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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 "Metal.h"
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/RDKitQueries.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/Substruct/SubstructUtils.h>
using namespace std;
using namespace RDKit;
namespace RDKit {
class RWMol;
class ROMol;
namespace MolStandardize {
MetalDisconnector::MetalDisconnector()
: metal_nof(
SmartsToMol("[Li,Na,K,Rb,Cs,Fr,Be,Mg,Ca,Sr,Ba,Ra,Sc,Ti,V,Cr,Mn,Fe,Co,"
"Ni,Cu,Zn,Al,Ga,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,In,Sn,Hf,Ta,"
"W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi]~[N,O,F]")),
metal_non(SmartsToMol(
"[Al,Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,Hf,Ta,"
"W,Re,Os,Ir,Pt,Au]~[B,C,Si,P,As,Sb,S,Se,Te,Cl,Br,I,At]")){
BOOST_LOG(rdInfoLog) << "Initializing MetalDisconnector\n";
};
MetalDisconnector::MetalDisconnector(const MetalDisconnector &other) {
metal_nof = other.metal_nof;
metal_non = other.metal_non;
};
MetalDisconnector::~MetalDisconnector(){};
ROMol *MetalDisconnector::getMetalNof() {return metal_nof.get();}
ROMol *MetalDisconnector::getMetalNon() {return metal_non.get();}
void MetalDisconnector::setMetalNof(const ROMol &mol) {
this->metal_nof = static_cast<ROMOL_SPTR>(new ROMol(mol));
}
void MetalDisconnector::setMetalNon(const ROMol &mol) {
this->metal_non = static_cast<ROMOL_SPTR>(new ROMol(mol));
}
ROMol *MetalDisconnector::disconnect(const ROMol &mol) {
auto *res = new RWMol(mol);
MetalDisconnector::disconnect(*res);
return static_cast<ROMol *>(res);
}
void MetalDisconnector::disconnect(RWMol &mol) {
BOOST_LOG(rdInfoLog) << "Running MetalDisconnector\n";
std::list<ROMOL_SPTR> metalList = {metal_nof, metal_non};
for (auto &query : metalList) {
std::vector<MatchVectType> matches;
unsigned int matched;
matched = SubstructMatch(mol, *query, matches);
for (size_t i = 0; i < matched; ++i) {
// disconnecting metal-R bond
int metal_idx = matches[i][0].second;
int non_idx = matches[i][1].second;
Bond *b = mol.getBondBetweenAtoms(metal_idx, non_idx);
double order = b->getBondTypeAsDouble();
mol.removeBond(metal_idx, non_idx);
// adjusting neighbouring charges
Atom *a1 = mol.getAtomWithIdx(metal_idx);
a1->setFormalCharge(a1->getFormalCharge() + int(order));
Atom *a2 = mol.getAtomWithIdx(non_idx);
a2->setFormalCharge(a2->getFormalCharge() - int(order));
BOOST_LOG(rdInfoLog) << "Removed covalent bond between "
<< a1->getSymbol() << " and " << a2->getSymbol() << "\n";
}
// std::cout << "After removing bond and charge adjustment: " <<
//MolToSmiles(mol) << std::endl;
}
MolOps::sanitizeMol(mol);
}
} // namespace MolStandardize
} // namespace RDKit
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