RDKit
Open-source cheminformatics and machine learning.
TargetMatch.h
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1 //
2 // Copyright (C) 2014 Novartis Institutes for BioMedical Research
3 //
4 // @@ All Rights Reserved @@
5 // This file is part of the RDKit.
6 // The contents are covered by the terms of the BSD license
7 // which is included in the file license.txt, found at the root
8 // of the RDKit source tree.
9 //
10 #pragma once
11 #include <vector>
12 #include "FMCS.h"
13 #include "MatchTable.h"
14 
15 namespace RDKit {
16  namespace FMCS {
17  struct TargetMatch {
18  bool Empty;
21  std::vector<unsigned> TargetAtomIdx;
22  std::vector<unsigned> TargetBondIdx;
23  std::vector<bool> VisitedTargetBonds;
24  std::vector<bool> VisitedTargetAtoms; // for checking rings
25  public:
26  TargetMatch() : Empty(true), MatchedAtomSize(0), MatchedBondSize(0) {}
27  TargetMatch(const TargetMatch& src) {
28  *this = src;
29  }
31  Empty = src.Empty;
32  if(!Empty) {
33  MatchedAtomSize = src.MatchedAtomSize;
34  MatchedBondSize = src.MatchedBondSize;
35  TargetAtomIdx.resize(src.TargetAtomIdx.size());
36  memcpy(&TargetAtomIdx[0], &src.TargetAtomIdx[0], sizeof(unsigned)*TargetAtomIdx.size());
37  TargetBondIdx.resize(src.TargetBondIdx.size());
38  memcpy(&TargetBondIdx[0], &src.TargetBondIdx[0], sizeof(unsigned)*TargetBondIdx.size());
39  VisitedTargetBonds = src.VisitedTargetBonds; // std::vector<bool> bitset
40  VisitedTargetAtoms = src.VisitedTargetAtoms; // std::vector<bool> bitset
41  }
42  return *this;
43  }
44  bool empty()const {
45  return Empty;
46  }
47  void clear() {
48  Empty = true;
49 
50  TargetAtomIdx.clear();
51  TargetBondIdx.clear();
52  VisitedTargetBonds.clear();
53  VisitedTargetAtoms.clear();
54  }
55  void init(const Seed& seed, const match_V_t& match, const ROMol& query, const Target& target) {
56  TargetAtomIdx.resize(query.getNumAtoms());
57  TargetBondIdx.resize(query.getNumBonds());
58  VisitedTargetBonds.resize(target.Molecule->getNumBonds());
59  VisitedTargetAtoms.resize(target.Molecule->getNumAtoms());
60 
61  memset(&TargetAtomIdx[0], 0xFF, sizeof(unsigned)*TargetAtomIdx.size());
62  memset(&TargetBondIdx[0], 0xFF, sizeof(unsigned)*TargetBondIdx.size());
63  /*
64  for(size_t i = 0; i < TargetAtomIdx.size(); i++)
65  TargetAtomIdx[i] = -1;
66  for(size_t i = 0; i < TargetBondIdx.size(); i++)
67  TargetBondIdx[i] = -1;
68  */
69  for(size_t i = 0; i < VisitedTargetBonds.size(); i++)
70  VisitedTargetBonds[i] = false;
71  for(size_t i = 0; i < VisitedTargetAtoms.size(); i++)
72  VisitedTargetAtoms[i] = false;
73 
74  MatchedAtomSize = match.size();
75  for(match_V_t::const_iterator mit = match.begin(); mit != match.end(); mit++) {
76  TargetAtomIdx[seed.MoleculeFragment.AtomsIdx[mit->first]] = mit->second;
77  VisitedTargetAtoms[mit->second] = true;
78  }
79 
80  MatchedBondSize = 0;
81  for(std::vector<const Bond*>::const_iterator bond = seed.MoleculeFragment.Bonds.begin(); bond != seed.MoleculeFragment.Bonds.end(); bond++) {
82  unsigned i = (*bond)->getBeginAtomIdx();
83  unsigned j = (*bond)->getEndAtomIdx();
84  unsigned ti= TargetAtomIdx[i];
85  unsigned tj= TargetAtomIdx[j];
86  const Bond* tb = target.Molecule->getBondBetweenAtoms(ti, tj);
87  if(tb) {
88  MatchedBondSize++;
89  TargetBondIdx[(*bond)->getIdx()] = tb->getIdx(); // add
90  VisitedTargetBonds[tb->getIdx()] = true;
91  }
92  }
93  Empty = false;
94  }
95  };
96  }
97 }
std::vector< unsigned > TargetBondIdx
Definition: TargetMatch.h:22
const ROMol * Molecule
Definition: Target.h:21
void init(const Seed &seed, const match_V_t &match, const ROMol &query, const Target &target)
Definition: TargetMatch.h:55
std::vector< unsigned > TargetAtomIdx
Definition: TargetMatch.h:21
unsigned int getNumAtoms(bool onlyExplicit=1) const
returns our number of atoms
std::vector< bool > VisitedTargetAtoms
Definition: TargetMatch.h:24
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:105
TargetMatch(const TargetMatch &src)
Definition: TargetMatch.h:27
Bond * getBondBetweenAtoms(unsigned int idx1, unsigned int idx2)
returns a pointer to the bond between two atoms, Null on failure
unsigned int getNumBonds(bool onlyHeavy=1) const
returns our number of Bonds
std::vector< bool > VisitedTargetBonds
Definition: TargetMatch.h:23
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
TargetMatch & operator=(const TargetMatch &src)
Definition: TargetMatch.h:30
class for representing a bond
Definition: Bond.h:46
std::vector< std::pair< FMCS::Graph::vertex_descriptor, FMCS::Graph::vertex_descriptor > > match_V_t
MolFragment MoleculeFragment
Definition: Seed.h:50
std::vector< const Bond * > Bonds
Definition: Seed.h:25
unsigned int getIdx() const
returns our index within the ROMol
Definition: Bond.h:156
std::vector< unsigned > AtomsIdx
Definition: Seed.h:26