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rdkit/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp
Schneider 8aac978f1b ChemReactions: Extented functionality of chemical reactions 
- Module to generate reaction fingerprints: structural FP for screening,
  difference FP for similarity search
- Add some utility functions to simplify handling of reactions
- Add new functionality to include agents in the reactions, some adaptions
  to parsers and writers had to be done
- Supports intra-bond breaks in products now
- Molecules with rxn role (atom property) can be parse as reaction now
2014-08-19 13:08:11 +02:00

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// $Id$
//
// Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <GraphMol/RDKitBase.h>
#include <string>
#include <iostream>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include "GraphMol/ChemReactions/ReactionFingerprints.h"
#include <DataStructs/BitOps.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>
#include <GraphMol/Fingerprints/AtomPairs.h>
using namespace RDKit;
void testStructuralFingerprintsReaction(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Reaction StructuralFingerprint" << std::endl;
{
std::string reaction, reactionq;
ChemicalReaction* rxn, *rxnq;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "C1CCCCC1>>C1CCNCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
ReactionFingerprintParams params;
params.fpType = PatternFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxnq->getNumReactantTemplates() == 1);
TEST_ASSERT(rxnq->getNumProductTemplates() == 1);
MOL_SPTR_VECT::const_iterator reacts_iter = rxn->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator reacts_iterq = rxnq->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator products_iter = rxn->beginProductTemplates();
MOL_SPTR_VECT::const_iterator products_iterq = rxnq->beginProductTemplates();
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*reacts_iter->get(),*reacts_iterq->get(),mv))
TEST_ASSERT(SubstructMatch(*products_iter->get(),*products_iterq->get(),mv))
delete rxn;
delete rxnq;
delete rxnFP;
delete rxnqFP;
}
{
std::string reaction, reactionq;
ChemicalReaction* rxn, *rxnq;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "C1CCCCC1>>C1CCOCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
ReactionFingerprintParams params;
params.fpType = PatternFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
TEST_ASSERT(!AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxnq->getNumReactantTemplates() == 1);
TEST_ASSERT(rxnq->getNumProductTemplates() == 1);
MOL_SPTR_VECT::const_iterator reacts_iter = rxn->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator reacts_iterq = rxnq->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator products_iter = rxn->beginProductTemplates();
MOL_SPTR_VECT::const_iterator products_iterq = rxnq->beginProductTemplates();
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*reacts_iter->get(),*reacts_iterq->get(),mv))
TEST_ASSERT(!SubstructMatch(*products_iter->get(),*products_iterq->get(),mv))
delete rxn;
delete rxnq;
delete rxnFP;
delete rxnqFP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = ">>C1CCNCC1";
reactionq2 = ">>C1CCOCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpType = PatternFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(!AllProbeBitsMatch(*rxnq2FP,*rxnFP));
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxnq->getNumReactantTemplates() == 0);
TEST_ASSERT(rxnq->getNumProductTemplates() == 1);
TEST_ASSERT(rxnq2->getNumReactantTemplates() == 0);
TEST_ASSERT(rxnq2->getNumProductTemplates() == 1);
MOL_SPTR_VECT::const_iterator products_iter = rxn->beginProductTemplates();
MOL_SPTR_VECT::const_iterator products_iterq = rxnq->beginProductTemplates();
MOL_SPTR_VECT::const_iterator products_iterq2 = rxnq2->beginProductTemplates();
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*products_iter->get(),*products_iterq->get(),mv))
TEST_ASSERT(!SubstructMatch(*products_iter->get(),*products_iterq2->get(),mv))
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "C1CCCCC1>>";
reactionq2 = "C1CCOCC1>>";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpType = PatternFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(!AllProbeBitsMatch(*rxnq2FP,*rxnFP));
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxnq->getNumReactantTemplates() == 1);
TEST_ASSERT(rxnq->getNumProductTemplates() == 0);
TEST_ASSERT(rxnq2->getNumReactantTemplates() == 1);
TEST_ASSERT(rxnq2->getNumProductTemplates() == 0);
MOL_SPTR_VECT::const_iterator react_iter = rxn->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator react_iterq = rxnq->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator react_iterq2 = rxnq2->beginReactantTemplates();
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*react_iter->get(),*react_iterq->get(),mv))
TEST_ASSERT(!SubstructMatch(*react_iter->get(),*react_iterq2->get(),mv))
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "CCC>>CNC";
reactionq2 = "CCCCC>>CCCCN";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpType = PatternFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(AllProbeBitsMatch(*rxnq2FP,*rxnFP));
TEST_ASSERT(rxn->getNumReactantTemplates() == 1);
TEST_ASSERT(rxn->getNumProductTemplates() == 1);
TEST_ASSERT(rxnq->getNumReactantTemplates() == 1);
TEST_ASSERT(rxnq->getNumProductTemplates() == 1);
TEST_ASSERT(rxnq2->getNumReactantTemplates() == 1);
TEST_ASSERT(rxnq2->getNumProductTemplates() == 1);
MOL_SPTR_VECT::const_iterator react_iter = rxn->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator react_iterq = rxnq->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator react_iterq2 = rxnq2->beginReactantTemplates();
MOL_SPTR_VECT::const_iterator products_iter = rxn->beginProductTemplates();
MOL_SPTR_VECT::const_iterator products_iterq = rxnq->beginProductTemplates();
MOL_SPTR_VECT::const_iterator products_iterq2 = rxnq2->beginProductTemplates();
MatchVectType mv;
TEST_ASSERT(SubstructMatch(*react_iter->get(),*react_iterq->get(),mv))
TEST_ASSERT(SubstructMatch(*react_iter->get(),*react_iterq2->get(),mv))
TEST_ASSERT(SubstructMatch(*products_iter->get(),*products_iterq->get(),mv))
TEST_ASSERT(SubstructMatch(*products_iter->get(),*products_iterq2->get(),mv))
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
unsigned int nWarn,nError,which;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "CCC>>CNC";
reactionq2 = "CCCCC>>CCCCN";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpType = PatternFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(AllProbeBitsMatch(*rxnq2FP,*rxnFP));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *rxnq));
TEST_ASSERT(hasReactionSubstructMatch(*rxn, *rxnq2));
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "C1CCCCC1>>C1CCNCC1";
reactionq2 = "C1CCCCC1>>C1CCOCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpType = MorganFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(!AllProbeBitsMatch(*rxnq2FP,*rxnFP));
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "C1CCCCC1>>C1CCNCC1";
reactionq2 = "C1CCCCC1>>C1CCOCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(!AllProbeBitsMatch(*rxnq2FP,*rxnFP));
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "C1CCCCC1>>C1CCNCC1";
reactionq2 = "C1CCCCC1>>C1CCOCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpType = TopologicalTorsion;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(!AllProbeBitsMatch(*rxnq2FP,*rxnFP));
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "C1CCCCC1>>C1CCNCC1";
reactionq2 = "C1CCCCC1>>C1CCOCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpType = RDKitFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(!AllProbeBitsMatch(*rxnq2FP,*rxnFP));
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>>C1CCNCC1";
reactionq = "C1CCCCC1>>C1CCNCC1";
reactionq2 = "C1CCCCC1>>C1CCOCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ReactionFingerprintParams params;
params.fpType = RDKitFP;
params.fpSize = 4096;
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, params);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, params);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, params);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(!AllProbeBitsMatch(*rxnq2FP,*rxnFP));
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>C(=O)O.[Na]>C1CCNCC1";
reactionq = "C1CCCCC1>C(=O)O.[Na]>C1CCNCC1";
reactionq2 = "C1CCCCC1>>C1CCNCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, DefaultStructuralFPParams);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, DefaultStructuralFPParams);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, DefaultStructuralFPParams);
TEST_ASSERT(AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(AllProbeBitsMatch(*rxnq2FP,*rxnFP));
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
{
std::string reaction, reactionq, reactionq2;
ChemicalReaction* rxn, *rxnq, *rxnq2;
reaction = "C1CCCCC1>[Na]>C1CCNCC1";
reactionq = "C1CCCCC1>C(=O)O.[Na]>C1CCNCC1";
reactionq2 = "C1CCCCC1>>C1CCNCC1";
rxn = RxnSmartsToChemicalReaction(reaction,0,true);
rxnq = RxnSmartsToChemicalReaction(reactionq,0,true);
rxnq2 = RxnSmartsToChemicalReaction(reactionq2,0,true);
TEST_ASSERT(rxn);
TEST_ASSERT(rxnq);
TEST_ASSERT(rxnq2);
ExplicitBitVect *rxnFP = StructuralFingerprintChemReaction(*rxn, DefaultStructuralFPParams);
ExplicitBitVect *rxnqFP = StructuralFingerprintChemReaction(*rxnq, DefaultStructuralFPParams);
ExplicitBitVect *rxnq2FP = StructuralFingerprintChemReaction(*rxnq2, DefaultStructuralFPParams);
TEST_ASSERT(!AllProbeBitsMatch(*rxnqFP,*rxnFP));
TEST_ASSERT(AllProbeBitsMatch(*rxnq2FP,*rxnFP));
delete rxn;
delete rxnq;
delete rxnq2;
delete rxnFP;
delete rxnqFP;
delete rxnq2FP;
}
}
void testDifferenceFingerprintsReaction(){
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Reaction DifferenceFingerprint" << std::endl;
{
std::string reaction1, reaction2;
ChemicalReaction* rxn1, *rxn2;
reaction1 = "C1CCCCC1>>C1CCCCC1";
reaction2 = "C1CCCCC1>>C1CCNCC1";
rxn1 = RxnSmartsToChemicalReaction(reaction1,0,true);
rxn2 = RxnSmartsToChemicalReaction(reaction2,0,true);
TEST_ASSERT(rxn1);
TEST_ASSERT(rxn2);
SparseIntVect<boost::uint32_t> *rxn1FP = DifferenceFingerprintChemReaction(*rxn1);
SparseIntVect<boost::uint32_t> *rxn2FP = DifferenceFingerprintChemReaction(*rxn2);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) == 0.0);;
delete rxn1;
delete rxn2;
delete rxn1FP;
delete rxn2FP;
}
{
std::string reaction1, reaction2;
ChemicalReaction* rxn1, *rxn2;
reaction1 = "C1CCCCC1>>C1CCOCC1";
reaction2 = "C1CCCCC1>>C1CCNCC1";
rxn1 = RxnSmartsToChemicalReaction(reaction1,0,true);
rxn2 = RxnSmartsToChemicalReaction(reaction2,0,true);
TEST_ASSERT(rxn1);
TEST_ASSERT(rxn2);
SparseIntVect<boost::uint32_t> *rxn1FP = DifferenceFingerprintChemReaction(*rxn1);
SparseIntVect<boost::uint32_t> *rxn2FP = DifferenceFingerprintChemReaction(*rxn2);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) > 0.0);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) <= 1.0);
delete rxn1;
delete rxn2;
delete rxn1FP;
delete rxn2FP;
}
{
std::string reaction1, reaction2;
ChemicalReaction* rxn1, *rxn2;
reaction1 = "c1ccccc1>>c1ccncn1";
reaction2 = "c1ccccc1>>c1ccncc1";
rxn1 = RxnSmartsToChemicalReaction(reaction1,0,true);
rxn2 = RxnSmartsToChemicalReaction(reaction2,0,true);
TEST_ASSERT(rxn1);
TEST_ASSERT(rxn2);
SparseIntVect<boost::uint32_t> *rxn1FP = DifferenceFingerprintChemReaction(*rxn1);
SparseIntVect<boost::uint32_t> *rxn2FP = DifferenceFingerprintChemReaction(*rxn2);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) > 0.0);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) <= 1.0);
delete rxn1;
delete rxn2;
delete rxn1FP;
delete rxn2FP;
}
{
std::string reaction1, reaction2;
ChemicalReaction* rxn1, *rxn2;
reaction1 = "c1ccccc1>>c1ccncn1";
reaction2 = "c1ccccc1>>c1ccncc1";
rxn1 = RxnSmartsToChemicalReaction(reaction1,0,true);
rxn2 = RxnSmartsToChemicalReaction(reaction2,0,true);
TEST_ASSERT(rxn1);
TEST_ASSERT(rxn2);
ReactionFingerprintParams params;
params.fpType = MorganFP;
SparseIntVect<boost::uint32_t> *rxn1FP = DifferenceFingerprintChemReaction(*rxn1, params);
SparseIntVect<boost::uint32_t> *rxn2FP = DifferenceFingerprintChemReaction(*rxn2, params);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) > 0.0);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) <= 1.0);
delete rxn1;
delete rxn2;
delete rxn1FP;
delete rxn2FP;
}
{
std::string reaction1, reaction2;
ChemicalReaction* rxn1, *rxn2;
reaction1 = "c1ccccc1>>c1ccncn1";
reaction2 = "c1ccccc1>>c1ccncc1";
rxn1 = RxnSmartsToChemicalReaction(reaction1,0,true);
rxn2 = RxnSmartsToChemicalReaction(reaction2,0,true);
TEST_ASSERT(rxn1);
TEST_ASSERT(rxn2);
ReactionFingerprintParams params;
params.fpType = TopologicalTorsion;
SparseIntVect<boost::uint32_t> *rxn1FP = DifferenceFingerprintChemReaction(*rxn1, params);
SparseIntVect<boost::uint32_t> *rxn2FP = DifferenceFingerprintChemReaction(*rxn2, params);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) > 0.0);
TEST_ASSERT(TanimotoSimilarity(*rxn1FP,*rxn2FP) <= 1.0);
delete rxn1;
delete rxn2;
delete rxn1FP;
delete rxn2FP;
}
}
int main() {
RDLog::InitLogs();
BOOST_LOG(rdInfoLog) << "********************************************************\n";
BOOST_LOG(rdInfoLog) << "Testing Chemical Reaction Fingerprints \n";
testStructuralFingerprintsReaction();
testDifferenceFingerprintsReaction();
BOOST_LOG(rdInfoLog) << "*******************************************************\n";
return(0);
}
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