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//
// Copyright (C) 2017 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 <iostream>
#include <string>
#include <map>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/MolBundle.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Resonance.h>
using namespace RDKit;
void testBaseFunctionality() {
BOOST_LOG(rdInfoLog) << "-----------------------\n"
<< " testBaseFunctionality" << std::endl;
ROMOL_SPTR mol(SmilesToMol("CC[C@H](C)F"));
{
MolBundle bundle;
TEST_ASSERT(bundle.size() == 0);
TEST_ASSERT(bundle.addMol(mol) == 1);
TEST_ASSERT(bundle.size() == 1);
TEST_ASSERT(bundle.addMol(ROMOL_SPTR(SmilesToMol("CC[C@@H](C)F"))) == 2);
TEST_ASSERT(bundle.size() == 2);
MolBundle bundle2(bundle);
TEST_ASSERT(bundle2.size() == 2);
TEST_ASSERT(bundle.getMol(0)->getNumAtoms() == 5);
TEST_ASSERT(bundle[0]->getNumAtoms() == 5);
}
{
FixedMolSizeMolBundle bundle;
TEST_ASSERT(bundle.size() == 0);
TEST_ASSERT(bundle.addMol(mol) == 1);
TEST_ASSERT(bundle.size() == 1);
TEST_ASSERT(bundle.addMol(ROMOL_SPTR(SmilesToMol("CC[C@@H](C)F"))) == 2);
TEST_ASSERT(bundle.size() == 2);
FixedMolSizeMolBundle bundle2(bundle);
TEST_ASSERT(bundle2.size() == 2);
}
BOOST_LOG(rdInfoLog) << " Done." << std::endl;
}
void testSubstructFunctionality() {
BOOST_LOG(rdInfoLog) << "-----------------------\n"
<< " testSubstructFunctionality" << std::endl;
{
MolBundle bundle;
TEST_ASSERT(bundle.addMol(ROMOL_SPTR(SmilesToMol("CC[C@H](Cl)F"))) == 1);
TEST_ASSERT(bundle.addMol(ROMOL_SPTR(SmilesToMol("CC[C@@H](Cl)F"))) == 2);
ROMOL_SPTR qry(SmilesToMol("C[C@@H](Cl)F"));
MatchVectType match;
TEST_ASSERT(SubstructMatch(bundle, *qry, match));
TEST_ASSERT(SubstructMatch(bundle, *qry, match, true, true));
ROMOL_SPTR qry2(SmilesToMol("C[C@@H](Br)F"));
TEST_ASSERT(!SubstructMatch(bundle, *qry2, match));
TEST_ASSERT(!SubstructMatch(bundle, *qry2, match, true, true));
std::vector<MatchVectType> matches;
TEST_ASSERT(SubstructMatch(bundle, *qry, matches) == 1);
TEST_ASSERT(SubstructMatch(bundle, *qry, matches, false, true, true) == 1);
TEST_ASSERT(SubstructMatch(bundle, *qry2, matches) == 0);
TEST_ASSERT(SubstructMatch(bundle, *qry2, matches, false, true, true) == 0);
}
{
MolBundle bundle;
TEST_ASSERT(bundle.addMol(ROMOL_SPTR(SmilesToMol("C[C@H](Cl)F"))) == 1);
TEST_ASSERT(bundle.addMol(ROMOL_SPTR(SmilesToMol("C[C@@H](Cl)F"))) == 2);
ROMOL_SPTR mol(SmilesToMol("CC[C@@H](Cl)F"));
MatchVectType match;
TEST_ASSERT(SubstructMatch(*mol, bundle, match));
TEST_ASSERT(SubstructMatch(*mol, bundle, match, true, true));
ROMOL_SPTR mol2(SmilesToMol("CC[C@@H](Br)F"));
TEST_ASSERT(!SubstructMatch(*mol2, bundle, match));
TEST_ASSERT(!SubstructMatch(*mol2, bundle, match, true, true));
std::vector<MatchVectType> matches;
TEST_ASSERT(SubstructMatch(*mol, bundle, matches) == 1);
TEST_ASSERT(SubstructMatch(*mol, bundle, matches, false, true, true) == 1);
TEST_ASSERT(SubstructMatch(*mol2, bundle, matches) == 0);
TEST_ASSERT(SubstructMatch(*mol2, bundle, matches, false, true, true) == 0);
}
{
MolBundle bundle;
TEST_ASSERT(bundle.addMol(ROMOL_SPTR(SmilesToMol("CC[C@H](Cl)F"))) == 1);
TEST_ASSERT(bundle.addMol(ROMOL_SPTR(SmilesToMol("CC[C@@H](Cl)F"))) == 2);
MolBundle qbundle;
TEST_ASSERT(qbundle.addMol(ROMOL_SPTR(SmilesToMol("C[13C@H](Cl)F"))) == 1);
TEST_ASSERT(qbundle.addMol(ROMOL_SPTR(SmilesToMol("C[C@@H](Cl)F"))) == 2);
MatchVectType match;
TEST_ASSERT(SubstructMatch(bundle, qbundle, match));
TEST_ASSERT(SubstructMatch(bundle, qbundle, match, true, true));
std::vector<MatchVectType> matches;
TEST_ASSERT(SubstructMatch(bundle, qbundle, matches) == 1);
TEST_ASSERT(SubstructMatch(bundle, qbundle, matches, false, true, true) ==
1);
}
BOOST_LOG(rdInfoLog) << " Done." << std::endl;
}
void testExceptions() {
BOOST_LOG(rdInfoLog) << "-----------------------\n"
<< " testExceptions" << std::endl;
ROMOL_SPTR mol(SmilesToMol("C1CCC1"));
{
// FixedMolSizeMolBundle requires all molecules to have the same size
FixedMolSizeMolBundle bundle;
TEST_ASSERT(bundle.size() == 0);
TEST_ASSERT(bundle.addMol(mol) == 1);
TEST_ASSERT(bundle.size() == 1);
{
bool ok = false;
try {
bundle.addMol(ROMOL_SPTR(SmilesToMol("C1CC1")));
} catch (const ValueErrorException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
bool ok = false;
try {
bundle.addMol(ROMOL_SPTR(SmilesToMol("CCCC")));
} catch (const ValueErrorException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
bool ok = false;
try {
bundle.getMol(1);
} catch (const IndexErrorException &) {
ok = true;
}
TEST_ASSERT(ok);
}
{
bool ok = false;
try {
bundle[1];
} catch (const IndexErrorException &) {
ok = true;
}
TEST_ASSERT(ok);
}
}
{
// MolBundle requires supports different size molecules
MolBundle bundle;
TEST_ASSERT(bundle.size() == 0);
TEST_ASSERT(bundle.addMol(mol) == 1);
TEST_ASSERT(bundle.size() == 1);
bundle.addMol(ROMOL_SPTR(SmilesToMol("C1CC1")));
bundle.addMol(ROMOL_SPTR(SmilesToMol("CCCC")));
TEST_ASSERT(bundle.size() == 3);
}
BOOST_LOG(rdInfoLog) << " Done." << std::endl;
}
int main() {
RDLog::InitLogs();
#if 1
testBaseFunctionality();
testSubstructFunctionality();
testExceptions();
#endif
return 0;
}
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