK(DGeomHelpers::EmbedMolecule(*m) == 0);
auto mb = MolToV3KMolBlock(*m);
// std::cerr << mb << std::endl;
std::unique_ptr<RWMol> m2(MolBlockToMol(mb));
MolOps::assignStereochemistryFrom3D(*m2);
CHECK(m2->getAtomWithIdx(1)->getChiralTag() ==
Atom::ChiralType::CHI_SQUAREPLANAR);
unsigned int perm = 100;
CHECK(m2->getAtomWithIdx(1)->getPropIfPresent(
common_properties::_chiralPermutation, perm));
CHECK(perm == 3);
}
}
#endif
}
TEST_CASE("problems with bounds matrix smoothing and aromatic sulfur") {
SECTION("basics") {
auto core = R"CTAB(test structure - renumbered
RDKit 3D
7 7 0 0 0 0 0 0 0 0999 V2000
48.6842 -14.8137 0.1450 C 0 0 0 0 0 0 0 0 0 0 0 0
48.0829 -13.5569 0.6868 C 0 0 0 0 0 0 0 0 0 0 0 0
48.0162 -12.0909 -0.1327 S 0 0 0 0 0 0 0 0 0 0 0 0
47.1565 -11.3203 1.0899 C 0 0 0 0 0 0 0 0 0 0 0 0
46.9350 -12.2470 2.1088 C 0 0 0 0 0 0 0 0 0 0 0 0
46.1942 -11.9293 3.3432 C 0 0 0 0 0 0 0 0 0 0 0 0
47.4440 -13.4879 1.8745 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 7 2 0
2 3 1 0
7 5 1 0
5 4 2 0
5 6 1 0
4 3 1 0
M END)CTAB"_ctab;
REQUIRE(core);
auto thiaz = "Cc1scc(C)n1"_smiles;
REQUIRE(thiaz);
MolOps::addHs(*thiaz);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
const auto conf = core->getConformer();
std::map<int, RDGeom::Point3D> cmap;
for (unsigned i = 0; i < core->getNumAtoms(); ++i) {
cmap[i] = conf.getAtomPos(i);
}
ps.coordMap = &cmap;
ps.randomSeed = 0xf00d;
auto cid = DGeomHelpers::EmbedMolecule(*thiaz, ps);
CHECK(cid >= 0);
}
SECTION("bulk") {
// run a bunch of molecules with S-containing aromatic heterocycles
std::vector<std::string> smileses = {
"[O-][S+](c1ccccn1)c1cncs1",
"Cn1cccc1C(=O)Nc1nccs1",
"Cc1csc(=N)n1-c1ccc(Cl)cc1",
"Nc1ncc([S+]([O-])c2ncccn2)s1",
"CCCN1CCC=C(c2csc(N)n2)C1",
"CNc1ncc([S+]([O-])c2ccccn2)s1",
"Cn1nnnc1SCc1nc2ccccc2s1",
"CCCC(C(=O)Nc1nccs1)c1ccccc1",
"Cc1ccc(NC(=O)c2sc(Cl)nc2C)c(C)c1",
"CCc1nc(-c2ccc(Cl)cc2)sc1C(=O)OC",
"Cc1nc(CNS(=O)(=O)c2ccc(Cl)cc2)cs1",
"Cc1ccc2sc(C)[n+](CCC(C)S(=O)(=O)[O-])c2c1",
"Nc1nc2c(s1)-c1ccccc1Sc1ccccc1-2",
"COc1ccccc1OCC(=O)Nc1nc(C)c(C)s1",
"COc1ccc(NC(=O)Nc2sc(=S)n(C)c2C)cc1",
"C=CCNc1nc(-c2c[nH]c3c(CC)cccc23)cs1",
};
auto patt = "[s]1*c[!#6]c1"_smarts;
REQUIRE(patt);
for (const auto &smi : smileses) {
INFO(smi);
std::unique_ptr<RWMol> mol{SmilesToMol(smi)};
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
REQUIRE(cid >= 0);
UFF::UFFOptimizeMolecule(*mol);
auto match = SubstructMatch(*mol, *patt);
REQUIRE(match.size() >= 1);
const auto conf = mol->getConformer();
std::map<int, RDGeom::Point3D> cmap;
for (auto &mi : match[0]) {
cmap[mi.second] = conf.getAtomPos(mi.second);
}
ps.coordMap = &cmap;
auto cid2 = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid2 >= 0);
}
}
SECTION("phosphorous") {
std::vector<std::string> smileses = {
"CCOC(=O)c1pc(P(Cl)Cl)c2n1[C@@H](C)C(=O)Nc1ccc(C)cc1-2",
"N(c1c(O)ccc2c(P(Cl)Cl)pc(C(=O)O)n12)[N+](=O)[O-]",
};
auto patt = "[p]1*c[!#6]c1"_smarts;
REQUIRE(patt);
for (const auto &smi : smileses) {
INFO(smi);
std::unique_ptr<RWMol> mol{SmilesToMol(smi)};
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
REQUIRE(cid >= 0);
UFF::UFFOptimizeMolecule(*mol);
auto match = SubstructMatch(*mol, *patt);
REQUIRE(match.size() >= 1);
const auto conf = mol->getConformer();
std::map<int, RDGeom::Point3D> cmap;
for (auto &mi : match[0]) {
cmap[mi.second] = conf.getAtomPos(mi.second);
}
ps.coordMap = &cmap;
auto cid2 = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid2 >= 0);
}
}
}
TEST_CASE("double bond stereo not honored in conformer generator") {
SECTION("mol 1 basics") {
// this test used to fail
// from the platinum set
auto m = "O=C1OCC/C=C/CC/C=C/C(=N/OCC(=O)N2CCCCC2)Cc2cc(O)cc(O)c21"_smiles;
REQUIRE(m);
RWMol cp(*m);
MolOps::addHs(cp);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d + 81;
auto cid = DGeomHelpers::EmbedMolecule(cp, ps);
REQUIRE(cid >= 0);
MolOps::assignStereochemistryFrom3D(cp);
// std::cerr << MolToMolBlock(cp) << std::endl;
for (const auto bnd : cp.bonds()) {
if (bnd->getBondType() == Bond::BondType::DOUBLE) {
INFO(bnd->getIdx());
CHECK(bnd->getStereo() ==
m->getBondWithIdx(bnd->getIdx())->getStereo());
}
}
}
SECTION("mol 1 multiple loops") {
// from the platinum set
auto m = "O=C1OCC/C=C/CC/C=C/C(=N/OCC(=O)N2CCCCC2)Cc2cc(O)cc(O)c21"_smiles;
REQUIRE(m);
RWMol cp(*m);
MolOps::addHs(cp);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
for (unsigned int iter = 0; iter < 10; ++iter) {
RWMol lcp(cp);
ps.randomSeed = 0xf00d + iter;
auto cid = DGeomHelpers::EmbedMolecule(lcp, ps);
REQUIRE(cid >= 0);
MolOps::assignStereochemistryFrom3D(lcp);
// std::cerr << MolToMolBlock(cp) << std::endl;
for (const auto bnd : lcp.bonds()) {
if (bnd->getBondType() == Bond::BondType::DOUBLE) {
INFO(iter);
CHECK(bnd->getStereo() ==
m->getBondWithIdx(bnd->getIdx())->getStereo());
}
}
}
}
SECTION("github #5913") {
auto m = "[H]/C(F)=C([H])\\C([H])=C(/[H])Br"_smiles;
REQUIRE(m);
RWMol cp(*m);
MolOps::addHs(cp);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
for (unsigned int iter = 0; iter < 50; ++iter) {
RWMol lcp(cp);
ps.randomSeed = 0 + iter;
auto cid = DGeomHelpers::EmbedMolecule(lcp, ps);
REQUIRE(cid >= 0);
MolOps::assignStereochemistryFrom3D(lcp);
// std::cerr << MolToMolBlock(cp) << std::endl;
for (const auto bnd : lcp.bonds()) {
if (bnd->getBondType() == Bond::BondType::DOUBLE) {
INFO(iter);
CHECK(bnd->getStereo() ==
m->getBondWithIdx(bnd->getIdx())->getStereo());
}
}
}
}
SECTION("github #5283") {
UseLegacyStereoPerceptionFixture useLegacy(false);
auto m =
"Cc3nn(CC(=O)N2CCN(c1ccccc1)CC2)c(C)c3/N=N\\c6ccc(CNC(=O)CCC(=O)Nc4cccc5C(=O)NCc45)cc6"_smiles;
REQUIRE(m);
RWMol cp(*m);
MolOps::addHs(cp);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.enforceChirality = false;
for (unsigned int iter = 0; iter < 10; ++iter) {
INFO(iter);
RWMol lcp(cp);
ps.randomSeed = 140 + iter;
auto cid = DGeomHelpers::EmbedMolecule(lcp, ps);
REQUIRE(cid >= 0);
MolOps::assignStereochemistryFrom3D(lcp, cid, true);
auto bnd = lcp.getBondBetweenAtoms(22, 23);
REQUIRE(bnd);
REQUIRE(bnd->getBondType() == Bond::BondType::DOUBLE);
CHECK(bnd->getStereo() == m->getBondWithIdx(bnd->getIdx())->getStereo());
}
}
}
TEST_CASE("tracking failure causes") {
SECTION("basics") {
auto mol =
"C=CC1=C(N)Oc2cc1c(-c1cc(C(C)O)cc(=O)cc1C1NCC(=O)N1)c(OC)c2OC"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.trackFailures = true;
ps.maxIterations = 50;
ps.randomSeed = 42;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid < 0);
CHECK(ps.failures[DGeomHelpers::EmbedFailureCauses::INITIAL_COORDS] > 5);
CHECK(ps.failures[DGeomHelpers::EmbedFailureCauses::ETK_MINIMIZATION] > 10);
auto fail_cp = ps.failures;
// make sure we reset the counts each time
cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(ps.failures == fail_cp);
}
SECTION("chirality") {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase +
"/Code/GraphMol/DistGeomHelpers/test_data/chirality_failure_test.mol";
std::unique_ptr<RWMol> mol{MolFileToMol(fname, true, false)};
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
ps.trackFailures = true;
ps.maxIterations = 50;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid < 0);
CHECK(ps.failures[DGeomHelpers::EmbedFailureCauses::INITIAL_COORDS] > 5);
CHECK(ps.failures[DGeomHelpers::EmbedFailureCauses::FINAL_CHIRAL_BOUNDS] >=
4);
}
#ifdef RDK_TEST_MULTITHREADED
SECTION("multithreaded") {
auto mol =
"C=CC1=C(N)Oc2cc1c(-c1cc(C(C)O)cc(=O)cc1C1NCC(=O)N1)c(OC)c2OC"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.trackFailures = true;
ps.maxIterations = 10;
ps.randomSeed = 42;
auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, 20, ps);
DGeomHelpers::EmbedParameters ps2 = ps;
ps2.numThreads = 4;
auto cids2 = DGeomHelpers::EmbedMultipleConfs(*mol, 20, ps2);
CHECK(cids2 == cids);
CHECK(ps.failures == ps2.failures);
}
#endif
}
TEST_CASE("Github #5883: confgen failing for chiral N in a three ring") {
SECTION("basics1") {
auto mol = "N1[C@H-]C1"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
mol->getAtomWithIdx(1)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 42;
ps.maxIterations = 1;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid >= 0);
}
SECTION("basics2") {
auto mol = "N1[N@H]C1"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
mol->getAtomWithIdx(1)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 42;
ps.maxIterations = 1;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid >= 0);
}
SECTION("no ring") {
auto mol = "N[C@H-]C"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
mol->getAtomWithIdx(1)->setChiralTag(Atom::ChiralType::CHI_TETRAHEDRAL_CCW);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 42;
ps.maxIterations = 1;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid >= 0);
}
}
TEST_CASE("Github #6365: cannot generate conformers for PF6- or SF6") {
SECTION("basics") {
std::vector<std::string> smileses = {"S(F)(F)(F)(F)(F)F",
"[P-](F)(F)(F)(F)(F)F"};
for (const auto &smi : smileses) {
std::unique_ptr<RWMol> mol{SmilesToMol(smi)};
REQUIRE(mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 42;
ps.useRandomCoords = true;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid >= 0);
}
}
}
TEST_CASE("Sequential random seeds") {
SECTION("basics") {
auto mol = "CCCCCCCCCCCC"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
RWMol mol2(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.enableSequentialRandomSeeds = true;
ps.useRandomCoords = true;
ps.randomSeed = 0xf00d;
auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, 10, ps);
CHECK(cids.size() == 10);
ps.randomSeed = 0xf00d + 5;
auto cids2 = DGeomHelpers::EmbedMultipleConfs(mol2, 5, ps);
CHECK(cids2.size() == 5);
compareConfs(mol.get(), &mol2, 5, 0);
}
}
TEST_CASE("Macrocycle bounds matrix") {
SECTION("basics") {
auto mol = "C1/C=C/C=C/CCCCCCCCC1"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(mol->getNumAtoms())};
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm, true, false, true);
CHECK(bm->getLowerBound(1, 18) > 2.6);
CHECK(bm->getLowerBound(1, 18) < 2.7);
CHECK(bm->getLowerBound(4, 17) > 2.6);
CHECK(bm->getLowerBound(4, 17) < 2.7);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid >= 0);
const auto conf = mol->getConformer(cid);
RDGeom::Point3D pos_1 = conf.getAtomPos(1);
RDGeom::Point3D pos_4 = conf.getAtomPos(4);
CHECK((pos_1 - pos_4).length() < 3.61);
CHECK((pos_1 - pos_4).length() > 3.5);
}
}
TEST_CASE("atropisomers and embedding") {
SECTION("basics") {
auto mol =
"Cc1cccc(O)c1-c1c(N)cccc1Cl |(-8.88571,2.09707,;-8.17143,3.33425,;-6.74286,3.33425,;-6.02857,4.57143,;-6.74286,5.80861,;-8.17143,5.80861,;-8.88571,7.04579,;-8.88571,4.57143,;-10.3143,4.57143,;-11.0286,5.80861,;-10.3143,7.04579,;-12.4571,5.80861,;-13.1714,4.57143,;-12.4571,3.33425,;-11.0286,3.33425,;-10.3143,2.09707,),wU:8.15|"_smiles;
REQUIRE(mol);
REQUIRE(mol->getBondWithIdx(7)->getBondType() == Bond::BondType::SINGLE);
REQUIRE(mol->getBondWithIdx(7)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW);
MolOps::addHs(*mol);
// mol->debugMol(std::cerr);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
{
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
REQUIRE(cid >= 0);
const auto conf = mol->getConformer(cid);
Atropisomers::AtropAtomAndBondVec abvs[2];
REQUIRE(Atropisomers::getAtropisomerAtomsAndBonds(mol->getBondWithIdx(7),
abvs, *mol));
auto pos_1 = conf.getAtomPos(7);
auto pos_2 = conf.getAtomPos(8);
auto pos_3 = conf.getAtomPos(1);
auto pos_4 = conf.getAtomPos(9);
auto v2 = pos_2 - pos_1;
auto v3 = pos_3 - pos_1;
auto v4 = pos_4 - pos_1;
auto chiralVol = v3.crossProduct(v4).dotProduct(v2);
CHECK(chiralVol < 0);
}
{
RWMol mol2(*mol);
mol2.getBondWithIdx(7)->setStereo(Bond::BondStereo::STEREOATROPCW);
auto cid = DGeomHelpers::EmbedMolecule(mol2, ps);
REQUIRE(cid >= 0);
const auto conf = mol2.getConformer(cid);
Atropisomers::AtropAtomAndBondVec abvs[2];
REQUIRE(Atropisomers::getAtropisomerAtomsAndBonds(mol2.getBondWithIdx(7),
abvs, mol2));
auto pos_1 = conf.getAtomPos(7);
auto pos_2 = conf.getAtomPos(8);
auto pos_3 = conf.getAtomPos(1);
auto pos_4 = conf.getAtomPos(9);
auto v2 = pos_2 - pos_1;
auto v3 = pos_3 - pos_1;
auto v4 = pos_4 - pos_1;
auto chiralVol = v3.crossProduct(v4).dotProduct(v2);
CHECK(chiralVol > 0);
}
}
}
TEST_CASE("atropisomers bulk") {
std::string rdbase = getenv("RDBASE");
std::string fname =
rdbase + "/Code/GraphMol/DistGeomHelpers/test_data/atropisomers.sdf";
SDMolSupplier sdsup(fname);
auto params = DGeomHelpers::ETKDGv3;
params.randomSeed = 0xf00d + 1;
for (auto i = 0u; i < sdsup.length(); ++i) {
std::unique_ptr<RWMol> mol(static_cast<RWMol *>(sdsup[i]));
REQUIRE(mol);
auto bondIdx = mol->getProp<unsigned int>("atrop bond");
REQUIRE((mol->getBondWithIdx(bondIdx)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW ||
mol->getBondWithIdx(bondIdx)->getStereo() ==
Bond::BondStereo::STEREOATROPCW));
auto atropInfo = mol->getProp<std::string>("atrop volume");
std::vector<std::string> tokens;
boost::split(tokens, atropInfo, boost::is_any_of(" \t"));
REQUIRE(tokens.size() == 5);
std::vector<unsigned int> atropAtoms(4);
for (auto j = 0u; j < 4u; ++j) {
atropAtoms[j] = std::stol(tokens[j]);
}
int vol = std::stol(tokens[4]);
MolOps::addHs(*mol);
unsigned int nconfs = 20;
{
auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, nconfs, params);
CHECK(cids.size() == nconfs);
for (auto cid : cids) {
const auto conf = mol->getConformer(cid);
std::vector<RDGeom::Point3D> pts;
for (auto idx : atropAtoms) {
pts.push_back(conf.getAtomPos(idx));
}
auto v2 = pts[1] - pts[0];
auto v3 = pts[2] - pts[0];
auto v4 = pts[3] - pts[0];
auto chiralVol = v3.crossProduct(v4).dotProduct(v2);
INFO(cid << MolToV3KMolBlock(*mol, true, cid));
CHECK(chiralVol * vol > 0);
CHECK(fabs(chiralVol) > 0.5);
}
} // now swap the stereo and see if it still works
mol->getBondWithIdx(bondIdx)->setStereo(
mol->getBondWithIdx(bondIdx)->getStereo() ==
Bond::BondStereo::STEREOATROPCCW
? Bond::BondStereo::STEREOATROPCW
: Bond::BondStereo::STEREOATROPCCW);
{
auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, nconfs, params);
CHECK(cids.size() == nconfs);
for (auto cid : cids) {
const auto conf = mol->getConformer(cid);
std::vector<RDGeom::Point3D> pts;
for (auto idx : atropAtoms) {
pts.push_back(conf.getAtomPos(idx));
}
auto v2 = pts[1] - pts[0];
auto v3 = pts[2] - pts[0];
auto v4 = pts[3] - pts[0];
auto chiralVol = v3.crossProduct(v4).dotProduct(v2);
INFO(cid << MolToV3KMolBlock(*mol, true, cid));
CHECK(chiralVol * vol < 0);
CHECK(fabs(chiralVol) > 0.5);
}
}
}
}
TEST_CASE(
"Github #7109: wrong stereochemistry in ring from stereospecific SMILES") {
SECTION("basics") {
auto m = "C1[C@H](C#CC#C)CC[C@H](C#CC#C)C1"_smiles;
REQUIRE(m);
MolOps::addHs(*m);
REQUIRE(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW);
REQUIRE(m->getAtomWithIdx(8)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::KDG;
{ // this always worked
ps.randomSeed = 0xC0FFEE;
auto cid = DGeomHelpers::EmbedMolecule(*m, ps);
CHECK(cid >= 0);
MolOps::assignStereochemistryFrom3D(*m, cid);
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW);
CHECK(m->getAtomWithIdx(8)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW);
}
{ // this failed
ps.randomSeed = 0xC0FFEE + 123;
auto cid = DGeomHelpers::EmbedMolecule(*m, ps);
CHECK(cid >= 0);
MolOps::assignStereochemistryFrom3D(*m, cid);
CHECK(m->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW);
CHECK(m->getAtomWithIdx(8)->getChiralTag() == Atom::CHI_TETRAHEDRAL_CCW);
}
}
}
TEST_CASE("Github #7181: ET terms applied to constrained atoms") {
SECTION("basics") {
auto templ =
"CNc1ccc(OC)cc1 |(-3.3363,0.129414,1.28582;-2.44714,-0.687978,0.507453;-1.11383,-0.29452,0.197587;-0.622766,0.911164,0.645083;0.652332,1.29026,0.350281;1.45603,0.462513,-0.400278;2.7718,0.891528,-0.684446;3.83908,0.0736652,-0.224516;0.984393,-0.734112,-0.850528;-0.300532,-1.12218,-0.556656)|"_smiles;
REQUIRE(templ);
auto mol = "COc1ccc(NC(C)C)cc1"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
auto matches = SubstructMatch(*mol, *templ);
REQUIRE(matches.size() == 1);
auto tconf = templ->getConformer();
std::map<int, RDGeom::Point3D> cmap;
for (auto [ti, mi] : matches[0]) {
cmap[mi] = tconf.getAtomPos(ti);
}
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xC0FFEE;
ps.coordMap = &cmap;
auto cid = DGeomHelpers::EmbedMolecule(*mol, ps);
CHECK(cid >= 0);
auto imatch = matches[0];
for (auto &[ti, mi] : imatch) {
std::swap(ti, mi);
}
auto rmsd = MolAlign::alignMol(*mol, *templ, cid, -1, &imatch);
CHECK(rmsd < 0.2);
}
}
TEST_CASE("terminal groups in pruning") {
SECTION("basics") {
std::vector<std::string> smiles = {"FCC(=O)O", "FCC(=O)[O-]",
"FCC(=N)[NH-]", "FCS(=O)(=O)O",
"FCP(=O)(O)O"};
for (const auto &smi : smiles) {
auto mol = v2::SmilesParse::MolFromSmiles(smi);
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xc0ffee;
ps.pruneRmsThresh = 0.5;
auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, 50, ps);
CHECK(cids.size() == 1);
ps.symmetrizeConjugatedTerminalGroupsForPruning = false;
cids = DGeomHelpers::EmbedMultipleConfs(*mol, 50, ps);
CHECK(cids.size() >= 2);
}
}
}
TEST_CASE("github #7552") {
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
SECTION("as reported") {
auto mol = "O=CCC1OC2COC12"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
CHECK(DGeomHelpers::EmbedMolecule(*mol, ps) == 0);
}
SECTION("as reported, bulk") {
std::vector<std::string> smileses{
"O=CCC1OC2COC12", "O=C1OC2CCC12C#N", "CC1C2CC3OC2C13O",
"CC12CC1C3(C)OCC23", "OC1C2COC13COC23", "OC1C2C3C2N4C3CC14",
"CC1OC12C3CC2(O)C3", "OC1C2CC3C2CCC13", "CN1CC2(O)C3CC3C12",
"C1OC2C3C4C5C4C12N35", "C1OC2CC3OC12C=C3", "C1C2OC3C1OC23",
"CC1(O)CC2CCC12", "CC12NC(=O)C1C3OC23", "OC1CC2(NCCC12)C#N",
"CC12C3C1C(=O)C3C2O", "C1C=C2C3OC4C3N1C24", "CC12C3C1C4=NC3C2O4",
"C1OC23C=CC4C2N4C13", "OCC12CNC1C(=O)N2", "CC1C2C3C1C(C#C)n23",
};
for (const auto &smiles : smileses) {
INFO(smiles);
auto mol = v2::SmilesParse::MolFromSmiles(smileses[0]);
REQUIRE(mol);
MolOps::addHs(*mol);
CHECK(DGeomHelpers::EmbedMolecule(*mol, ps) == 0);
}
}
}
TEST_CASE("No overlapping atoms") {
auto ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 1;
ps.enableSequentialRandomSeeds = true;
auto mol = "COc1cc2cc(OC)c1OCCOC[C@H](C)OC(=O)[C@@H]CNC(=O)[C@H]2"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(mol->getNumAtoms())};
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm, true, false, true);
auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, 10, ps);
CHECK(cids.size() == 10);
for (const auto &cid : cids) {
CHECK(cid >= 0);
const auto conf = mol->getConformer(cid);
for (unsigned int i = 1; i < mol->getNumAtoms(); ++i) {
for (unsigned int j = 0; j < i; ++j) {
const auto minDist = bm->getLowerBound(i, j);
const auto length = (conf.getAtomPos(i) - conf.getAtomPos(j)).length();
CHECK((minDist - length) < .375);
}
}
}
}
TEST_CASE("github #8001: RMS pruning misses conformers") {
auto mol = "OCCCCCCC"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::KDG;
ps.randomSeed = 1;
ps.pruneRmsThresh = 0.5;
auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, 200, ps);
CHECK(cids.size() == 88);
ps.pruneRmsThresh = 1.0;
cids = DGeomHelpers::EmbedMultipleConfs(*mol, 200, ps);
CHECK(cids.size() == 4);
}
#ifdef RDK_TEST_MULTITHREADED
using namespace std::chrono_literals;
TEST_CASE("test interrupt") {
auto mol = "OCCCCCCCCCCCCCCCCCCCCCC"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 1;
ps.numThreads = 8;
std::vector<int> cids;
// one thread for conformer generation
std::thread cgThread(
[&]() { cids = DGeomHelpers::EmbedMultipleConfs(*mol, 1000, ps); });
// another thread to raise SIGINT
std::thread interruptThread([]() {
// sleep for a bit to make sure the conformer generation has made some
// progress
std::this_thread::sleep_for(500ms);
std::raise(SIGINT);
});
cgThread.join();
interruptThread.join();
CHECK(cids.empty());
}
#endif
TEST_CASE("github #8250: Seg fault in EmbedMultipleConfs") {
auto mol = R"CTAB(segmentation_fault
RDKit 3D
14 16 0 0 1 0 0 0 0 0999 V2000
-2.6383 -1.3457 -2.3147 C 0 0 2 0 0 0 0 0 0 0 0 0
-2.6416 0.2493 -2.4783 C 0 0 2 0 0 0 0 0 0 0 0 0
-1.4682 0.5200 0.1489 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1790 -1.5540 -0.8344 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7790 3.4105 -1.7076 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.0867 2.1687 -1.5159 C 0 0 2 0 0 0 0 0 0 0 0 0
-2.2251 -0.8303 -3.3823 N 0 0 0 0 0 2 0 0 0 0 0 0
-1.3466 1.1554 -2.5476 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.6987 -0.4961 -0.2729 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.2293 -2.6650 -2.6584 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.3198 -2.6432 -0.3452 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.3334 1.7234 -0.1738 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.1653 -0.2280 0.9964 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.7484 0.9579 -2.1397 O 0 0 0 0 0 1 0 0 0 0 0 0
1 10 1 6
1 4 1 0
2 1 1 0
2 14 1 6
3 9 1 0
3 13 1 1
4 11 2 0
4 9 1 0
6 5 1 6
12 6 1 0
7 2 1 0
7 1 1 0
8 2 1 0
8 6 1 0
9 13 1 0
12 3 1 0
M RAD 2 7 2 14 2
M END)CTAB"_ctab;
REQUIRE(mol);
MolOps::addHs(*mol);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
// with the bug, this would segfault
auto cids = DGeomHelpers::EmbedMultipleConfs(*mol, 10, ps);
CHECK(cids.size() == 10);
}
TEST_CASE("allenes and cumulenes") {
SECTION("allene") {
auto m = "C=C=C"_smiles;
REQUIRE(m);
MolOps::addHs(*m);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
auto cid = DGeomHelpers::EmbedMolecule(*m, ps);
CHECK(cid >= 0);
auto conf = m->getConformer(cid);
{
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(1);
auto v2 = conf.getAtomPos(2) - conf.getAtomPos(1);
CHECK_THAT(v1.angleTo(v2), Catch::Matchers::WithinAbs(M_PI, 0.2));
}
}
SECTION("cumulene") {
auto m = "C=C=C=C"_smiles;
REQUIRE(m);
MolOps::addHs(*m);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
auto cid = DGeomHelpers::EmbedMolecule(*m, ps);
CHECK(cid >= 0);
auto conf = m->getConformer(cid);
{
auto v1 = conf.getAtomPos(0) - conf.getAtomPos(1);
auto v2 = conf.getAtomPos(2) - conf.getAtomPos(1);
CHECK_THAT(v1.angleTo(v2), Catch::Matchers::WithinAbs(M_PI, 0.2));
}
{
auto v1 = conf.getAtomPos(1) - conf.getAtomPos(2);
auto v2 = conf.getAtomPos(3) - conf.getAtomPos(2);
CHECK_THAT(v1.angleTo(v2), Catch::Matchers::WithinAbs(M_PI, 0.2));
}
}
SECTION("azide") {
auto m = "CN=[N+]=[N-]"_smiles;
REQUIRE(m);
MolOps::addHs(*m);
DGeomHelpers::EmbedParameters ps = DGeomHelpers::ETKDGv3;
ps.randomSeed = 0xf00d;
auto cid = DGeomHelpers::EmbedMolecule(*m, ps);
CHECK(cid >= 0);
auto conf = m->getConformer(cid);
{
auto v1 = conf.getAtomPos(1) - conf.getAtomPos(2);
auto v2 = conf.getAtomPos(3) - conf.getAtomPos(2);
CHECK_THAT(v1.angleTo(v2), Catch::Matchers::WithinAbs(M_PI, 0.2));
}
}
}
namespace RDKit {
namespace DGeomHelpers {
namespace EmbeddingOps {
RDKIT_DISTGEOMHELPERS_EXPORT void findDoubleBonds(
const ROMol &mol,
std::vector<std::tuple<unsigned int, unsigned int, unsigned int>>
&doubleBondEnds,
std::vector<std::pair<std::vector<unsigned int>, int>> &stereoDoubleBonds,
const std::map<int, RDGeom::Point3D> *coordMap);
}
} // namespace DGeomHelpers
} // namespace RDKit
TEST_CASE("FindDoubleBonds") {
SECTION("Allene") {
auto m = "C=C=C"_smiles;
REQUIRE(m);
MolOps::addHs(*m);
std::vector<std::tuple<unsigned int, unsigned int, unsigned int>>
doubleBondEnds;
std::vector<std::pair<std::vector<unsigned int>, int>> stereoDoubleBonds;
DGeomHelpers::EmbeddingOps::findDoubleBonds(*m, doubleBondEnds,
stereoDoubleBonds, nullptr);
// This is 4, we still have two double bonds to Hydrogens on each
// side that should not be linear but the C=C=C should be, so not 5.
CHECK(doubleBondEnds.size() == 4);
CHECK(stereoDoubleBonds.empty());
}
SECTION("Sulfone") {
auto m = "CS(=O)(=O)C"_smiles;
REQUIRE(m);
MolOps::addHs(*m);
std::vector<std::tuple<unsigned int, unsigned int, unsigned int>>
doubleBondEnds;
std::vector<std::pair<std::vector<unsigned int>, int>> stereoDoubleBonds;
DGeomHelpers::EmbeddingOps::findDoubleBonds(*m, doubleBondEnds,
stereoDoubleBonds, nullptr);
// We want 6 and not 4, the angle between O=S=O should not be linear
// (the current implementation counts it twice, hence not 5).
CHECK(doubleBondEnds.size() == 6);
CHECK(stereoDoubleBonds.empty());
}
}
TEST_CASE("Github #8559: seg fault in setTopolBounds") {
SECTION("as reported") {
auto mol =
"CC1CN([C@H]2C[C@H](O[PH](O)(O)OC[C@H]3O[C@@H](N4CNC5C(N)NCNC54)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CC(C)C(O)NC4O)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CNC5C(N)NCNC54)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CCC(N)NC4O)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CNC5C(O)NC(N)NC54)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CNC5C(N)NCNC54)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CNC5C(N)NCNC54)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CNC5C(O)NC(N)NC54)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CC(C)C(O)NC4O)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CC(C)C(O)NC4O)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CNC5C(N)NCNC54)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CC(C)C(O)NC4O)C[C@@H]3O[PH](O)(O)OC[C@H]3O[C@@H](N4CCC(N)NC4O)C[C@@H]3O)[C@@H](CO[PH](O)(O)O[C@H]3C[C@H](N4CCC(N)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(O)NC(N)NC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CC(C)C(O)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(N)NCNC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CC(C)C(O)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(O)NC(N)NC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CC(C)C(O)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(N)NCNC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(N)NCNC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CC(C)C(O)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(N)NCNC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CC(C)C(O)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(O)NC(N)NC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CCC(N)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CC(C)C(O)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CCC(O)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CCC(N)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(N)NCNC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(N)NCNC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CC(C)C(O)NC4O)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(N)NCNC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CNC5C(O)NC(N)NC54)O[C@@H]3CO[PH](O)(O)O[C@H]3C[C@H](N4CCC(N)NC4O)O[C@@H]3CO)O2)C(O)NC1O"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
DistGeom::BoundsMatPtr bm{new DistGeom::BoundsMatrix(mol->getNumAtoms())};
DGeomHelpers::initBoundsMat(bm, 0.0, 1000.0);
DGeomHelpers::setTopolBounds(*mol, bm);
}
}
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