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//
// Copyright (C) 2018-2021 Susan H. Leung and other RDKit contributors
//
// @@ 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 "Normalize.h"
#include <string>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ChemReactions/Reaction.h>
#include <GraphMol/ChemReactions/ReactionParser.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SanitException.h>
#include <GraphMol/ChemTransforms/ChemTransforms.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/flyweight.hpp>
#include <boost/flyweight/key_value.hpp>
#include <boost/flyweight/no_tracking.hpp>
#include <RDGeneral/BoostEndInclude.h>
using namespace std;
using namespace RDKit;
namespace RDKit {
class RWMol;
class ROMol;
namespace MolStandardize {
typedef boost::flyweight<
boost::flyweights::key_value<std::string, TransformCatalogParams>,
boost::flyweights::no_tracking>
param_filename_flyweight;
typedef boost::flyweight<boost::flyweights::key_value<
std::vector<std::pair<std::string, std::string>>,
TransformCatalogParams>,
boost::flyweights::no_tracking>
param_data_flyweight;
// unsigned int MAX_RESTARTS = 200;
// constructor
Normalizer::Normalizer() {
BOOST_LOG(rdInfoLog) << "Initializing Normalizer\n";
const TransformCatalogParams *tparams = &(
param_filename_flyweight(defaultCleanupParameters.normalizations).get());
this->d_tcat = new TransformCatalog(tparams);
this->MAX_RESTARTS = 200;
}
// overloaded constructor
Normalizer::Normalizer(const std::string normalizeFile,
const unsigned int maxRestarts) {
BOOST_LOG(rdInfoLog) << "Initializing Normalizer\n";
const TransformCatalogParams *tparams =
&(param_filename_flyweight(normalizeFile).get());
this->d_tcat = new TransformCatalog(tparams);
this->MAX_RESTARTS = maxRestarts;
}
// overloaded constructor
Normalizer::Normalizer(std::istream &normalizeStream,
const unsigned int maxRestarts) {
BOOST_LOG(rdInfoLog) << "Initializing Normalizer\n";
TransformCatalogParams tparams(normalizeStream);
this->d_tcat = new TransformCatalog(&tparams);
this->MAX_RESTARTS = maxRestarts;
}
// overloaded constructor
Normalizer::Normalizer(
const std::vector<std::pair<std::string, std::string>> &normalizations,
const unsigned int maxRestarts) {
BOOST_LOG(rdInfoLog) << "Initializing Normalizer\n";
const TransformCatalogParams *tparams =
&(param_data_flyweight(normalizations).get());
this->d_tcat = new TransformCatalog(tparams);
this->MAX_RESTARTS = maxRestarts;
}
// destructor
Normalizer::~Normalizer() { delete d_tcat; }
ROMol *Normalizer::normalize(const ROMol &mol) {
BOOST_LOG(rdInfoLog) << "Running Normalizer\n";
PRECONDITION(this->d_tcat, "");
const TransformCatalogParams *tparams = this->d_tcat->getCatalogParams();
PRECONDITION(tparams, "");
if (!mol.getNumAtoms()) {
return new ROMol(mol);
}
const std::vector<std::shared_ptr<ChemicalReaction>> &transforms =
tparams->getTransformations();
bool sanitizeFrags = false;
MOL_SPTR_VECT frags = MolOps::getMolFrags(mol, sanitizeFrags);
MOL_SPTR_VECT nfrags; //( frags.size() );
for (const auto &frag : frags) {
frag->updatePropertyCache(false);
ROMOL_SPTR nfrag(this->normalizeFragment(*frag, transforms));
nfrags.push_back(nfrag);
}
auto *outmol = new ROMol(*(nfrags.back()));
nfrags.pop_back();
for (const auto &nfrag : nfrags) {
ROMol *tmol = combineMols(*outmol, *nfrag);
delete outmol;
outmol = tmol;
// delete nfrag;
}
return outmol;
}
ROMOL_SPTR Normalizer::normalizeFragment(
const ROMol &mol,
const std::vector<std::shared_ptr<ChemicalReaction>> &transforms) const {
ROMOL_SPTR nfrag(new ROMol(mol));
MolOps::fastFindRings(
*nfrag); // this doesn't do anything if rings are already there
std::set<std::string> seenProductSmiles;
for (unsigned int i = 0; i < MAX_RESTARTS; ++i) {
bool loop_break = false;
// Iterate through Normalization transforms and apply each in order
for (auto &transform : transforms) {
SmilesMolPair product = applyTransform(nfrag, *transform);
if (!product.first.empty() && !seenProductSmiles.count(product.first)) {
seenProductSmiles.insert(product.first);
BOOST_LOG(rdInfoLog)
<< "Rule applied: "
<< transform->getProp<std::string>(common_properties::_Name)
<< "\n";
nfrag = product.second;
loop_break = true;
break;
}
}
// For loop finishes normally, all applicable transforms have been applied
if (!loop_break) {
return nfrag;
}
}
BOOST_LOG(rdInfoLog) << "Gave up normalization after " << MAX_RESTARTS
<< " restarts.\n";
return nfrag;
}
SmilesMolPair Normalizer::applyTransform(const ROMOL_SPTR &mol,
ChemicalReaction &transform) const {
// Repeatedly apply normalization transform to molecule until no changes
// occur.
//
// It is possible for multiple products to be produced when a rule is applied.
// The rule is applied repeatedly to each of the products, until no further
// changes occur or after 20 attempts.
//
// If there are multiple unique products after the final application, the
// first product (sorted alphabetically by SMILES) is chosen.
SmilesMolPair smilesMolPair{std::string(), mol};
if (!transform.isInitialized()) {
transform.initReactantMatchers();
}
// REVIEW: what's the source of the 20 in the next line?
for (unsigned int i = 0; i < 20; ++i) {
std::map<std::string, ROMOL_SPTR> pdts;
std::vector<MOL_SPTR_VECT> products =
transform.runReactants({smilesMolPair.second});
for (auto &pdt : products) {
// shared_ptr<ROMol> p0( new RWMol(*pdt[0]) );
// std::cout << MolToSmiles(*p0) <<
// std::endl;
unsigned int failed;
try {
auto *tmol = static_cast<RWMol *>(pdt.front().get());
// we'll allow atoms with a valence that's too high to make it
// through, but we should fail if we just created something that
// can't, for example, be kekulized.
unsigned int sanitizeOps = MolOps::SANITIZE_ALL ^
MolOps::SANITIZE_CLEANUP ^
MolOps::SANITIZE_PROPERTIES;
MolOps::sanitizeMol(*tmol, failed, sanitizeOps);
pdts[MolToSmiles(*tmol)] = pdt.front();
} catch (MolSanitizeException &) {
BOOST_LOG(rdInfoLog) << "FAILED sanitizeMol.\n";
}
}
if (!pdts.empty()) {
smilesMolPair = std::move(*pdts.begin());
} else {
if (i) {
return smilesMolPair;
}
return std::make_pair(std::string(), nullptr);
}
}
return smilesMolPair;
}
} // namespace MolStandardize
} // namespace RDKit
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