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https://github.com/rdkit/rdkit.git
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276 lines
9.2 KiB
C++
276 lines
9.2 KiB
C++
#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
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// this in one cpp file
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#include "catch.hpp"
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/Chirality.h>
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#include <GraphMol/FileParsers/FileParsers.h>
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/SmilesParse/SmartsWrite.h>
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using namespace RDKit;
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TEST_CASE("SMILES Parsing works", "[molops]") {
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std::unique_ptr<RWMol> mol(SmilesToMol("C1CC1"));
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REQUIRE(mol);
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REQUIRE(mol->getNumAtoms() == 3);
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}
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TEST_CASE("Sanitization tests", "[molops]") {
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std::unique_ptr<RWMol> mol(SmilesToMol("C1=CC=CC=C1Cc2ccccc2", false, false));
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REQUIRE(mol);
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REQUIRE(mol->getNumAtoms() == 13);
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SECTION("properties") {
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mol->updatePropertyCache();
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CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 1);
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CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
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CHECK(mol->getAtomWithIdx(7)->getIsAromatic());
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SECTION("aromaticity") {
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unsigned int opThatFailed;
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MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_SETAROMATICITY);
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// mol->debugMol(std::cerr);
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CHECK(mol->getAtomWithIdx(7)->getIsAromatic());
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// blocked by #1730
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// CHECK(mol->getAtomWithIdx(0)->getIsAromatic());
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}
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SECTION("kekulize") {
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unsigned int opThatFailed;
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MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_KEKULIZE);
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CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
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CHECK(!mol->getAtomWithIdx(7)->getIsAromatic());
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}
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}
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}
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TEST_CASE("Github #2062", "[bug, molops]") {
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SmilesParserParams ps;
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ps.removeHs = false;
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ps.sanitize = true;
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std::unique_ptr<RWMol> mol(SmilesToMol("[C:1][C:2]([H:3])([H])[O:4][H]", ps));
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REQUIRE(mol);
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CHECK(mol->getNumAtoms() == 6);
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mol->getAtomWithIdx(1)->setProp("intProp", 42);
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MolOps::mergeQueryHs(*mol);
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CHECK(mol->getNumAtoms() == 3);
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SECTION("basics") { CHECK(mol->getAtomWithIdx(1)->getAtomMapNum() == 2); }
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SECTION("other props") {
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REQUIRE(mol->getAtomWithIdx(1)->hasProp("intProp"));
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CHECK(mol->getAtomWithIdx(1)->getProp<int>("intProp") == 42);
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}
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}
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TEST_CASE("Github #2086", "[bug, molops]") {
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SECTION("reported version") {
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auto mol = "C1CCCC1"_smiles;
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REQUIRE(mol);
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MolOps::addHs(*mol);
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REQUIRE(mol->getNumAtoms() == 15);
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mol->removeBond(4, 13);
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MolOps::removeHs(*mol);
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REQUIRE(mol->getNumAtoms() == 6);
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}
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}
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TEST_CASE("github #299", "[bug, molops, SSSR]") {
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SECTION("simplified") {
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auto mol =
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"C13%13%14.C124%18.C25%13%15.C368%17.C4679.C75%10%17.C8%11%14%16.C9%11%12%18.C%10%12%15%16"_smiles;
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REQUIRE(mol);
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REQUIRE(mol->getNumAtoms() == 9);
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}
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SECTION("old example from molopstest") {
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auto mol = "C123C45C11C44C55C22C33C14C523"_smiles;
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REQUIRE(mol);
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REQUIRE(mol->getNumAtoms() == 9);
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}
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SECTION("carborane") {
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std::unique_ptr<RWMol> mol(
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SmilesToMol("[B]1234[B]567[B]118[B]229[B]33%10[B]454[B]656[B]711[B]822["
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"C]933[B]%1045[C]6123",
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0, false));
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REQUIRE(mol);
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CHECK(mol->getNumAtoms() == 12);
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mol->updatePropertyCache(false);
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MolOps::findSSSR(*mol);
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REQUIRE(mol->getRingInfo()->isInitialized());
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}
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SECTION("original report from ChEbI") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/GraphMol/test_data/";
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std::unique_ptr<RWMol> mol(
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MolFileToMol(pathName + "ChEBI_50252.mol", false));
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REQUIRE(mol);
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CHECK(mol->getNumAtoms() == 80);
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mol->updatePropertyCache(false);
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MolOps::findSSSR(*mol);
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REQUIRE(mol->getRingInfo()->isInitialized());
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}
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}
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TEST_CASE("github #2224", "[bug, molops, removeHs, query]") {
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SECTION("the original report") {
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std::string pathName = getenv("RDBASE");
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pathName += "/Code/GraphMol/test_data/";
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std::unique_ptr<RWMol> mol(MolFileToMol(pathName + "github2224_1.mol"));
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REQUIRE(mol);
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REQUIRE(mol->getNumAtoms() == 7);
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}
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SECTION("basics") {
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SmilesParserParams ps;
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ps.removeHs = false;
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ps.sanitize = true;
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std::unique_ptr<ROMol> mol(SmilesToMol("C[H]", ps));
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REQUIRE(mol);
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REQUIRE(mol->getNumAtoms() == 2);
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{ // The H without a query is removed
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std::unique_ptr<ROMol> m2(MolOps::removeHs(*mol));
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CHECK(m2->getNumAtoms() == 1);
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}
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{ // but if we add a query feature it's not removed
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RWMol m2(*mol);
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auto *qa = new QueryAtom(1);
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m2.replaceAtom(1, qa);
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m2.getAtomWithIdx(1)->setAtomicNum(1);
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MolOps::removeHs(m2);
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CHECK(m2.getNumAtoms() == 2);
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delete qa;
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}
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}
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}
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TEST_CASE(
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"github #2268: Recognize N in three-membered rings as potentially chiral",
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"[bug,stereo]") {
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SECTION("basics: N in a 3 ring") {
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const auto mol = "C[N@]1CC1C"_smiles;
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REQUIRE(mol);
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CHECK(mol->getAtomWithIdx(1)->getChiralTag() != Atom::CHI_UNSPECIFIED);
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}
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SECTION("basics: N in a 4 ring") {
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const auto mol = "C[N@]1CCC1C"_smiles;
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REQUIRE(mol);
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CHECK(mol->getAtomWithIdx(1)->getChiralTag() == Atom::CHI_UNSPECIFIED);
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}
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SECTION("the original molecule") {
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std::string mb = R"CTAB(
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Mrv1810 02131915062D
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18 20 0 0 1 0 999 V2000
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-0.7207 -1.3415 0.0000 N 0 0 1 0 0 0 0 0 0 0 0 0
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-0.0583 -0.8416 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
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-0.0083 -1.7540 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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-1.3956 -0.8666 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0
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-0.3250 -0.0667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.1955 -0.6499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-1.1499 -0.0792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.6541 -0.4292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.7830 -1.2291 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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-1.6081 -1.6623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-2.4080 0.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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1.3665 -0.8374 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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0.6416 0.3958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.1996 0.3708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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-3.4121 1.1624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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1.3498 0.8207 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.0790 -0.4167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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2.0665 0.4083 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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2 1 1 0 0 0 0
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1 3 1 1 0 0 0
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4 1 1 0 0 0 0
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5 2 1 0 0 0 0
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4 6 1 0 0 0 0
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7 4 1 0 0 0 0
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2 8 1 6 0 0 0
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9 6 2 0 0 0 0
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4 10 1 1 0 0 0
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11 6 1 0 0 0 0
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12 8 2 0 0 0 0
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13 8 1 0 0 0 0
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14 11 1 0 0 0 0
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15 14 1 0 0 0 0
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16 13 2 0 0 0 0
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17 12 1 0 0 0 0
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18 16 1 0 0 0 0
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2 3 1 0 0 0 0
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5 7 1 0 0 0 0
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17 18 2 0 0 0 0
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M END
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)CTAB";
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std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
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REQUIRE(mol);
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CHECK(mol->getAtomWithIdx(0)->getChiralTag() != Atom::CHI_UNSPECIFIED);
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}
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}
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TEST_CASE("github #2244", "[bug, molops, stereo]") {
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SECTION("the original report") {
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auto mol = "CC=CC=CC"_smiles;
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REQUIRE(mol);
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MolOps::findPotentialStereoBonds(*mol, true);
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CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOANY);
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CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
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mol->getBondWithIdx(3)->setStereo(Bond::STEREONONE);
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MolOps::findPotentialStereoBonds(*mol, true);
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CHECK(mol->getBondWithIdx(1)->getStereo() == Bond::STEREOANY);
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CHECK(mol->getBondWithIdx(3)->getStereo() == Bond::STEREOANY);
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}
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}
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TEST_CASE(
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"github #2258: heterocycles with exocyclic bonds not failing valence check",
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"[bug, molops]") {
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SECTION("the original report") {
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std::vector<std::string> smiles = {"C=n1ccnc1", "C#n1ccnc1"};
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for (auto smi : smiles) {
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CHECK_THROWS_AS(SmilesToMol(smi), MolSanitizeException);
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}
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}
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}
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TEST_CASE("github #908: AddHs() using 3D coordinates with 2D conformations",
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"[bug, molops]") {
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SECTION("basics: single atom mols") {
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std::vector<std::string> smiles = {"Cl", "O", "N", "C"};
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for (auto smi : smiles) {
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// std::cerr << smi << std::endl;
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std::unique_ptr<RWMol> mol(SmilesToMol(smi));
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REQUIRE(mol);
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auto conf = new Conformer(1);
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conf->set3D(false);
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conf->setAtomPos(0, RDGeom::Point3D(0, 0, 0));
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mol->addConformer(conf, true);
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bool explicitOnly = false;
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bool addCoords = true;
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MolOps::addHs(*mol, explicitOnly, addCoords);
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for (size_t i = 0; i < mol->getNumAtoms(); ++i) {
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// std::cerr << " " << i << " " << conf->getAtomPos(i) << std::endl;
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CHECK(conf->getAtomPos(i).z == 0.0);
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}
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}
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}
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}
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TEST_CASE(
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"github #2423: Incorrect assignment of explicit Hs to Al+3 read from mol "
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"block",
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"[bug, molops]") {
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SECTION("basics: single atom mols") {
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std::string mb = R"CTAB(2300
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-OEChem-01301907122D
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1 0 0 0 0 0 0 0 0999 V2000
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-66.7000 999.0000 0.0000 Al 0 1 0 0 0 0 0 0 0 0 0 0
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M CHG 1 1 3
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M END)CTAB";
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std::unique_ptr<ROMol> mol(MolBlockToMol(mb));
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REQUIRE(mol);
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CHECK(mol->getAtomWithIdx(0)->getFormalCharge() == 3);
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CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 0);
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}
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}
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