mirror of
https://github.com/rdkit/rdkit.git
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ec366c1ab7
* a round of cleanups courtesy of PVS studio * add a test to make sure that a warning is a false alarm * bug fix * Fix a UFF bug * more PVS studio cleanups * next round of PVS studio cleanups * completely remove the chances for that bug * changes in response to review * add an additional test + a bit of reformatting that snuck in
96 lines
3.1 KiB
C++
96 lines
3.1 KiB
C++
//
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// Copyright (C) 2018 Susan H. Leung
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include "Metal.h"
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#include <GraphMol/SmilesParse/SmilesParse.h>
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#include <GraphMol/SmilesParse/SmilesWrite.h>
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <GraphMol/RDKitQueries.h>
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#include <GraphMol/Substruct/SubstructMatch.h>
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#include <GraphMol/Substruct/SubstructUtils.h>
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using namespace std;
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using namespace RDKit;
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namespace RDKit {
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class RWMol;
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class ROMol;
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namespace MolStandardize {
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MetalDisconnector::MetalDisconnector()
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: metal_nof(
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SmartsToMol("[Li,Na,K,Rb,Cs,Fr,Be,Mg,Ca,Sr,Ba,Ra,Sc,Ti,V,Cr,Mn,Fe,Co,"
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"Ni,Cu,Zn,Al,Ga,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,In,Sn,Hf,Ta,"
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"W,Re,Os,Ir,Pt,Au,Hg,Tl,Pb,Bi]~[N,O,F]")),
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metal_non(SmartsToMol(
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"[Al,Sc,Ti,V,Cr,Mn,Fe,Co,Ni,Cu,Zn,Y,Zr,Nb,Mo,Tc,Ru,Rh,Pd,Ag,Cd,Hf,Ta,"
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"W,Re,Os,Ir,Pt,Au]~[B,C,Si,P,As,Sb,S,Se,Te,Cl,Br,I,At]")) {
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BOOST_LOG(rdInfoLog) << "Initializing MetalDisconnector\n";
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};
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MetalDisconnector::MetalDisconnector(const MetalDisconnector &other) {
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metal_nof = other.metal_nof;
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metal_non = other.metal_non;
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};
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MetalDisconnector::~MetalDisconnector(){};
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ROMol *MetalDisconnector::getMetalNof() { return metal_nof.get(); }
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ROMol *MetalDisconnector::getMetalNon() { return metal_non.get(); }
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void MetalDisconnector::setMetalNof(const ROMol &mol) {
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this->metal_nof.reset(new ROMol(mol));
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}
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void MetalDisconnector::setMetalNon(const ROMol &mol) {
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this->metal_non.reset(new ROMol(mol));
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}
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ROMol *MetalDisconnector::disconnect(const ROMol &mol) {
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auto *res = new RWMol(mol);
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MetalDisconnector::disconnect(*res);
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return static_cast<ROMol *>(res);
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}
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void MetalDisconnector::disconnect(RWMol &mol) {
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BOOST_LOG(rdInfoLog) << "Running MetalDisconnector\n";
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std::list<ROMOL_SPTR> metalList = {metal_nof, metal_non};
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for (auto &query : metalList) {
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std::vector<MatchVectType> matches;
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unsigned int matched;
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matched = SubstructMatch(mol, *query, matches);
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for (size_t i = 0; i < matched; ++i) {
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// disconnecting metal-R bond
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int metal_idx = matches[i][0].second;
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int non_idx = matches[i][1].second;
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Bond *b = mol.getBondBetweenAtoms(metal_idx, non_idx);
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double order = b->getBondTypeAsDouble();
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mol.removeBond(metal_idx, non_idx);
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// adjusting neighbouring charges
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Atom *a1 = mol.getAtomWithIdx(metal_idx);
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a1->setFormalCharge(a1->getFormalCharge() + int(order));
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Atom *a2 = mol.getAtomWithIdx(non_idx);
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a2->setFormalCharge(a2->getFormalCharge() - int(order));
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BOOST_LOG(rdInfoLog) << "Removed covalent bond between "
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<< a1->getSymbol() << " and " << a2->getSymbol()
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<< "\n";
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}
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// std::cout << "After removing bond and charge adjustment: " <<
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// MolToSmiles(mol) << std::endl;
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}
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}
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} // namespace MolStandardize
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} // namespace RDKit
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