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//
// Copyright (C) David Cosgrove 2024.
//
// @@ 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 <DataStructs/ExplicitBitVect.h>
#include <GraphMol/Chirality.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/MolPickler.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/FileParsers/FileWriters.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/SynthonSpaceSearch/Synthon.h>
#include <GraphMol/SynthonSpaceSearch/SynthonSpaceSearch_details.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmartsWrite.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
namespace RDKit::SynthonSpaceSearch {
Synthon::Synthon(const std::string &smi) : d_smiles(smi) {
v2::SmilesParse::SmilesParserParams params;
params.sanitize = false;
dp_origMol = v2::SmilesParse::MolFromSmiles(d_smiles, params);
if (!dp_origMol) {
// This should be rare, as it should be possible to assume that
// the people who made the SynthonSpace know what they're doing.
// Therefore, it's probably a corrupted or incorrect file, so
// bring it all down.
throw ValueErrorException("Unparsable synthon SMILES " + d_smiles);
}
calcProperties();
}
Synthon::Synthon(const Synthon &other)
: d_smiles(other.d_smiles),
dp_origMol(std::make_unique<ROMol>(*other.dp_origMol)),
dp_searchMol(std::make_unique<ROMol>(*other.dp_searchMol)),
dp_pattFP(std::make_unique<ExplicitBitVect>(*other.dp_pattFP)),
dp_FP(std::make_unique<ExplicitBitVect>(*other.dp_FP)),
d_connRegions(other.d_connRegions),
d_numDummies(other.d_numDummies),
d_numHeavyAtoms(other.d_numHeavyAtoms),
d_numChiralAtoms(other.d_numChiralAtoms),
d_numChiralAtomsExcDummies(other.d_numChiralAtomsExcDummies),
d_molWt(other.d_molWt) {}
Synthon &Synthon::operator=(const Synthon &other) {
if (this == &other) {
return *this;
}
d_smiles = other.d_smiles;
if (other.dp_origMol) {
dp_origMol = std::make_unique<ROMol>(*other.dp_origMol);
} else {
dp_origMol.reset();
}
if (other.dp_searchMol) {
dp_searchMol = std::make_unique<ROMol>(*other.dp_searchMol);
} else {
dp_searchMol.reset();
}
if (other.dp_pattFP) {
dp_pattFP = std::make_unique<ExplicitBitVect>(*other.dp_pattFP);
} else {
dp_pattFP.reset();
}
if (other.dp_FP) {
dp_FP = std::make_unique<ExplicitBitVect>(*other.dp_FP);
} else {
dp_FP.reset();
}
if (!other.d_connRegions.empty()) {
d_connRegions.clear();
std::transform(
other.d_connRegions.begin(), other.d_connRegions.end(),
std::back_inserter(d_connRegions),
[](const std::shared_ptr<ROMol> &m) -> std::shared_ptr<ROMol> {
return std::make_shared<ROMol>(*m);
});
} else {
d_connRegions.clear();
}
d_numDummies = other.d_numDummies;
d_numHeavyAtoms = other.d_numHeavyAtoms;
d_numChiralAtoms = other.d_numChiralAtoms;
d_numChiralAtomsExcDummies = other.d_numChiralAtomsExcDummies;
d_molWt = other.d_molWt;
return *this;
}
const std::unique_ptr<ROMol> &Synthon::getOrigMol() const { return dp_origMol; }
const std::unique_ptr<ROMol> &Synthon::getSearchMol() const {
return dp_searchMol;
}
const std::unique_ptr<ExplicitBitVect> &Synthon::getPattFP() const {
return dp_pattFP;
}
const std::unique_ptr<ExplicitBitVect> &Synthon::getFP() const { return dp_FP; }
const std::vector<std::shared_ptr<ROMol>> &Synthon::getConnRegions() const {
return d_connRegions;
}
void Synthon::setSearchMol(std::unique_ptr<ROMol> mol) {
dp_searchMol = std::move(mol);
// There are probably extraneous props on the atoms and bonds
for (auto &atom : dp_searchMol->atoms()) {
atom->clearProp("molNum");
atom->clearProp("idx");
}
for (auto &bond : dp_searchMol->bonds()) {
bond->clearProp("molNum");
bond->clearProp("idx");
}
finishInitialization();
}
void Synthon::setFP(std::unique_ptr<ExplicitBitVect> fp) {
dp_FP = std::move(fp);
}
void Synthon::writeToDBStream(std::ostream &os) const {
streamWrite(os, d_smiles);
MolPickler::pickleMol(*dp_origMol, os, PicklerOps::AllProps);
MolPickler::pickleMol(*dp_searchMol, os, PicklerOps::AllProps);
const auto pattFPstr = getPattFP()->toString();
streamWrite(os, pattFPstr);
streamWrite(os, static_cast<std::uint64_t>(getConnRegions().size()));
for (const auto &cr : getConnRegions()) {
MolPickler::pickleMol(*cr, os, PicklerOps::AllProps);
}
if (dp_FP) {
streamWrite(os, true);
streamWrite(os, dp_FP->toString());
} else {
streamWrite(os, false);
}
streamWrite(os, d_numDummies);
streamWrite(os, d_numHeavyAtoms);
streamWrite(os, d_numChiralAtoms);
streamWrite(os, d_molWt);
}
void Synthon::readFromDBStream(std::istream &is, std::uint32_t version) {
streamRead(is, d_smiles, 0);
dp_origMol = std::make_unique<ROMol>();
MolPickler::molFromPickle(is, *dp_origMol);
dp_searchMol = std::make_unique<ROMol>();
MolPickler::molFromPickle(is, *dp_searchMol);
std::string pickle;
streamRead(is, pickle, 0);
dp_pattFP = std::make_unique<ExplicitBitVect>(pickle);
size_t numConnRegs;
streamRead(is, numConnRegs);
d_connRegions.resize(numConnRegs);
for (size_t i = 0; i < numConnRegs; ++i) {
d_connRegions[i] = std::make_shared<ROMol>();
MolPickler::molFromPickle(is, *d_connRegions[i]);
}
bool haveFP = false;
streamRead(is, haveFP);
if (haveFP) {
std::string pickle;
streamRead(is, pickle, 0);
dp_FP = std::make_unique<ExplicitBitVect>(pickle);
}
if (version > 3000) {
streamRead(is, d_numDummies);
streamRead(is, d_numHeavyAtoms);
streamRead(is, d_numChiralAtoms);
streamRead(is, d_molWt);
} else {
calcProperties();
}
}
void Synthon::finishInitialization() {
dp_pattFP.reset(PatternFingerprintMol(*dp_searchMol, PATT_FP_NUM_BITS));
d_connRegions.clear();
if (const auto cr = details::buildConnRegion(*dp_searchMol); cr) {
std::vector<std::unique_ptr<ROMol>> tmpFrags;
MolOps::getMolFrags(*cr, tmpFrags, false);
for (auto &f : tmpFrags) {
d_connRegions.push_back(std::shared_ptr<ROMol>(f.release()));
}
}
}
void Synthon::calcProperties() {
d_numDummies = 0;
d_numHeavyAtoms = 0;
MolOps::assignStereochemistry(*dp_origMol);
for (const auto atom : dp_origMol->atoms()) {
if (atom->getAtomicNum() == 0) {
d_numDummies++;
} else if (atom->getAtomicNum() > 1) {
d_numHeavyAtoms++;
}
}
Chirality::findPotentialStereo(*dp_origMol, true, true);
d_numChiralAtoms =
details::countChiralAtoms(*dp_origMol, &d_numChiralAtomsExcDummies);
d_molWt = Descriptors::calcAMW(*dp_origMol);
}
} // namespace RDKit::SynthonSpaceSearch
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