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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 "MolStandardize.h"
#include "Metal.h"
#include "Normalize.h"
#include "Tautomer.h"
#include "Fragment.h"
#include <GraphMol/RDKitBase.h>
#include <iostream>
#include <GraphMol/ROMol.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.h>
#include "Charge.h"
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
using namespace std;
namespace RDKit {
namespace MolStandardize {
const CleanupParameters defaultCleanupParameters;
RWMol *cleanup(const RWMol &mol, const CleanupParameters ¶ms) {
RWMol m(mol);
MolOps::sanitizeMol(m);
MolOps::removeHs(m);
MolStandardize::MetalDisconnector md;
md.disconnect(m);
RWMOL_SPTR normalized(MolStandardize::normalize(&m, params));
RWMol *reionized = MolStandardize::reionize(normalized.get(), params);
MolOps::assignStereochemistry(*reionized);
return reionized;
}
void tautomerParent(RWMol &mol, const CleanupParameters ¶ms) {
RDUNUSED_PARAM(mol);
RDUNUSED_PARAM(params);
UNDER_CONSTRUCTION("Not yet implmented");
}
// Return the fragment parent of a given molecule.
// The fragment parent is the largest organic covalent unit in the molecule.
//
RWMol *fragmentParent(const RWMol &mol, const CleanupParameters ¶ms,
bool skip_standardize) {
const RWMol *cleaned = nullptr;
if (!skip_standardize) {
cleaned = cleanup(mol, params);
} else {
cleaned = &mol;
}
LargestFragmentChooser lfragchooser(params.preferOrganic);
ROMol nm(*cleaned);
ROMOL_SPTR lfrag(lfragchooser.choose(nm));
delete cleaned;
return new RWMol(*lfrag);
}
void stereoParent(RWMol &mol, const CleanupParameters ¶ms) {
RDUNUSED_PARAM(mol);
RDUNUSED_PARAM(params);
UNDER_CONSTRUCTION("Not yet implmented");
}
void isotopeParent(RWMol &mol, const CleanupParameters ¶ms) {
RDUNUSED_PARAM(mol);
RDUNUSED_PARAM(params);
UNDER_CONSTRUCTION("Not yet implmented");
}
RWMol *chargeParent(const RWMol &mol, const CleanupParameters ¶ms,
bool skip_standardize) {
// Return the charge parent of a given molecule.
// The charge parent is the uncharged version of the fragment parent.
RWMol *m = nullptr;
if (!skip_standardize) {
m = cleanup(mol, params);
}
RWMOL_SPTR fragparent(fragmentParent(*m, params, true));
// if fragment...
ROMol nm(*fragparent);
Uncharger uncharger;
ROMOL_SPTR uncharged(uncharger.uncharge(nm));
RWMol *omol = cleanup(static_cast<RWMol>(*uncharged), params);
return omol;
}
void superParent(RWMol &mol, const CleanupParameters ¶ms) {
RDUNUSED_PARAM(mol);
RDUNUSED_PARAM(params);
UNDER_CONSTRUCTION("Not yet implmented");
}
RWMol *normalize(const RWMol *mol, const CleanupParameters ¶ms) {
Normalizer normalizer(params.normalizations, params.maxRestarts);
ROMol m(*mol);
ROMol *normalized = normalizer.normalize(m);
return static_cast<RWMol *>(normalized);
}
RWMol *reionize(const RWMol *mol, const CleanupParameters ¶ms) {
RDUNUSED_PARAM(params);
Reionizer reionizer;
ROMol m(*mol);
ROMol *reionized = reionizer.reionize(m);
return static_cast<RWMol *>(reionized);
}
std::string standardizeSmiles(const std::string &smiles) {
RWMOL_SPTR mol(SmilesToMol(smiles, 0, false));
if (!mol) {
std::string message =
"SMILES Parse Error: syntax error for input: " + smiles;
throw ValueErrorException(message);
}
CleanupParameters params;
RWMOL_SPTR cleaned(cleanup(*mol, params));
return MolToSmiles(*cleaned);
}
std::vector<std::string> enumerateTautomerSmiles(
const std::string &smiles, const CleanupParameters ¶ms) {
std::shared_ptr<RWMol> mol(SmilesToMol(smiles, 0, false));
cleanup(*mol, params);
MolOps::sanitizeMol(*mol);
auto *tautparams = new TautomerCatalogParams(params.tautomerTransforms);
// unsigned int ntautomers = tautparams->getNumTautomers();
TautomerCatalog tautcat(tautparams);
TautomerEnumerator te;
std::vector<ROMOL_SPTR> res =
te.enumerate(static_cast<ROMol>(*mol), &tautcat);
std::vector<std::string> tsmiles;
for (const auto &r : res) {
tsmiles.push_back(MolToSmiles(*r));
}
return tsmiles;
}
} // end of namespace MolStandardize
} // end of namespace RDKit
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