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//
// Copyright (C) 2023 David Cosgrove 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/RWMol.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
using namespace RDKit;
TEST_CASE("convert haptic bond to explicit dative bonds") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/MolStandardize/test_data/";
std::vector<std::tuple<std::string, int, int, int>> test_data{
{"ferrocene.mol", 10, 26, 10},
{"MOL_00002.mol", 14, 26, 10},
{"MOL_00010.mol", 5, 46, 5}};
{
// doing in place
for (const auto &td : test_data) {
std::unique_ptr<RWMol> mol(MolFileToMol(pathName + std::get<0>(td)));
REQUIRE(mol);
MolOps::hapticBondsToDative(*mol);
int numDats = 0, numMetDats = 0;
for (const auto &b : mol->bonds()) {
if (b->getBondType() == Bond::DATIVE) {
++numDats;
if (b->getEndAtom()->getAtomicNum() == get<2>(td)) {
++numMetDats;
}
}
}
CHECK(numDats == std::get<1>(td));
CHECK(numMetDats == std::get<3>(td));
}
}
{
// doing via temporary
for (const auto &td : test_data) {
std::unique_ptr<ROMol> mol(MolFileToMol(pathName + std::get<0>(td)));
REQUIRE(mol);
std::unique_ptr<ROMol> newMol(MolOps::hapticBondsToDative(*mol));
int numDats = 0, numMetDats = 0;
for (const auto &b : newMol->bonds()) {
if (b->getBondType() == Bond::DATIVE) {
++numDats;
if (b->getEndAtom()->getAtomicNum() == get<2>(td)) {
++numMetDats;
}
}
}
CHECK(numDats == std::get<1>(td));
CHECK(numMetDats == std::get<3>(td));
}
}
}
TEST_CASE("convert explicit dative bonds to haptic bond") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/MolStandardize/test_data/";
std::vector<std::string> test_data{"ferrocene.mol", "MOL_00002.mol",
"MOL_00010.mol"};
// MOL_00010.mol only has 1 dummy, so duplicating the test to fit in.
std::vector<std::tuple<int, int, float, float, float, float>> exp_res{
{11, 12, -36.5, 13.5, -36.4, 8.6},
{43, 44, -36.5, 13.5, -36.4, 8.6},
{82, 82, -1.0, -0.7, -1.0, -0.7}};
{
// doing in place
for (size_t i = 0; i < 3; ++i) {
std::unique_ptr<RWMol> mol(MolFileToMol(pathName + test_data[i]));
REQUIRE(mol);
auto initSmi = MolToSmiles(*mol);
MolOps::hapticBondsToDative(*mol);
MolOps::dativeBondsToHaptic(*mol);
CHECK(initSmi == MolToSmiles(*mol));
// Check the dummy atoms are in the right place.
auto [d1, d2, d1x, d1y, d2x, d2y] = exp_res[i];
auto dummy1pos = mol->getConformer().getAtomPos(d1);
REQUIRE_THAT(dummy1pos.x, Catch::Matchers::WithinAbs(d1x, 0.1));
REQUIRE_THAT(dummy1pos.y, Catch::Matchers::WithinAbs(d1y, 0.1));
auto dummy2pos = mol->getConformer().getAtomPos(d2);
REQUIRE_THAT(dummy2pos.x, Catch::Matchers::WithinAbs(d2x, 0.1));
REQUIRE_THAT(dummy2pos.y, Catch::Matchers::WithinAbs(d2y, 0.1));
}
}
{
// doing via temporary
for (const auto &td : test_data) {
std::unique_ptr<ROMol> mol(MolFileToMol(pathName + td));
REQUIRE(mol);
auto initSmi = MolToSmiles(*mol);
std::unique_ptr<ROMol> mol1{MolOps::hapticBondsToDative(*mol)};
std::unique_ptr<ROMol> mol2{MolOps::dativeBondsToHaptic(*mol1)};
CHECK(initSmi == MolToSmiles(*mol2));
}
}
}
TEST_CASE("get haptic bond end points") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/MolStandardize/test_data/";
bool sanitize = false;
std::unique_ptr<RWMol> mol(
MolFileToMol(pathName + "MOL_00002.mol", sanitize));
REQUIRE(mol);
auto bond = mol->getBondWithIdx(0);
auto endPts = MolOps::details::hapticBondEndpoints(bond);
CHECK(std::vector<int>{1, 2, 3, 4, 0} == endPts);
bond = mol->getBondWithIdx(11);
endPts = MolOps::details::hapticBondEndpoints(bond);
CHECK(std::vector<int>{6, 7, 8, 9, 5} == endPts);
// dative but not haptic
bond = mol->getBondWithIdx(49);
endPts = MolOps::details::hapticBondEndpoints(bond);
CHECK(std::vector<int>{} == endPts);
// not dative
bond = mol->getBondWithIdx(1);
endPts = MolOps::details::hapticBondEndpoints(bond);
CHECK(std::vector<int>{} == endPts);
}
TEST_CASE("Rings and dative bonds") {
SECTION("ferrocene") {
auto m =
"C12->[Fe+2]3456789(<-C1=C->3[CH-]->4C->5=2)<-C1=C->6[CH-]->7C->8=C->91"_smiles;
REQUIRE(m);
std::vector<std::vector<int>> rings;
auto nrings = MolOps::symmetrizeSSSR(*m, rings);
CHECK(nrings == 2);
CHECK(rings[0].size() == 5);
CHECK(rings[1].size() == 5);
}
}
TEST_CASE("aromaticity and dative bonds") {
SECTION("ferrocene") {
auto m =
"C12->[Fe+2]3456789(<-C1=C->3[CH-]->4C->5=2)<-C1=C->6[CH-]->7C->8=C->91"_smiles;
REQUIRE(m);
CHECK(m->getAtomWithIdx(0)->getIsAromatic());
CHECK(!m->getAtomWithIdx(1)->getIsAromatic());
}
}
TEST_CASE("Github 6252 - wrong endpoints after dativeBondsToHaptic") {
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/MolStandardize/test_data/";
std::string ferroccene = pathName + "ferrocene.mol";
{
std::unique_ptr<RWMol> mol(MolFileToMol(ferroccene));
REQUIRE(mol);
auto initSmi = MolToSmiles(*mol);
MolOps::hapticBondsToDative(*mol);
MolOps::dativeBondsToHaptic(*mol);
CHECK(initSmi == MolToSmiles(*mol));
std::string endpts;
std::string attach;
auto bond10 = mol->getBondWithIdx(10);
CHECK(bond10->getBondType() == Bond::DATIVE);
CHECK(bond10->getPropIfPresent(common_properties::_MolFileBondEndPts,
endpts));
CHECK(endpts == "(5 2 3 1 4 5)");
auto bond11 = mol->getBondWithIdx(11);
CHECK(bond11->getBondType() == Bond::DATIVE);
CHECK(bond11->getPropIfPresent(common_properties::_MolFileBondEndPts,
endpts));
CHECK(endpts == "(5 7 8 6 9 10)");
}
}
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