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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 "Fragment.h"
#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h>
#include <boost/tokenizer.hpp>
typedef boost::tokenizer<boost::char_separator<char>> tokenizer;
#include <GraphMol/ChemTransforms/ChemTransforms.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <RDGeneral/types.h>
namespace RDKit {
namespace MolStandardize {
//constructor
FragmentRemover::FragmentRemover(){
BOOST_LOG(rdInfoLog) << "Initializing FragmentRemover\n" ;
FragmentCatalogParams fparams(defaultCleanupParameters.fragmentFile);
// unsigned int numfg = fparams->getNumFuncGroups();
// TEST_ASSERT(fparams->getNumFuncGroups() == 61);
this->d_fcat = new FragmentCatalog(&fparams);
this->LEAVE_LAST = true;
}
//overloaded constructor
FragmentRemover::FragmentRemover(const std::string fragmentFile, const bool leave_last){
FragmentCatalogParams fparams(fragmentFile);
this->d_fcat = new FragmentCatalog(&fparams);
this->LEAVE_LAST = leave_last;
}
//Destructor
FragmentRemover::~FragmentRemover(){
delete d_fcat;
};
ROMol *FragmentRemover::remove(const ROMol &mol) {
BOOST_LOG(rdInfoLog) << "Running FragmentRemover\n" ;
PRECONDITION(this->d_fcat, "");
const FragmentCatalogParams *fparams = this->d_fcat->getCatalogParams();
PRECONDITION(fparams, "");
const std::vector<std::shared_ptr<ROMol>> &fgrps = fparams->getFuncGroups();
auto *removed = new ROMol(mol);
for (auto &fgci : fgrps) {
std::vector<boost::shared_ptr<ROMol>> frags = MolOps::getMolFrags(*removed);
// If nothing is left or leave_last and only one fragment, end here
if (removed->getNumAtoms() == 0 ||
(this->LEAVE_LAST && frags.size() <= 1)) {
break;
}
std::string fname;
fgci->getProp(common_properties::_Name, fname);
ROMol *tmp = RDKit::deleteSubstructs(*removed, *fgci, true);
if (tmp->getNumAtoms() != removed->getNumAtoms()) {
BOOST_LOG(rdInfoLog) << "Removed fragment: " << fname << "\n";
}
if (this->LEAVE_LAST && tmp->getNumAtoms() == 0) {
// All the remaining fragments match this pattern - leave them all
delete tmp;
break;
}
delete removed;
removed = tmp;
}
return removed;
}
bool isOrganic(const ROMol &frag) {
// Returns true if fragment contains at least one carbon atom.
for (const auto at : frag.atoms()) {
if (at->getAtomicNum() == 6) {
return true;
}
}
return false;
}
LargestFragmentChooser::LargestFragmentChooser(
const LargestFragmentChooser &other) {
BOOST_LOG(rdInfoLog) << "Initializing LargestFragmentChooser\n";
PREFER_ORGANIC = other.PREFER_ORGANIC;
}
ROMol *LargestFragmentChooser::choose(const ROMol &mol) {
BOOST_LOG(rdInfoLog) << "Running LargestFragmentChooser\n";
std::vector<boost::shared_ptr<ROMol>> frags = MolOps::getMolFrags(mol);
LargestFragmentChooser::Largest l;
for (const auto &frag : frags) {
std::string smiles = MolToSmiles(*frag);
BOOST_LOG(rdInfoLog) << "Fragment: " << smiles << "\n";
bool organic = isOrganic(*frag);
if (this->PREFER_ORGANIC) {
// Skip this fragment if not organic and we already have an organic
// fragment as the largest so far
if (l.Fragment != nullptr && l.Organic && !organic) continue;
// Reset largest if it wasn't organic and this fragment is organic
// if largest and organic and not largest['organic']:
if (l.Fragment != nullptr && organic && !l.Organic) {
l.Fragment = nullptr;
}
}
unsigned int numatoms = 0;
for (const auto at : frag->atoms()) {
numatoms += 1 + at->getTotalNumHs();
}
// Skip this fragment if fewer atoms than the largest
if (l.Fragment != nullptr && (numatoms < l.NumAtoms)) continue;
// Skip this fragment if equal number of atoms but weight is lower
double weight = Descriptors::calcExactMW(*frag);
if (l.Fragment != nullptr && (numatoms == l.NumAtoms) &&
(weight < l.Weight))
continue;
// Skip this fragment if equal number of atoms and equal weight but smiles
// comes last alphabetically
if (l.Fragment != nullptr && (numatoms == l.NumAtoms) &&
(weight == l.Weight) && (smiles > l.Smiles))
continue;
BOOST_LOG(rdInfoLog) << "New largest fragment: " << smiles << " (" <<
numatoms << ")\n";
// Otherwise this is the largest so far
l.Smiles = smiles;
l.Fragment = frag;
l.NumAtoms = numatoms;
l.Weight = weight;
l.Organic = organic;
}
return new ROMol(*(l.Fragment));
}
LargestFragmentChooser::Largest::Largest()
: Smiles(""), Fragment(nullptr), NumAtoms(0), Weight(0), Organic(false) {}
LargestFragmentChooser::Largest::Largest(
std::string &smiles, const boost::shared_ptr<ROMol> &fragment,
unsigned int &numatoms, double &weight, bool &organic)
: Smiles(smiles),
Fragment(fragment),
NumAtoms(numatoms),
Weight(weight),
Organic(organic) {}
} // namespace MolStandardize
} // namespace RDKit
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