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17323d11bf
* Modify removeHs so that it does not remove degree 0 atoms Update the docs at the same time. * include a warning when not removing some Hs * clear up a problem with the warning log
75 lines
2.4 KiB
C++
75 lines
2.4 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/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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