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//
// Copyright (c) 2014, 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 <GraphMol/RDKitBase.h>
#include <DataStructs/ExplicitBitVect.h>
#include <DataStructs/BitOps.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/Fingerprints/AtomPairs.h>
#include "GraphMol/ChemReactions/ReactionFingerprints.h"
#include <GraphMol/Fingerprints/MACCS.h>
#include <GraphMol/Fingerprints/MorganFingerprints.h>
#include <DataStructs/SparseIntVect.h>
#include <GraphMol/ChemReactions/ReactionUtils.h>
namespace {
RDKit::SparseIntVect<std::uint32_t> *generateFingerprint(
RDKit::ROMol &mol, unsigned int fpSize, RDKit::FingerprintType t) {
mol.updatePropertyCache(false);
RDKit::SparseIntVect<std::uint32_t> *res;
switch (t) {
case RDKit::AtomPairFP: {
RDKit::SparseIntVect<std::int32_t> *tmp1 =
RDKit::AtomPairs::getHashedAtomPairFingerprint(mol, fpSize);
res = new RDKit::SparseIntVect<std::uint32_t>(fpSize);
for (auto val : tmp1->getNonzeroElements()) {
res->setVal(static_cast<std::uint32_t>(val.first), val.second);
}
delete tmp1;
} break;
case RDKit::TopologicalTorsion: {
RDKit::SparseIntVect<boost::int64_t> *tmp2 =
RDKit::AtomPairs::getHashedTopologicalTorsionFingerprint(mol, fpSize);
res = new RDKit::SparseIntVect<std::uint32_t>(fpSize);
for (auto val : tmp2->getNonzeroElements()) {
res->setVal(static_cast<std::uint32_t>(val.first), val.second);
}
delete tmp2;
} break;
case RDKit::MorganFP: {
if (!mol.getRingInfo()->isInitialized()) {
mol.updatePropertyCache();
RDKit::MolOps::findSSSR(mol);
}
res = RDKit::MorganFingerprints::getHashedFingerprint(mol, 2, fpSize);
} break;
default:
std::stringstream err;
err << ">> unsupported fingerprint type" << std::endl;
throw RDKit::ChemicalReactionException(err.str());
}
return res;
}
ExplicitBitVect *generateFingerprintAsBitVect(RDKit::ROMol &mol,
unsigned int fpSize,
RDKit::FingerprintType t) {
mol.updatePropertyCache(false);
ExplicitBitVect *res;
switch (t) {
case RDKit::AtomPairFP:
res =
RDKit::AtomPairs::getHashedAtomPairFingerprintAsBitVect(mol, fpSize);
break;
case RDKit::RDKitFP:
res = RDKit::RDKFingerprintMol(mol, 1, 7, fpSize);
break;
case RDKit::TopologicalTorsion:
res = RDKit::AtomPairs::getHashedTopologicalTorsionFingerprintAsBitVect(
mol, fpSize);
break;
case RDKit::MorganFP: {
if (!mol.getRingInfo()->isInitialized()) {
mol.updatePropertyCache();
RDKit::MolOps::findSSSR(mol);
}
res = RDKit::MorganFingerprints::getFingerprintAsBitVect(mol, 2, fpSize);
} break;
case RDKit::PatternFP:
res = RDKit::PatternFingerprintMol(mol, fpSize);
break;
default:
std::stringstream err;
err << ">> unsupported fingerprint type" << std::endl;
throw RDKit::ChemicalReactionException(err.str());
}
return res;
}
} // namespace
namespace RDKit {
const ReactionFingerprintParams DefaultStructuralFPParams(true, 0.2, 1, 1, 4096,
PatternFP);
const ReactionFingerprintParams DefaultDifferenceFPParams(true, 0.0, 10, 1,
2048, AtomPairFP);
SparseIntVect<std::uint32_t> *generateFingerprintChemReactionAsCountVect(
const ChemicalReaction &rxn, unsigned int fpSize, FingerprintType t,
ReactionMoleculeType mt) {
PRECONDITION(fpSize != 0, "fpSize==0");
auto *result = new SparseIntVect<std::uint32_t>(fpSize);
auto begin = getStartIterator(rxn, mt);
auto end = getEndIterator(rxn, mt);
for (; begin != end; ++begin) {
SparseIntVect<std::uint32_t> *tmp = generateFingerprint(**begin, fpSize, t);
(*result) += *tmp;
delete tmp;
}
return result;
}
ExplicitBitVect *generateFingerprintChemReactionAsBitVect(
const ChemicalReaction &rxn, unsigned int fpSize, FingerprintType t,
ReactionMoleculeType mt) {
PRECONDITION(fpSize != 0, "fpSize==0");
auto *result = new ExplicitBitVect(fpSize);
auto begin = getStartIterator(rxn, mt);
auto end = getEndIterator(rxn, mt);
for (; begin != end; ++begin) {
ExplicitBitVect *tmp = generateFingerprintAsBitVect(**begin, fpSize, t);
(*result) |= *tmp;
delete tmp;
}
return result;
}
// caller owns the result, it must be deleted
ExplicitBitVect *StructuralFingerprintChemReaction(
const ChemicalReaction &rxn, const ReactionFingerprintParams ¶ms) {
PRECONDITION(params.fpSize != 0, "fpSize==0");
unsigned int fpSize_final = params.fpSize / 2;
if (params.includeAgents) {
unsigned agent_fp_size = params.fpSize / 3;
if (params.bitRatioAgents < 1.0) {
agent_fp_size =
int(ceil(static_cast<double>(params.fpSize) * params.bitRatioAgents));
}
unsigned scaling = !(agent_fp_size % 2) ? agent_fp_size : agent_fp_size - 1;
fpSize_final = (params.fpSize - scaling) / 2;
}
unsigned int fpSize_agent = params.fpSize - 2 * fpSize_final;
ExplicitBitVect *reactantFP = generateFingerprintChemReactionAsBitVect(
rxn, fpSize_final, params.fpType, Reactant);
ExplicitBitVect *productFP = generateFingerprintChemReactionAsBitVect(
rxn, fpSize_final, params.fpType, Product);
auto *res = new ExplicitBitVect;
/* concatenate the two bitvectors */
(*res) = *reactantFP + *productFP;
if (fpSize_agent > 0) {
ExplicitBitVect *agentFP = generateFingerprintChemReactionAsBitVect(
rxn, fpSize_agent, params.fpType, Agent);
(*res) += *agentFP;
delete agentFP;
}
delete reactantFP;
delete productFP;
return res;
}
SparseIntVect<std::uint32_t> *DifferenceFingerprintChemReaction(
const ChemicalReaction &rxn, const ReactionFingerprintParams ¶ms) {
PRECONDITION(params.fpSize != 0, "fpSize==0");
PRECONDITION(params.fpType > 0 && params.fpType < 4,
"Fingerprinttype not supported");
SparseIntVect<std::uint32_t> *reactantFP =
generateFingerprintChemReactionAsCountVect(rxn, params.fpSize,
params.fpType, Reactant);
SparseIntVect<std::uint32_t> *productFP =
generateFingerprintChemReactionAsCountVect(rxn, params.fpSize,
params.fpType, Product);
auto *res = new SparseIntVect<std::uint32_t>;
if (params.includeAgents) {
SparseIntVect<std::uint32_t> *agentFP =
generateFingerprintChemReactionAsCountVect(rxn, params.fpSize,
params.fpType, Agent);
(*productFP) *= params.nonAgentWeight;
(*reactantFP) *= params.nonAgentWeight;
(*agentFP) *= params.agentWeight;
(*res) = *productFP - *reactantFP + *agentFP;
delete agentFP;
}
/* subtract product FP from reactant FP */
else {
(*res) = *productFP - *reactantFP;
}
delete reactantFP;
delete productFP;
return res;
}
} // namespace RDKit
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