mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-05 22:04:27 +08:00
1dc268bf4a
* support tracking where the conformer generation code fails * less verbose output * tests now pass * fix a stupid typo * fix SWIG wrappers * changes in response to review
583 lines
22 KiB
C++
583 lines
22 KiB
C++
//
|
|
// Copyright (C) 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 <RDGeneral/test.h>
|
|
#include "catch.hpp"
|
|
|
|
#include <RDGeneral/RDLog.h>
|
|
#include <GraphMol/RDKitBase.h>
|
|
#include <GraphMol/Chirality.h>
|
|
#include <GraphMol/Substruct/SubstructMatch.h>
|
|
#include <GraphMol/ForceFieldHelpers/UFF/UFF.h>
|
|
#include <GraphMol/FileParsers/FileParsers.h>
|
|
#include <GraphMol/SmilesParse/SmilesParse.h>
|
|
#include <GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h>
|
|
#include "Embedder.h"
|
|
#include "BoundsMatrixBuilder.h"
|
|
#include <tuple>
|
|
|
|
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) == Approx(M_PI / 2).margin(0.15));
|
|
}
|
|
}
|
|
}
|
|
|
|
TEST_CASE(
|
|
"github #4346: Specified cis/trans stereo being ignored during "
|
|
"conformation generation in macrocycles") {
|
|
SECTION("basics 1") {
|
|
auto m1 = "C1C/C=C/CCCCCCCC1"_smiles;
|
|
REQUIRE(m1);
|
|
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
|
|
Bond::BondStereo::STEREOE);
|
|
MolOps::addHs(*m1);
|
|
DGeomHelpers::EmbedParameters params = DGeomHelpers::KDG;
|
|
params.randomSeed = 0xf00d;
|
|
CHECK(DGeomHelpers::EmbedMolecule(*m1, params) != -1);
|
|
MolOps::assignStereochemistryFrom3D(*m1);
|
|
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
|
|
Bond::BondStereo::STEREOE);
|
|
}
|
|
SECTION("basics 2") {
|
|
auto m1 = "C1C/C=C\\CCCCCCCC1"_smiles;
|
|
REQUIRE(m1);
|
|
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
|
|
Bond::BondStereo::STEREOZ);
|
|
MolOps::addHs(*m1);
|
|
DGeomHelpers::EmbedParameters params = DGeomHelpers::KDG;
|
|
params.randomSeed = 0xf00d;
|
|
CHECK(DGeomHelpers::EmbedMolecule(*m1, params) != -1);
|
|
MolOps::assignStereochemistryFrom3D(*m1);
|
|
CHECK(m1->getBondBetweenAtoms(2, 3)->getStereo() ==
|
|
Bond::BondStereo::STEREOZ);
|
|
}
|
|
}
|
|
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);
|
|
}
|
|
|
|
{
|
|
auto m = "Cl[Pt@SP1]([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("tracking failure causes") {
|
|
SECTION("basics") {
|
|
// auto mol = "CCNS(=O)(=O)c1ccccc1"_smiles;
|
|
// auto mol = "c2cccc3c2OC2=CC=CC[C@H]23"_smiles;
|
|
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.randomSeed = 0xf00d;
|
|
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") {
|
|
auto mol = R"CTAB(
|
|
Ketcher 1102315302D 1 1.00000 0.00000 0
|
|
|
|
10 11 0 0 1 0 0 0 0 0999 V2000
|
|
10.1340 -11.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
10.1340 -12.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11.0000 -12.5250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11.8660 -12.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11.8660 -11.0250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11.0000 -10.5250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11.0000 -11.5250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
|
|
11.2588 -12.4909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
9.2680 -10.5250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
12.7629 -12.4673 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
1 6 1 0 0 0
|
|
1 2 1 0 0 0
|
|
2 3 1 0 0 0
|
|
3 4 1 0 0 0
|
|
4 5 1 0 0 0
|
|
5 6 1 0 0 0
|
|
1 7 1 0 0 0
|
|
7 8 1 0 0 0
|
|
8 4 1 0 0 0
|
|
1 9 1 1 0 0
|
|
4 10 1 1 0 0
|
|
M END
|
|
)CTAB"_ctab;
|
|
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] >
|
|
5);
|
|
}
|
|
|
|
#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.randomSeed = 0xf00d;
|
|
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
|
|
} |