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//
// Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
// @@ 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 <RDGeneral/export.h>
#pragma once
#include <vector>
#include "FMCS.h"
#include "MatchTable.h"
namespace RDKit {
namespace FMCS {
struct TargetMatch {
bool Empty;
size_t MatchedAtomSize;
size_t MatchedBondSize;
std::vector<unsigned> TargetAtomIdx;
std::vector<unsigned> TargetBondIdx;
std::vector<bool> VisitedTargetBonds;
std::vector<bool> VisitedTargetAtoms; // for checking rings
public:
TargetMatch() : Empty(true), MatchedAtomSize(0), MatchedBondSize(0) {}
TargetMatch(const TargetMatch& src) { *this = src; }
TargetMatch& operator=(const TargetMatch& src) {
Empty = src.Empty;
if (!Empty) {
MatchedAtomSize = src.MatchedAtomSize;
MatchedBondSize = src.MatchedBondSize;
TargetAtomIdx.resize(src.TargetAtomIdx.size());
memcpy(&TargetAtomIdx[0], &src.TargetAtomIdx[0],
sizeof(unsigned) * TargetAtomIdx.size());
TargetBondIdx.resize(src.TargetBondIdx.size());
memcpy(&TargetBondIdx[0], &src.TargetBondIdx[0],
sizeof(unsigned) * TargetBondIdx.size());
VisitedTargetBonds = src.VisitedTargetBonds; // std::vector<bool> bitset
VisitedTargetAtoms = src.VisitedTargetAtoms; // std::vector<bool> bitset
}
return *this;
}
bool empty() const { return Empty; }
void clear() {
Empty = true;
TargetAtomIdx.clear();
TargetBondIdx.clear();
VisitedTargetBonds.clear();
VisitedTargetAtoms.clear();
}
void init(const Seed& seed, const match_V_t& match, const ROMol& query,
const Target& target) {
TargetAtomIdx.resize(query.getNumAtoms());
TargetBondIdx.resize(query.getNumBonds());
VisitedTargetBonds.resize(target.Molecule->getNumBonds());
VisitedTargetAtoms.resize(target.Molecule->getNumAtoms());
memset(&TargetAtomIdx[0], 0xFF, sizeof(unsigned) * TargetAtomIdx.size());
memset(&TargetBondIdx[0], 0xFF, sizeof(unsigned) * TargetBondIdx.size());
/*
for(size_t i = 0; i < TargetAtomIdx.size(); i++)
TargetAtomIdx[i] = -1;
for(size_t i = 0; i < TargetBondIdx.size(); i++)
TargetBondIdx[i] = -1;
*/
for (size_t i = 0; i < VisitedTargetBonds.size(); i++)
VisitedTargetBonds[i] = false;
for (size_t i = 0; i < VisitedTargetAtoms.size(); i++)
VisitedTargetAtoms[i] = false;
MatchedAtomSize = match.size();
for (match_V_t::const_iterator mit = match.begin(); mit != match.end();
mit++) {
TargetAtomIdx[seed.MoleculeFragment.AtomsIdx[mit->first]] = mit->second;
VisitedTargetAtoms[mit->second] = true;
}
MatchedBondSize = 0;
for (std::vector<const Bond*>::const_iterator bond =
seed.MoleculeFragment.Bonds.begin();
bond != seed.MoleculeFragment.Bonds.end(); bond++) {
unsigned i = (*bond)->getBeginAtomIdx();
unsigned j = (*bond)->getEndAtomIdx();
unsigned ti = TargetAtomIdx[i];
unsigned tj = TargetAtomIdx[j];
const Bond* tb = target.Molecule->getBondBetweenAtoms(ti, tj);
if (tb) {
MatchedBondSize++;
TargetBondIdx[(*bond)->getIdx()] = tb->getIdx(); // add
VisitedTargetBonds[tb->getIdx()] = true;
}
}
Empty = false;
}
};
}
}
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