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// $Id$
//
// Copyright (C) 2013 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.
//
#include <RDGeneral/test.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/ReducedGraphs/ReducedGraphs.h>
#include <DataStructs/ExplicitBitVect.h>
#include <RDGeneral/RDLog.h>
#include <string>
using namespace RDKit;
void test1() {
BOOST_LOG(rdInfoLog) << "testing basics" << std::endl;
{
std::string smi = "c1ccccc1CCO";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
{
std::string smi = "c1cnccc1CCO";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
{
std::string smi = "OCCC1=CC2=C(C=CC=C2)C=C1";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
{
std::string smi = "OCCC1=CC2=C(C=CC=C2)N=C1";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
{
std::string smi = "OCCC1=CC2=C(CCCC2)N=C1";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
{
std::string smi = "OCCc1ccc(CC(C)C)cc1";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
{
std::string smi = "OCCC1CCC(CC(C)C)CC1";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
{
std::string smi = "OCCC1=CCC(CC(C)C)CC1";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
{
std::string smi = "OCCC1=CCC(CC(C)C)C=C1";
ROMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m1);
std::cerr << *fp << std::endl;
delete fp;
delete m1;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void test2() {
BOOST_LOG(rdInfoLog) << "testing basics2" << std::endl;
{
std::string smi1 = "c1ccccc1CCO";
std::string smi2 = "C1=CC=CCC1CCO";
ROMol *m1 = SmilesToMol(smi1);
TEST_ASSERT(m1);
ROMol *m2 = SmilesToMol(smi2);
TEST_ASSERT(m2);
RDNumeric::DoubleVector *fp1 = ReducedGraphs::getErGFingerprint(*m1);
RDNumeric::DoubleVector *fp2 = ReducedGraphs::getErGFingerprint(*m2);
TEST_ASSERT(feq(RDNumeric::TanimotoSimilarity(*fp1, *fp2), 1.0, 0.001));
delete fp1;
delete fp2;
delete m1;
delete m2;
}
{
std::string smi1 = "c1ccccc1CCO";
std::string smi2 = "C1CC=CCC1CCO";
ROMol *m1 = SmilesToMol(smi1);
TEST_ASSERT(m1);
ROMol *m2 = SmilesToMol(smi2);
TEST_ASSERT(m2);
RDNumeric::DoubleVector *fp1 = ReducedGraphs::getErGFingerprint(*m1);
RDNumeric::DoubleVector *fp2 = ReducedGraphs::getErGFingerprint(*m2);
TEST_ASSERT(!feq(RDNumeric::TanimotoSimilarity(*fp1, *fp2), 1.0, 0.001));
delete fp1;
delete fp2;
delete m1;
delete m2;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testCanRetrieveProp() {
BOOST_LOG(rdInfoLog) << "testing retrieving _ErGAtomTypes from property"
<< std::endl;
auto m = "OCCc1ccccc1"_smiles;
std::vector<std::vector<int>> expected{{0, 1}, {}, {}, {}, {5}};
std::vector<std::vector<int>> res;
std::unique_ptr<ROMol> mrg(
ReducedGraphs::generateMolExtendedReducedGraph(*m));
for (const auto atom : mrg->atoms()) {
std::vector<int> atomTypes;
TEST_ASSERT(atom->getPropIfPresent("_ErGAtomTypes", atomTypes));
res.push_back(atomTypes);
}
TEST_ASSERT(res == expected);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testGithub8201() {
BOOST_LOG(rdInfoLog) << "testing Github8201 : not filling last bits."
<< std::endl;
const auto m = "c4ccc(C(CCCCCCCCCCC(c1ccccc1)C2CCNCC2)C3CCNCC3)cc4"_smiles;
TEST_ASSERT(m);
RDNumeric::DoubleVector *fp = ReducedGraphs::getErGFingerprint(*m);
TEST_ASSERT(fp->size() == 315);
TEST_ASSERT((*fp)[314] == 1.0);
BOOST_LOG(rdInfoLog) << "done" << std::endl;
delete fp;
}
int main(int argc, char *argv[]) {
(void)argc;
(void)argv;
RDLog::InitLogs();
test1();
test2();
testCanRetrieveProp();
testGithub8201();
return 0;
}
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