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//
// Copyright (C) 2019 Greg Landrum
//
// @@ 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.
//
#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
// this in one cpp file
#include "catch.hpp"
#include <memory>
#include <RDGeneral/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/Fingerprints/MorganFingerprints.h>
#include <RDGeneral/Exceptions.h>
#include <GraphMol/Fingerprints/RDKitFPGenerator.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <DataStructs/ExplicitBitVect.h>
#include <DataStructs/BitOps.h>
#include <string>
using namespace RDKit;
TEST_CASE("Github 2051", "[patternfp][bug]") {
auto mol = "CCC1CC1"_smiles;
std::unique_ptr<ExplicitBitVect> mfp(PatternFingerprintMol(*mol));
REQUIRE(mfp);
SECTION("basics1") {
auto qmol = "**"_smarts;
std::unique_ptr<ExplicitBitVect> qfp(PatternFingerprintMol(*qmol));
REQUIRE(qfp);
CHECK(AllProbeBitsMatch(*qfp, *mfp));
}
SECTION("basics2") {
auto qmol = "*"_smarts;
std::unique_ptr<ExplicitBitVect> qfp(PatternFingerprintMol(*qmol));
REQUIRE(qfp);
CHECK(AllProbeBitsMatch(*qfp, *mfp));
}
}
TEST_CASE("Github 2614", "[patternfp][bug]") {
SECTION("basics") {
auto mol =
"F[P-](F)(F)(F)(F)F.F[P-](F)(F)(F)(F)F.F[P-](F)(F)(F)(F)F.F[P-](F)(F)(F)(F)F.F[P-](F)(F)(F)(F)F.F[P-](F)(F)(F)(F)F.F[P-](F)(F)(F)(F)F.F[P-](F)(F)(F)(F)F.F[P-](F)(F)(F)(F)F.c1ccc2ccccc2c1"_smiles;
REQUIRE(mol);
std::unique_ptr<ExplicitBitVect> mfp(PatternFingerprintMol(*mol));
REQUIRE(mfp);
auto query = "c1ccc2ccccc2c1"_smiles;
REQUIRE(query);
std::unique_ptr<ExplicitBitVect> qfp(PatternFingerprintMol(*query));
REQUIRE(qfp);
CHECK(AllProbeBitsMatch(*qfp, *mfp));
}
}
TEST_CASE("Github 1761", "[patternfp][bug]") {
SECTION("throw ValueErrorException") {
auto mol = "CCC1CC1"_smiles;
try
{
RDKit::MorganFingerprints::getHashedFingerprint(*mol, 0, 0);
FAIL("Expected ValueErrorException");
}
catch (const ValueErrorException &e)
{
REQUIRE(std::string(e.what()) == "nBits can not be zero");
}
}
}
TEST_CASE("RDKit bits per feature", "[fpgenerator][rdkit]") {
auto m1 = "CCCO"_smiles;
REQUIRE(m1);
SECTION("defaults") {
unsigned int minPath = 1;
unsigned int maxPath = 2;
std::unique_ptr<FingerprintGenerator<std::uint64_t>> fpGenerator(
RDKitFP::getRDKitFPGenerator<std::uint64_t>(minPath, maxPath));
REQUIRE(fpGenerator);
std::unique_ptr<ExplicitBitVect> fp(fpGenerator->getFingerprint(*m1));
REQUIRE(fp);
CHECK(fp->getNumBits() == 2048);
CHECK(fp->getNumOnBits() == 8);
CHECK(fpGenerator->infoString().find("bitsPerFeature=2") !=
std::string::npos);
}
SECTION("change numBitsPerFeature") {
// I won't lie: having to do this makes my head hurt, but fixing it to create a
// ctor that takes a Parameters object is more effort than I can devote at the moment
unsigned int minPath = 1;
unsigned int maxPath = 2;
bool useHs = true;
bool branchedPaths = true;
bool useBondOrder = true;
AtomInvariantsGenerator *atomInvariantsGenerator = nullptr;
bool countSimulation = false;
const std::vector<std::uint32_t> countBounds = {1, 2, 4, 8};
std::uint32_t fpSize = 2048;
std::uint32_t numBitsPerFeature = 1;
std::unique_ptr<FingerprintGenerator<std::uint64_t>> fpGenerator(
RDKitFP::getRDKitFPGenerator<std::uint64_t>(
minPath, maxPath, useHs, branchedPaths, useBondOrder,
atomInvariantsGenerator, countSimulation, countBounds, fpSize,
numBitsPerFeature));
REQUIRE(fpGenerator);
std::unique_ptr<ExplicitBitVect> fp(fpGenerator->getFingerprint(*m1));
REQUIRE(fp);
CHECK(fp->getNumBits() == 2048);
CHECK(fp->getNumOnBits() == 4);
CHECK(fpGenerator->infoString().find("bitsPerFeature=1") !=
std::string::npos);
}
}
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