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#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
// this in one cpp file
#include "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
using namespace RDKit;
TEST_CASE("SMILES Parsing works", "[molops]") {
std::unique_ptr<RWMol> mol(SmilesToMol("C1CC1"));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 3);
}
TEST_CASE("Sanitization tests", "[molops]") {
std::unique_ptr<RWMol> mol(SmilesToMol("C1=CC=CC=C1Cc2ccccc2", false, false));
REQUIRE(mol);
REQUIRE(mol->getNumAtoms() == 13);
SECTION("properties") {
mol->updatePropertyCache();
CHECK(mol->getAtomWithIdx(0)->getTotalNumHs() == 1);
CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
CHECK(mol->getAtomWithIdx(7)->getIsAromatic());
SECTION("aromaticity") {
unsigned int opThatFailed;
MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_SETAROMATICITY);
// mol->debugMol(std::cerr);
CHECK(mol->getAtomWithIdx(7)->getIsAromatic());
// blocked by #1730
// CHECK(mol->getAtomWithIdx(0)->getIsAromatic());
}
SECTION("kekulize") {
unsigned int opThatFailed;
MolOps::sanitizeMol(*mol, opThatFailed, MolOps::SANITIZE_KEKULIZE);
CHECK(!mol->getAtomWithIdx(0)->getIsAromatic());
CHECK(!mol->getAtomWithIdx(7)->getIsAromatic());
}
}
}
TEST_CASE("Github #2062", "[bug, molops]") {
SmilesParserParams ps;
ps.removeHs = false;
ps.sanitize = true;
std::unique_ptr<RWMol> mol(SmilesToMol("[C:1][C:2]([H:3])([H])[O:4][H]", ps));
REQUIRE(mol);
CHECK(mol->getNumAtoms() == 6);
mol->getAtomWithIdx(1)->setProp("intProp", 42);
MolOps::mergeQueryHs(*mol);
CHECK(mol->getNumAtoms() == 3);
SECTION("basics") { CHECK(mol->getAtomWithIdx(1)->getAtomMapNum() == 2); }
SECTION("other props") {
REQUIRE(mol->getAtomWithIdx(1)->hasProp("intProp"));
CHECK(mol->getAtomWithIdx(1)->getProp<int>("intProp") == 42);
}
}
TEST_CASE("Github #2086", "[bug, molops]") {
SECTION("reported version") {
auto mol = "C1CCCC1"_smiles;
REQUIRE(mol);
MolOps::addHs(*mol);
REQUIRE(mol->getNumAtoms() == 15);
mol->removeBond(4, 13);
MolOps::removeHs(*mol);
REQUIRE(mol->getNumAtoms() == 6);
}
}
TEST_CASE("github #299", "[bug, molops, SSSR]"){
SECTION("simplified"){
auto mol = "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;
REQUIRE(mol);
REQUIRE(mol->getNumAtoms()==9);
}
SECTION("old example from molopstest"){
auto mol = "C123C45C11C44C55C22C33C14C523"_smiles;
REQUIRE(mol);
REQUIRE(mol->getNumAtoms()==9);
}
SECTION("carborane"){
std::unique_ptr<RWMol> mol(SmilesToMol("[B]1234[B]567[B]118[B]229[B]33%10[B]454[B]656[B]711[B]822[C]933[B]%1045[C]6123",0,false));
REQUIRE(mol);
CHECK(mol->getNumAtoms()==12);
mol->updatePropertyCache(false);
MolOps::findSSSR(*mol);
REQUIRE(mol->getRingInfo()->isInitialized());
}
SECTION("original report from ChEbI"){
std::string pathName = getenv("RDBASE");
pathName += "/Code/GraphMol/test_data/";
std::unique_ptr<RWMol> mol(MolFileToMol(pathName + "ChEBI_50252.mol",false));
REQUIRE(mol);
CHECK(mol->getNumAtoms()==80);
mol->updatePropertyCache(false);
MolOps::findSSSR(*mol);
REQUIRE(mol->getRingInfo()->isInitialized());
}
}
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