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TargetMatch.h
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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 <boost/dynamic_bitset.hpp>
#include "FMCS.h"
#include "MatchTable.h"
namespace RDKit {
namespace FMCS {
struct TargetMatch {
bool Empty{true};
size_t MatchedAtomSize{0};
size_t MatchedBondSize{0};
std::vector<unsigned int> TargetAtomIdx;
std::vector<unsigned int> TargetBondIdx;
boost::dynamic_bitset<> VisitedTargetBonds;
boost::dynamic_bitset<> VisitedTargetAtoms; // for checking rings
public:
TargetMatch() {}
TargetMatch(const TargetMatch& src) { *this = src; }
TargetMatch& operator=(const TargetMatch& src) {
Empty = src.Empty;
if (!Empty) {
MatchedAtomSize = src.MatchedAtomSize;
MatchedBondSize = src.MatchedBondSize;
TargetAtomIdx = src.TargetAtomIdx;
TargetBondIdx = src.TargetBondIdx;
VisitedTargetBonds = src.VisitedTargetBonds;
VisitedTargetAtoms = src.VisitedTargetAtoms;
}
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.clear();
TargetAtomIdx.resize(query.getNumAtoms(), NotSet);
TargetBondIdx.clear();
TargetBondIdx.resize(query.getNumBonds(), NotSet);
VisitedTargetBonds.resize(target.Molecule->getNumBonds());
VisitedTargetAtoms.resize(target.Molecule->getNumAtoms());
VisitedTargetBonds.reset();
VisitedTargetAtoms.reset();
MatchedAtomSize = match.size();
for (const auto& m : match) {
TargetAtomIdx[seed.MoleculeFragment.Atoms.at(m.first)->getIdx()] =
m.second;
VisitedTargetAtoms.set(m.second);
}
MatchedBondSize = 0;
for (const auto bond : seed.MoleculeFragment.Bonds) {
unsigned int i = bond->getBeginAtomIdx();
unsigned int j = bond->getEndAtomIdx();
unsigned int ti = TargetAtomIdx.at(i);
unsigned int tj = TargetAtomIdx.at(j);
const auto tb = target.Molecule->getBondBetweenAtoms(ti, tj);
if (tb) {
++MatchedBondSize;
TargetBondIdx[bond->getIdx()] = tb->getIdx(); // add
VisitedTargetBonds.set(tb->getIdx());
}
}
Empty = false;
}
};
} // namespace FMCS
} // namespace RDKit
FMCS.h
MatchTable.h
RDKit::FMCS::Seed
Definition Seed.h:60
RDKit::ROMol
Definition ROMol.h:199
RDKit::ROMol::getNumBonds
unsigned int getNumBonds(bool onlyHeavy=1) const
returns our number of Bonds
RDKit::ROMol::getNumAtoms
unsigned int getNumAtoms() const
returns our number of atoms
Definition ROMol.h:421
export.h
RDKit::FMCS::NotSet
const unsigned int NotSet
Definition SubstructMatchCustom.h:23
RDKit::FMCS::match_V_t
std::vector< std::pair< FMCS::Graph::vertex_descriptor, FMCS::Graph::vertex_descriptor > > match_V_t
Definition SubstructMatchCustom.h:22
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::rdvalue_is
bool rdvalue_is(const RDValue_cast_t)
Definition RDValue-doublemagic.h:372
RDKit::FMCS::TargetMatch
Definition TargetMatch.h:19
RDKit::FMCS::TargetMatch::TargetAtomIdx
std::vector< unsigned int > TargetAtomIdx
Definition TargetMatch.h:23
RDKit::FMCS::TargetMatch::TargetMatch
TargetMatch(const TargetMatch &src)
Definition TargetMatch.h:29
RDKit::FMCS::TargetMatch::empty
bool empty() const
Definition TargetMatch.h:42
RDKit::FMCS::TargetMatch::operator=
TargetMatch & operator=(const TargetMatch &src)
Definition TargetMatch.h:30
RDKit::FMCS::TargetMatch::MatchedBondSize
size_t MatchedBondSize
Definition TargetMatch.h:22
RDKit::FMCS::TargetMatch::MatchedAtomSize
size_t MatchedAtomSize
Definition TargetMatch.h:21
RDKit::FMCS::TargetMatch::TargetBondIdx
std::vector< unsigned int > TargetBondIdx
Definition TargetMatch.h:24
RDKit::FMCS::TargetMatch::VisitedTargetAtoms
boost::dynamic_bitset VisitedTargetAtoms
Definition TargetMatch.h:26
RDKit::FMCS::TargetMatch::clear
void clear()
Definition TargetMatch.h:43
RDKit::FMCS::TargetMatch::Empty
bool Empty
Definition TargetMatch.h:20
RDKit::FMCS::TargetMatch::VisitedTargetBonds
boost::dynamic_bitset VisitedTargetBonds
Definition TargetMatch.h:25
RDKit::FMCS::TargetMatch::init
void init(const Seed &seed, const match_V_t &match, const ROMol &query, const Target &target)
Definition TargetMatch.h:51
RDKit::FMCS::TargetMatch::TargetMatch
TargetMatch()
Definition TargetMatch.h:28
RDKit::FMCS::Target
Definition Target.h:21