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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]~[#7,#8,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.reset(new ROMol(mol));
}
void MetalDisconnector::setMetalNon(const ROMol &mol) {
this->metal_non.reset(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};
std::map<int, NonMetal> nonMetals;
std::map<int, int> metalChargeExcess;
for (auto &query : metalList) {
std::vector<MatchVectType> matches;
SubstructMatch(mol, *query, matches);
for (const auto &match : matches) {
int metal_idx = match[0].second;
metalChargeExcess[metal_idx] = 0;
auto metal = mol.getAtomWithIdx(metal_idx);
int non_idx = match[1].second;
auto nonMetal = mol.getAtomWithIdx(non_idx);
Bond *b = mol.getBondBetweenAtoms(metal_idx, non_idx);
int order = (b->getBondType() >= Bond::DATIVEONE &&
b->getBondType() <= Bond::DATIVER)
? 0
: static_cast<int>(b->getBondTypeAsDouble());
// disconnecting metal-R bond
mol.removeBond(metal_idx, non_idx);
// increment the cut bond count for this non-metal atom
// and store the metal it was bonded to. We will need this
// later to adjust the metal charge
auto &value = nonMetals[non_idx];
value.cutBonds += order;
auto it = std::lower_bound(value.boundMetalIndices.begin(),
value.boundMetalIndices.end(), metal_idx);
if (it == value.boundMetalIndices.end() || *it != metal_idx) {
value.boundMetalIndices.insert(it, metal_idx);
}
BOOST_LOG(rdInfoLog) << "Removed covalent bond between "
<< metal->getSymbol() << " and "
<< nonMetal->getSymbol() << "\n";
}
// std::cout << "After removing bond and charge adjustment: " <<
// MolToSmiles(mol) << std::endl;
}
for (auto it = nonMetals.begin(); it != nonMetals.end(); ++it) {
auto a = mol.getAtomWithIdx(it->first);
// do not blindly trust the original formal charge as it is often wrong
// instead, find out the most appropriate formal charge based
// on the allowed element valences and on its current valence/lone electrons
// if there are no standard valences we assume the original
// valence was correct and the non-metal element was neutral
int valenceBeforeCut = a->getTotalValence();
int radBeforeCut = a->getNumRadicalElectrons();
int fcAfterCut = -it->second.cutBonds;
int valenceAfterCut = 0;
int loneElectrons = 0;
const auto &valens =
PeriodicTable::getTable()->getValenceList(a->getAtomicNum());
if (!valens.empty() && valens.front() != -1) {
for (auto v = valens.begin(); v != valens.end(); ++v) {
valenceAfterCut = valenceBeforeCut + radBeforeCut - it->second.cutBonds;
if (valenceAfterCut > *v) {
if (v + 1 != valens.end()) {
continue;
}
valenceAfterCut = *v;
break;
}
fcAfterCut = valenceAfterCut - *v;
// if there were radicals before and now we have
// a negative formal charge, then it's a carbene-like
// system (e.g., [Me]-[C]=O), or there was something silly
// such as [Me]-[S]=X or [Me]-[P](X)(X)X
if ((radBeforeCut % 2) && fcAfterCut < 0) {
++fcAfterCut;
++loneElectrons;
// no radical doublets on N and higher
a->setNumRadicalElectrons(a->getAtomicNum() < 7 ? radBeforeCut + 1
: 0);
}
break;
}
}
// do not put a negative charge on sp2 carbon
if (fcAfterCut == -1 &&
valenceAfterCut == static_cast<int>(a->getTotalDegree()) + 1) {
fcAfterCut = 0;
}
a->setFormalCharge(fcAfterCut);
if (!it->second.cutBonds ||
(fcAfterCut == -1 && a->getAtomicNum() == 6 &&
valenceAfterCut == static_cast<int>(a->getTotalDegree()) + 2)) {
// do not take electrons from the metal if it was a dative bond
// (e.g., [C-]#[O+] coordinated to metal)
fcAfterCut = 0;
}
std::sort(it->second.boundMetalIndices.begin(),
it->second.boundMetalIndices.end(),
[&metalChargeExcess](int a, int b) {
return (metalChargeExcess.at(a) < metalChargeExcess.at(b));
});
fcAfterCut += loneElectrons;
while (fcAfterCut < 0) {
for (auto i : it->second.boundMetalIndices) {
// if the bond was not dative, the non-metal stole electrons
// from the metal(s), so we need to take electrons from
// once-bonded metal(s)
if (fcAfterCut++ >= 0) {
break;
}
++metalChargeExcess[i];
}
}
a->updatePropertyCache();
}
// adjust formal charges of metal atoms
for (auto it = metalChargeExcess.begin(); it != metalChargeExcess.end();
++it) {
auto a = mol.getAtomWithIdx(it->first);
auto currentFc = a->getFormalCharge();
const auto &valens =
PeriodicTable::getTable()->getValenceList(a->getAtomicNum());
int fcAfterCut = it->second;
if (currentFc > 0) {
// if the original formal charge on the metal was positive, we trust it
// and add it to the charge excess
fcAfterCut += currentFc;
}
if (!valens.empty() && valens.front() != -1) {
for (auto v = valens.begin(); v != valens.end(); ++v) {
if (fcAfterCut > *v) {
auto next = v + 1;
if (next != valens.end() && fcAfterCut >= *v) {
continue;
}
fcAfterCut = *v;
break;
}
}
}
if (fcAfterCut > currentFc) {
a->setFormalCharge(fcAfterCut);
}
// make sure that radical electrons on metals are 0
// and are not added to metals by sanitization
// by setting NoImplicit to false
a->setNumRadicalElectrons(0);
a->setNumExplicitHs(0);
a->setNoImplicit(false);
a->updatePropertyCache();
}
}
} // namespace MolStandardize
} // namespace RDKit
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