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//
// Copyright (C) 2018 Susan H. Leung
//
// @@ 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>
using namespace std;
using namespace RDKit;
namespace RDKit {
class RWMol;
class ROMol;
namespace MolStandardize {
// unsigned int MAX_RESTARTS = 200;
// constructor
Normalizer::Normalizer() {
BOOST_LOG(rdInfoLog) << "Initializing Normalizer\n";
TransformCatalogParams tparams(defaultCleanupParameters.normalizations);
// unsigned int ntransforms = tparams->getNumTransformations();
// TEST_ASSERT(ntransforms == 22);
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";
TransformCatalogParams tparams(normalizeFile);
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, "");
const std::vector<std::shared_ptr<ChemicalReaction>> &transforms =
tparams->getTransformations();
std::vector<boost::shared_ptr<ROMol>> frags = MolOps::getMolFrags(mol);
std::vector<ROMOL_SPTR> nfrags; //( frags.size() );
for (const auto &frag : frags) {
ROMOL_SPTR nfrag(this->normalizeFragment(*frag, transforms));
nfrags.push_back(nfrag);
}
ROMol *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 *Normalizer::normalizeFragment(
const ROMol &mol,
const std::vector<std::shared_ptr<ChemicalReaction>> &transforms) {
ROMol *nfrag = new ROMol(mol);
for (unsigned int i = 0; i < MAX_RESTARTS; ++i) {
bool loop_brake = false;
// Iterate through Normalization transforms and apply each in order
for (auto &transform : transforms) {
std::string tname;
transform->getProp(common_properties::_Name, tname);
boost::shared_ptr<ROMol> product =
this->applyTransform(*nfrag, *transform);
if (product != nullptr) {
BOOST_LOG(rdInfoLog) << "Rule applied: " << tname << "\n";
delete nfrag;
nfrag = new ROMol(*product);
loop_brake = true;
break;
}
}
// For loop finishes normally, all applicable transforms have been applied
if (!loop_brake) {
return nfrag;
}
}
BOOST_LOG(rdInfoLog) << "Gave up normalization after " << MAX_RESTARTS
<< " restarts.\n";
return nfrag;
}
boost::shared_ptr<ROMol> Normalizer::applyTransform(
const ROMol &mol, ChemicalReaction &transform) {
// 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.
boost::shared_ptr<ROMol> tmp(new ROMol(mol));
MOL_SPTR_VECT mols;
mols.push_back(tmp);
transform.initReactantMatchers();
// REVIEW: what's the source of the 20 in the next line?
for (unsigned int i = 0; i < 20; ++i) {
std::vector<Normalizer::Product> pdts;
for (auto &m : mols) {
std::vector<MOL_SPTR_VECT> products = transform.runReactants({m});
for (auto &pdt : products) {
// shared_ptr<ROMol> p0( new RWMol(*pdt[0]) );
// std::cout << MolToSmiles(*p0) <<
// std::endl;
unsigned int failed;
try {
MolOps::sanitizeMol(*static_cast<RWMol *>(pdt[0].get()), failed);
Normalizer::Product np(MolToSmiles(*pdt[0]), pdt[0]);
pdts.push_back(np);
} catch (MolSanitizeException &) {
BOOST_LOG(rdInfoLog) << "FAILED sanitizeMol.\n";
}
}
}
if (pdts.size() != 0) {
std::sort(pdts.begin(), pdts.end());
mols.clear();
for (const auto &pdt : pdts) {
mols.push_back(pdt.Mol);
}
} else {
if (i > 0) {
return mols[0];
} else {
return nullptr;
}
}
}
if (mols.size())
return mols[0];
else
return nullptr;
}
} // namespace MolStandardize
} // namespace RDKit
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