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d90a73aa6bd5f0f602f36b4f69e6ce3e56791bbc
rdkit/Code/GraphMol/ChemTransforms/catch_tests.cpp
Ricardo Rodriguez d90a73aa6b Leak fixes for 2026.03.1 (#9198) 
* fix mols leaked in tests

* own invariant generators

* clean up MorganFeatureAtomInvGenerator patterns

* address review suggestions
2026-03-25 05:56:26 +01:00

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//
// Copyright (c) 2019-2025 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 <catch2/catch_all.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/test_fixtures.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <algorithm>
#include <regex>
using namespace RDKit;
using std::unique_ptr;
TEST_CASE("Github #1039") {
const auto useLegacy = GENERATE(true, false);
UseLegacyStereoPerceptionFixture fx(useLegacy);
SECTION("double bond") {
auto m1 = "C/C=C/C=C/C"_smiles;
REQUIRE(m1);
std::vector<unsigned int> bonds = {2};
std::unique_ptr<ROMol> pieces(MolFragmenter::fragmentOnBonds(*m1, bonds));
REQUIRE(pieces);
CHECK(pieces->getNumAtoms() == 8);
REQUIRE(pieces->getBondBetweenAtoms(3, 6));
REQUIRE(pieces->getBondBetweenAtoms(2, 7));
CHECK(pieces->getBondBetweenAtoms(3, 6)->getBondType() == Bond::SINGLE);
CHECK(pieces->getBondBetweenAtoms(3, 6)->getBondDir() == Bond::ENDUPRIGHT);
CHECK(pieces->getBondBetweenAtoms(2, 7)->getBondType() == Bond::SINGLE);
CHECK(pieces->getBondBetweenAtoms(2, 7)->getBondDir() == Bond::ENDUPRIGHT);
CHECK(MolToSmiles(*pieces) == "[2*]/C=C/C.[3*]/C=C/C");
}
SECTION("atomic stereo") {
auto m1 = "C(C)(F)(Cl)O"_smiles;
REQUIRE(m1);
m1->getBondWithIdx(0)->setBondDir(Bond::BEGINWEDGE);
std::vector<unsigned int> bonds = {0};
std::unique_ptr<ROMol> pieces(MolFragmenter::fragmentOnBonds(*m1, bonds));
REQUIRE(pieces);
CHECK(pieces->getNumAtoms() == 7);
REQUIRE(pieces->getBondBetweenAtoms(0, 6));
REQUIRE(pieces->getBondBetweenAtoms(1, 5));
CHECK(pieces->getBondBetweenAtoms(0, 6)->getBondDir() == Bond::BEGINWEDGE);
CHECK(pieces->getBondBetweenAtoms(1, 5)->getBondDir() == Bond::NONE);
// no actual stereo in the SMILES here since we haven't assigned it (need a
// conformer to do that using wedging)
CHECK(MolToSmiles(*pieces) == "*C.[1*]C(O)(F)Cl");
}
SECTION("bond stereo") {
auto m = "O/C=N/C=C"_smiles;
std::vector<std::pair<unsigned int, unsigned int>> dummyLabels{{1, 1}};
std::vector<unsigned int> bonds{0};
auto resa = RDKit::MolFragmenter::fragmentOnBonds(*m, bonds);
CHECK(MolToSmiles(*resa) == "*/C=N/C=C.[1*]O");
// make sure we still have stereo atoms
std::vector<std::vector<int>> expected_stereo_atoms{
{5, 3}, // 5 is the new dummy atom, it was 0 before
{}, {}, {}, {},
};
std::vector<std::vector<int>> received_stereo;
for (auto *bond : resa->bonds()) {
received_stereo.push_back(bond->getStereoAtoms());
}
CHECK(received_stereo == expected_stereo_atoms);
delete resa;
}
{ // break non stereo atom bond
auto m = "C/C(O)=N/C=C"_smiles;
std::vector<std::pair<unsigned int, unsigned int>> dummyLabels{{1, 1}};
std::vector<unsigned int> bonds{0};
auto resa = RDKit::MolFragmenter::fragmentOnBonds(*m, bonds);
CHECK(MolToSmiles(*resa) == "*/C(O)=N/C=C.[1*]C");
// make sure we still have stereo atoms
std::vector<std::vector<int>> expected_stereo_atoms;
if (useLegacy) {
expected_stereo_atoms = {{}, {2, 4}, {}, {}, {}, {}};
} else {
expected_stereo_atoms = {{}, {6, 4}, {}, {}, {}, {}};
}
std::vector<std::vector<int>> received_stereo;
for (auto *bond : resa->bonds()) {
received_stereo.push_back(bond->getStereoAtoms());
}
CHECK(received_stereo == expected_stereo_atoms);
delete resa;
}
{ // bond stereo should only be removed when deleting the double bond with
// E/Z
auto m = "O/C=N/C=C"_smiles;
std::vector<std::pair<unsigned int, unsigned int>> dummyLabels{{1, 1}};
std::vector<std::string> expected = {
"*/C=N/C=C.[1*]O",
"[1*]=NC=C.[2*]=CO", // bond stereo gone
"[2*]C=C.[3*]/N=C/O", "[3*]=C.[4*]=C/N=C/O"};
for (unsigned int i = 0; i < m->getNumBonds(); ++i) {
std::vector<unsigned int> bonds{i};
auto resa = RDKit::MolFragmenter::fragmentOnBonds(*m, bonds);
auto smiles = MolToSmiles(*resa);
CHECK(smiles == expected[i]);
delete resa;
}
}
{ // bond stereo should only be removed when deleting the double bond with
// E/Z
// chiral stereo should stay
auto m = "O/C=N/[C@H](I)F"_smiles;
std::vector<std::pair<unsigned int, unsigned int>> dummyLabels{{1, 1}};
std::vector<std::string> expected = {
"*/C=N/[C@@H](F)I.[1*]O",
"[1*]=N[C@@H](F)I.[2*]=CO", // bond stereo gone
"[2*][C@@H](F)I.[3*]/N=C/O", "[3*]I.[4*][C@H](F)/N=C/O",
"[3*]F.[5*][C@@H](I)/N=C/O"};
for (unsigned int i = 0; i < m->getNumBonds(); ++i) {
std::vector<unsigned int> bonds{i};
auto resa = RDKit::MolFragmenter::fragmentOnBonds(*m, bonds);
auto smiles = MolToSmiles(*resa);
CHECK(smiles == expected[i]);
delete resa;
}
}
}
TEST_CASE("molzip") {
const auto useLegacy = GENERATE(true, false);
CAPTURE(useLegacy);
UseLegacyStereoPerceptionFixture fx(useLegacy);
SECTION("basic tests") {
{
auto a = "C[*:1]"_smiles;
auto b = "N[*:1]"_smiles;
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "CN");
}
{
// 0 isotopes aren't mapped
auto a = "C[*]"_smiles;
auto b = "N[*]"_smiles;
MolzipParams p;
auto mol = molzip(*a, *b, p);
CHECK(MolToSmiles(*mol) == "*C.*N");
}
{
auto a = "C[1*]"_smiles;
auto b = "N[1*]"_smiles;
MolzipParams p;
p.label = MolzipLabel::Isotope;
auto mol = molzip(*a, *b, p);
CHECK(MolToSmiles(*mol) == "CN");
}
{
auto a = "[C@H](Br)([*:1])F"_smiles;
auto b = "[*:1]N"_smiles;
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "N[C@@H](F)Br");
}
{
auto a = "[C@H]([*:1])(Br)F"_smiles;
auto b = "[*:1]N"_smiles;
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "N[C@H](F)Br");
}
{
auto a = "[C@H]([*:1])(F)([*:2])"_smiles;
auto b = "[*:1]N.[*:2]I"_smiles;
auto mol = molzip(*a, *b);
REQUIRE(MolToSmiles(*mol) == "N[C@@H](F)I");
}
{
auto a = "[C@H]([Xe])(F)([V])"_smiles;
auto b = "[Xe]N.[V]I"_smiles;
MolzipParams params;
params.label = MolzipLabel::AtomType;
params.atomSymbols = {"Xe", "V"};
auto mol = molzip(*a, *b, params);
CHECK(MolToSmiles(*mol) == "N[C@@H](F)I");
}
{
auto m = "OOO[C@](F)(I)N"_smiles;
std::vector<std::pair<unsigned int, unsigned int>> dummyLabels{{1, 1},
{2, 2}};
for (unsigned int i = 0; i < m->getNumBonds(); ++i) {
for (unsigned int j = 0; j < m->getNumBonds(); ++j) {
if (i != j) {
std::vector<unsigned int> bonds{i, j};
auto resa = RDKit::MolFragmenter::fragmentOnBonds(*m, bonds);
MolzipParams p;
p.label = MolzipLabel::FragmentOnBonds;
CHECK(MolToSmiles(*molzip(*resa, p)) == MolToSmiles(*m));
delete resa;
// Now try using atom labels
auto res = RDKit::MolFragmenter::fragmentOnBonds(*m, bonds, true,
&dummyLabels);
for (auto *atom : res->atoms()) {
if (atom->getIsotope()) {
atom->setAtomMapNum(atom->getIsotope());
}
}
CHECK(MolToSmiles(*molzip(*res)) == MolToSmiles(*m));
delete res;
}
}
}
}
}
SECTION("use atom property as label") {
auto a = "[C@H]([*])(F)([*])"_smiles;
auto b = "[*]N.[*]I"_smiles;
a->getAtomWithIdx(1)->setProp<unsigned int>("foo", 1);
a->getAtomWithIdx(3)->setProp<unsigned int>("foo", 2);
b->getAtomWithIdx(0)->setProp<unsigned int>("foo", 1);
b->getAtomWithIdx(2)->setProp<unsigned int>("foo", 2);
MolzipParams p;
p.label = MolzipLabel::AtomProperty;
p.atomProperty = "foo";
auto mol = molzip(*a, *b, p);
// chirality is "lost" here because [C@H]([*])(F)([*]) is considered
// achiral
CHECK(MolToSmiles(*mol) == "NC(F)I");
}
SECTION("test bond stereo") {
{
auto a = "F/C=C/[*:1]"_smiles;
auto b = "[*:1]F"_smiles;
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "F/C=C/F");
}
{
auto a = "C=C/N=C/[*:1]"_smiles;
auto b = "O[*:1]"_smiles;
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "C=C/N=C/O");
}
{
auto a = "C=C[*:1].O/C=N/[*:1]"_smiles;
auto mol = molzip(*a);
CHECK(MolToSmiles(*mol) == "C=C/N=C/O");
}
{ // test single mol isotope labels
auto a = "C=C[1*].O/C=N/[1*]"_smiles;
MolzipParams p;
p.label = MolzipLabel::Isotope;
auto mol = molzip(*a, p);
CHECK(MolToSmiles(*mol) == "C=C/N=C/O");
}
{
// double bondd stereo not handled
// auto m = "O/C=N/C=C/F"_smiles;
auto m = "O/C=N/C=C"_smiles;
std::vector<std::pair<unsigned int, unsigned int>> dummyLabels{{1, 1}};
for (unsigned int i = 0; i < m->getNumBonds(); ++i) {
std::vector<unsigned int> bonds{i};
{
std::unique_ptr<ROMol> resa{
RDKit::MolFragmenter::fragmentOnBonds(*m, bonds)};
auto smiles = MolToSmiles(*resa);
if (std::count(smiles.begin(), smiles.end(), '/') != 2) {
continue; // we removed bond stereo in fragment to bonds!
}
MolzipParams p;
p.label = MolzipLabel::FragmentOnBonds;
CHECK(MolToSmiles(*molzip(*resa, p)) == MolToSmiles(*m));
}
{
// Now try using atom labels
std::unique_ptr<ROMol> res{RDKit::MolFragmenter::fragmentOnBonds(
*m, bonds, true, &dummyLabels)};
auto smiles = MolToSmiles(*res);
if (std::count(smiles.begin(), smiles.end(), '/') != 2) {
continue; // we removed bond stereo in fragment to bonds!
}
for (auto *atom : res->atoms()) {
if (atom->getIsotope()) {
atom->setAtomMapNum(atom->getIsotope());
}
}
CHECK(MolToSmiles(*molzip(*res)) == MolToSmiles(*m));
}
}
}
}
SECTION("unzippable molecules") {
auto a = "C[*:1]"_smiles;
auto b = "N[*:2]"_smiles;
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "C[*:1].N[*:2]");
}
{
auto a = "[*:2]OC[*:1]"_smiles;
auto b = "N[*:1]"_smiles;
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "NCO[*:2]");
}
{
auto a = "[*:1]OC[*:1]"_smiles;
auto b = "N[*:1]"_smiles;
bool caught = false;
try {
auto mol = molzip(*a, *b);
} catch (Invar::Invariant &e) {
CHECK(e.toUserString().find(
"molzip: bond info already exists for end atom with label:1") !=
std::string::npos);
caught = true;
}
CHECK(caught == true);
}
{
// check to see we can make a non sanitizable zipped mol
MolzipParams p;
p.enforceValenceRules = false;
auto a = "CC(=[*:1])N"_smiles;
auto b = "[*:1]-N=C"_smiles;
auto mol = molzip(*a, *b, p);
}
{
// check atom property zipping
auto a = "C=C*.O/C=N/*"_smiles;
a->getAtomWithIdx(2)->setProp<unsigned int>("fuse", 1);
a->getAtomWithIdx(6)->setProp<unsigned int>("fuse", 1);
MolzipParams p;
p.atomProperty = "fuse";
p.label = MolzipLabel::AtomProperty;
auto mol = molzip(*a, p);
CHECK(MolToSmiles(*mol) == "C=C/N=C/O");
}
SECTION("MolZip saves bonddir") {
{ // a-* b<*
auto a = "CC[*:1]"_smiles;
auto b = "N[*:1]"_smiles;
b->getBondWithIdx(0)->setBondDir(Bond::BondDir::BEGINWEDGE);
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "CCN");
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::BondDir::BEGINWEDGE);
CHECK(mol->getBondWithIdx(1)->getBeginAtom()->getIdx() == 2);
}
{ // a>* b-*
auto a = "[*:1]CC"_smiles;
auto b = "N[*:1]"_smiles;
a->getBondWithIdx(0)->setBondDir(Bond::BondDir::BEGINWEDGE);
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "CCN");
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::BondDir::BEGINWEDGE);
CHECK(mol->getBondWithIdx(1)->getBeginAtom()->getIdx() == 2);
}
{ // a<* b-*
auto a = "CC[*:1]"_smiles;
auto b = "N[*:1]"_smiles;
a->getBondWithIdx(1)->setBondDir(Bond::BondDir::BEGINWEDGE);
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "CCN");
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::BondDir::BEGINWEDGE);
CHECK(mol->getBondWithIdx(1)->getBeginAtom()->getIdx() == 1);
}
{ // a>* b-*
auto a = "[*:1]CC"_smiles;
auto b = "N[*:1]"_smiles;
a->getBondWithIdx(0)->setBondDir(Bond::BondDir::BEGINWEDGE);
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "CCN");
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::BondDir::BEGINWEDGE);
CHECK(mol->getBondWithIdx(1)->getBeginAtom()->getIdx() == 2);
}
{ // a-* b<*
auto a = "CC[*:1]"_smiles;
auto b = "[*:1]N"_smiles;
b->getBondWithIdx(0)->setBondDir(Bond::BondDir::BEGINWEDGE);
auto mol = molzip(*a, *b);
CHECK(MolToSmiles(*mol) == "CCN");
CHECK(mol->getBondWithIdx(1)->getBondDir() == Bond::BondDir::BEGINWEDGE);
CHECK(mol->getBondWithIdx(1)->getBeginAtom()->getIdx() == 1);
}
}
}
TEST_CASE(
"Github4825: ReplaceCore should set stereo on ring bonds when it breaks "
"rings") {
SECTION("basics") {
auto m = "C1C=CCC2=C1C=CC=N2"_smiles;
REQUIRE(m);
auto core = "c1ncccc1"_smiles;
REQUIRE(core);
std::unique_ptr<ROMol> res{replaceCore(*m, *core)};
REQUIRE(res);
auto mb = MolToV3KMolBlock(*res);
CHECK(mb.find("CFG=2") == std::string::npos);
}
SECTION("adjacent") {
auto m = "C1CC2=C(C=C1)C=CC=N2"_smiles;
REQUIRE(m);
auto core = "c1ncccc1"_smiles;
REQUIRE(core);
std::unique_ptr<ROMol> res{replaceCore(*m, *core)};
REQUIRE(res);
auto mb = MolToV3KMolBlock(*res);
CHECK(mb.find("CFG=2") == std::string::npos);
}
SECTION("don't do larger rings") {
auto m = "C1C=CCCCC2=C1C=CC=N2"_smiles;
REQUIRE(m);
auto core = "c1ncccc1"_smiles;
REQUIRE(core);
std::unique_ptr<ROMol> res{replaceCore(*m, *core)};
REQUIRE(res);
auto mb = MolToV3KMolBlock(*res);
CHECK(mb.find("CFG=2") != std::string::npos);
}
}
TEST_CASE(
"Github5334: ReplaceCore should set stereo on ring bonds when it breaks "
"rings") {
SECTION("segfault") {
auto a = "C([*:1])[*:2].[C@@H](Cl)([1*:1])[2*:2]"_smiles;
bool caught = false;
try {
auto mol = molzip(*a);
CHECK(false);
} catch (Invar::Invariant &e) {
CHECK(
e.toUserString().find(
"molzip: zipped Bond already exists, perhaps labels are duplicated") !=
std::string::npos);
caught = true;
}
CHECK(caught);
}
}
TEST_CASE(
"ReplaceCore handles chiral center with multiple bonds from core to chiral center") {
auto structure = "C1CSCN[C@@]12(NCCCO2)"_smiles;
auto core = "NCSCC"_smarts;
std::unique_ptr<ROMol> res{replaceCore(*structure, *core, true, true)};
REQUIRE(res);
auto resultSmiles = MolToSmiles(*res);
REQUIRE(resultSmiles == "*[C@]1([4*])NCCCO1");
}
TEST_CASE("Molzip with 2D coordinates", "[molzip]") {
std::vector<std::string> frags = {"c1nc([1*:1])c([2*:2])c([3*:3])n1",
"CC(C)(C#N)c1ccc([1*:1])cc1",
"Nc1ccc(C#C[2*:2])cn1", "OCC[3*:3]"};
std::vector<ROMOL_SPTR> mols = {
ROMOL_SPTR(SmilesToMol(frags[0])), ROMOL_SPTR(SmilesToMol(frags[1])),
ROMOL_SPTR(SmilesToMol(frags[2])), ROMOL_SPTR(SmilesToMol(frags[3]))};
MolzipParams params;
params.generateCoordinates = true;
const auto zippedMol = molzip(mols, params);
for (auto &mol : mols) {
for (auto &atom : mol->atoms()) {
atom->setIsotope(0);
atom->setAtomMapNum(0);
}
}
const auto &zippedConformer = zippedMol->getConformer();
for (size_t i = 0; i < frags.size(); i++) {
const auto sma =
std::regex_replace(frags[i], std::regex(R"(\[\d\*\:\d\])"), "*");
const auto query = SmartsToMol(sma);
const auto &mol = mols[i];
const auto &molConformer = mol->getConformer();
const auto molMatches = SubstructMatch(*mol, *query);
const auto zippedMatches = SubstructMatch(*zippedMol, *query);
REQUIRE(molMatches.size() == 1);
REQUIRE(zippedMatches.size() == 1);
const auto molMatch = molMatches[0];
const auto zippedMatch = zippedMatches[0];
for (size_t j = 0; j < molMatch.size(); j++) {
const auto &position1 = molConformer.getAtomPos(molMatch[i].second);
const auto &position2 = zippedConformer.getAtomPos(zippedMatch[i].second);
CHECK(position1.x == position2.x);
CHECK(position1.y == position2.y);
CHECK(position1.z == position2.z);
}
delete query;
}
}
TEST_CASE("Molzip with split rings from rgroup", "[molzip]") {
std::vector<std::string> frags = {"[*:1]CC[*:2]", "[*:1]NN[*:2]",
"[*:1]NN[*:2]"};
std::vector<ROMOL_SPTR> mols;
for (auto smi : frags) {
mols.push_back(ROMOL_SPTR(SmilesToMol(smi)));
}
const auto zippedMol = molzip(mols);
CHECK(MolToSmiles(*zippedMol) == "C1CNN1");
}
TEST_CASE("Github #6034: FragmentOnBonds may create unexpected radicals") {
auto m = "C[C@H](Cl)c1ccccc1"_smiles;
REQUIRE(m);
REQUIRE(m->getNumAtoms() == 9);
REQUIRE(m->getAtomWithIdx(1)->getNoImplicit() == true);
bool add_dummies = false;
std::vector<unsigned int> bonds = {0};
std::vector<std::pair<unsigned, unsigned>> *dummyLabels = nullptr;
const std::vector<Bond::BondType> *bondTypes = nullptr;
std::vector<unsigned> nCutsPerAtom(m->getNumAtoms(), 0);
std::unique_ptr<ROMol> pieces(MolFragmenter::fragmentOnBonds(
*m, bonds, add_dummies, dummyLabels, bondTypes, &nCutsPerAtom));
REQUIRE(pieces);
REQUIRE(nCutsPerAtom == std::vector<unsigned>{1, 1, 0, 0, 0, 0, 0, 0, 0});
for (auto at : pieces->atoms()) {
INFO("atom " + std::to_string(at->getIdx()));
if (at->getAtomicNum() == 6) {
CHECK(at->getNoImplicit() == (at->getIdx() == 1));
CHECK(at->getTotalValence() == 4);
}
}
}
TEST_CASE(
"GitHub #7327: SaltRemover may clear computed properties even if no atoms are removed",
"[bug]") {
auto m = "C=CC=O"_smiles;
REQUIRE(m);
REQUIRE(m->getRingInfo()->isSymmSssr());
auto q = "[O,N]"_smarts;
REQUIRE(q);
bool onlyFrags = true;
std::unique_ptr<ROMol> m2{deleteSubstructs(*m, *q, onlyFrags)};
REQUIRE(m2);
CHECK(m2->getNumAtoms() == m->getNumAtoms()); // No atoms removed
CHECK(m2->getRingInfo()->isSymmSssr());
}
TEST_CASE(
"Github #8288: molzip add linker bond functionality (fixes memory issue)",
"[feature,bug]") {
auto m = "[*:1][*:2].C[*:1].S[*:2]"_smiles;
auto res = molzip(*m);
CHECK(MolToSmiles(*res) == "CS");
}
TEST_CASE(
"Github #8389: FragmentOnBonds does not preserve bond stereo when useLegacy=False") {
auto useLegacy = GENERATE(true, false);
CAPTURE(useLegacy);
UseLegacyStereoPerceptionFixture fx(useLegacy);
SECTION("as reported ") {
auto m = "CC/C=C/N"_smiles;
REQUIRE(m);
std::unique_ptr<ROMol> res(
MolFragmenter::fragmentOnBonds(*m, std::vector<unsigned int>{1}));
REQUIRE(res);
CHECK(res->getBondWithIdx(1)->getBondType() == Bond::BondType::DOUBLE);
if (useLegacy) {
CHECK(res->getBondWithIdx(1)->getStereo() == Bond::BondStereo::STEREOE);
} else {
CHECK(res->getBondWithIdx(1)->getStereo() ==
Bond::BondStereo::STEREOTRANS);
}
CHECK(MolToSmiles(*res) == "[1*]/C=C/N.[2*]CC");
}
}
TEST_CASE(
"Github #9009: fragmentOnBonds should transfer queries on deleted bonds") {
// Basic test
auto m1 = "c1ccccc1-C1CCCCC1"_smarts;
REQUIRE(m1);
auto bond1 = m1->getBondWithIdx(1);
REQUIRE(bond1);
REQUIRE(bond1->hasQuery());
std::unique_ptr<ROMol> splitM1(
MolFragmenter::fragmentOnBonds(*m1, std::vector<unsigned int>{1, 5}));
REQUIRE(splitM1);
auto nb1 = splitM1->getBondWithIdx(11);
REQUIRE(nb1);
CHECK(nb1->hasQuery());
CHECK(nb1->getQuery()->getDescription() == "SingleOrAromaticBond");
auto nb2 = splitM1->getBondWithIdx(12);
REQUIRE(nb2);
CHECK(nb2->hasQuery());
CHECK(nb2->getQuery()->getDescription() == "SingleOrAromaticBond");
auto nb3 = splitM1->getBondWithIdx(13);
REQUIRE(nb3);
CHECK(nb3->hasQuery());
CHECK(nb3->getQuery()->getDescription() == "BondOrder");
auto nb4 = splitM1->getBondWithIdx(14);
REQUIRE(nb4);
CHECK(nb4->hasQuery());
CHECK(nb4->getQuery()->getDescription() == "BondOrder");
// Check it does nothing if there isn't a query
auto m2 = "c1ccccc1"_smiles;
REQUIRE(m2);
auto bond2 = m2->getBondWithIdx(1);
REQUIRE(bond2);
REQUIRE(!bond2->hasQuery());
std::unique_ptr<ROMol> splitM2(
MolFragmenter::fragmentOnBonds(*m2, std::vector<unsigned int>{1}));
REQUIRE(splitM2);
auto nb5 = splitM2->getBondWithIdx(5);
REQUIRE(nb5);
CHECK(!nb5->hasQuery());
auto nb6 = splitM2->getBondWithIdx(6);
REQUIRE(nb6);
CHECK(!nb6->hasQuery());
// Check it does nothing if bond types are specified
auto m3 = "c1ccccc1"_smiles;
REQUIRE(m3);
auto bond3 = m3->getBondWithIdx(1);
REQUIRE(bond3);
REQUIRE(!bond3->hasQuery());
auto dummyLabels =
std::vector<std::pair<unsigned int, unsigned int>>{{25, 26}};
auto newTypes = std::vector<Bond::BondType>{Bond::DOUBLE};
std::unique_ptr<ROMol> splitM3(MolFragmenter::fragmentOnBonds(
*m3, std::vector<unsigned int>{1}, true, &dummyLabels, &newTypes));
REQUIRE(splitM3);
auto nb7 = splitM3->getBondWithIdx(5);
REQUIRE(nb7);
CHECK(!nb7->hasQuery());
auto nb8 = splitM3->getBondWithIdx(6);
REQUIRE(nb8);
CHECK(!nb8->hasQuery());
}
TEST_CASE("align fragments") {
SECTION("basics") {
auto m = "CC[1*].O[1*] |(1,0,0;2,0,0;3.5,0,0;0,1,0;0,2.1,0)|"_smiles;
REQUIRE(m);
REQUIRE(m->getNumConformers() == 1);
MolzipParams params;
params.alignCoordinates = true;
params.label = MolzipLabel::Isotope;
auto res = molzip(*m, params);
REQUIRE(res);
REQUIRE(res->getNumConformers() == 1);
CHECK(MolToXYZBlock(*res) == R"XYZ(3
C 1.000000 0.000000 0.000000
C 2.000000 0.000000 0.000000
O 3.100000 0.000000 0.000000
)XYZ");
}
SECTION("2D multiple attachment points") {
auto m =
"[2*]CCC[1*].[2*]O[1*] |(2,1.2;1,1;1,0;2,0;3,0;\
0,0;0,1;0,2.1)|"_smiles;
REQUIRE(m);
REQUIRE(m->getNumConformers() == 1);
MolzipParams params;
params.alignCoordinates = true;
params.label = MolzipLabel::Isotope;
auto res = molzip(*m, params);
REQUIRE(res);
REQUIRE(res->getNumConformers() == 1);
CHECK(MolToXYZBlock(*res) == R"XYZ(4
C 1.000000 1.000000 0.000000
C 1.000000 0.000000 0.000000
C 2.000000 0.000000 0.000000
O 3.100000 0.000000 0.000000
)XYZ");
}
SECTION("3D, more real") {
auto m1 =
"[6*]C1CCCCC1 |(-1.08968,0.169713,-0.700677;0.254816,-0.328544,-0.482737;0.56879,-1.01027,0.899618;1.09147,0.21675,1.40903;2.37628,0.102667,0.427592;2.29478,-0.272363,-1.13357;1.24328,0.638789,-1.31851)|"_smiles;
REQUIRE(m1);
auto conf1 = m1->getConformer();
auto m2 =
"[6*]C1CCC1 |(3.18447,1.72863,2.51726;1.96576,1.94984,2.29932;1.43402,2.74418,3.09468;0.109542,1.58059,3.19096;0.655465,0.761837,2.3866)|"_smiles;
REQUIRE(m2);
auto conf2 = m2->getConformer();
auto origv = conf2.getAtomPos(0) - conf2.getAtomPos(1);
MolzipParams params;
params.alignCoordinates = true;
params.label = MolzipLabel::Isotope;
auto res = molzip(*m1, *m2, params);
REQUIRE(res);
REQUIRE(res->getNumConformers() == 1);
auto resconf = res->getConformer();
// check that the first fragment's coords are unchanged
CHECK_THAT(resconf.getAtomPos(0).x,
Catch::Matchers::WithinAbs(conf1.getAtomPos(1).x, 1e-4));
CHECK_THAT(resconf.getAtomPos(0).y,
Catch::Matchers::WithinAbs(conf1.getAtomPos(1).y, 1e-4));
CHECK_THAT(resconf.getAtomPos(0).z,
Catch::Matchers::WithinAbs(conf1.getAtomPos(1).z, 1e-4));
// make sure the bond length is right:
auto v = resconf.getAtomPos(0) - resconf.getAtomPos(6);
CHECK_THAT(v.length(), Catch::Matchers::WithinAbs(origv.length(), 1e-2));
}
SECTION("on top") {
auto m3 =
"[1*]c1ccccc1.[1*]c1ncccc1 |(2.57143,0,;1.07143,0,;0.321429,-1.29904,;-1.17857,-1.29904,;-1.92857,0,;-1.17857,1.29904,;0.321429,1.29904,;12.5714,0,;11.0714,0,;10.3214,1.29904,;8.82143,1.29904,;8.07143,0,;8.82143,-1.29904,;10.3214,-1.29904,)|"_smiles;
MolzipParams params;
params.alignCoordinates = true;
params.label = MolzipLabel::Isotope;
auto res = molzip(*m3, params);
INFO(MolToCXSmiles(*res));
auto resconf = res->getConformer();
// check that we don't have overlapping atoms:
for (unsigned int i = 0; i < res->getNumAtoms(); ++i) {
auto api = resconf.getAtomPos(i);
for (unsigned int j = i + 1; j < res->getNumAtoms(); ++j) {
auto apj = resconf.getAtomPos(j);
CHECK((api - apj).length() > 1.0);
}
}
}
SECTION("first fragment should not move") {
auto m3 =
"[1*]c1ccccc1.[1*]c1ncccc1 |(2.57143,0,;1.07143,0,;0.321429,-1.29904,;-1.17857,-1.29904,;-1.92857,0,;-1.17857,1.29904,;0.321429,1.29904,;12.5714,0,;11.0714,0,;10.3214,1.29904,;8.82143,1.29904,;8.07143,0,;8.82143,-1.29904,;10.3214,-1.29904,)|"_smiles;
MolzipParams params;
params.alignCoordinates = true;
params.label = MolzipLabel::Isotope;
auto res = molzip(*m3, params);
INFO(MolToCXSmiles(*res));
auto resconf = res->getConformer();
auto molconf = m3->getConformer();
for (unsigned int i = 0; i < 6; ++i) {
auto rap = resconf.getAtomPos(i);
auto map = molconf.getAtomPos(i + 1);
CHECK_THAT(rap.x, Catch::Matchers::WithinAbs(map.x, 1e-4));
CHECK_THAT(rap.y, Catch::Matchers::WithinAbs(map.y, 1e-4));
CHECK_THAT(rap.z, Catch::Matchers::WithinAbs(map.z, 1e-4));
}
}
}
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