RDKit: TargetMatch.h Source File

| RDKit Open-source cheminformatics and machine learning.

- Main Page
- Namespaces
- Classes
- Files

- File List
- File Members

TargetMatch.h
Go to the documentation of this file.
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;
19 size_t MatchedAtomSize;
20 size_t MatchedBondSize;
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) { *this = src; }
28 TargetMatch& operator=(const TargetMatch& src) {
29 Empty = src.Empty;
30 if (!Empty) {
31 MatchedAtomSize = src.MatchedAtomSize;
32 MatchedBondSize = src.MatchedBondSize;
33 TargetAtomIdx.resize(src.TargetAtomIdx.size());
34 memcpy(&TargetAtomIdx[0], &src.TargetAtomIdx[0],
35 sizeof(unsigned) * TargetAtomIdx.size());
36 TargetBondIdx.resize(src.TargetBondIdx.size());
37 memcpy(&TargetBondIdx[0], &src.TargetBondIdx[0],
38 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 { return Empty; }
45 void clear() {
46 Empty = true;
47
48 TargetAtomIdx.clear();
49 TargetBondIdx.clear();
50 VisitedTargetBonds.clear();
51 VisitedTargetAtoms.clear();
52 }
53 void init(const Seed& seed, const match_V_t& match, const ROMol& query,
54 const Target& target) {
55 TargetAtomIdx.resize(query.getNumAtoms());
56 TargetBondIdx.resize(query.getNumBonds());
57 VisitedTargetBonds.resize(target.Molecule->getNumBonds());
58 VisitedTargetAtoms.resize(target.Molecule->getNumAtoms());
59
60 memset(&TargetAtomIdx[0], 0xFF, sizeof(unsigned) * TargetAtomIdx.size());
61 memset(&TargetBondIdx[0], 0xFF, sizeof(unsigned) * TargetBondIdx.size());
62 /*
63 for(size_t i = 0; i < TargetAtomIdx.size(); i++)
64 TargetAtomIdx[i] = -1;
65 for(size_t i = 0; i < TargetBondIdx.size(); i++)
66 TargetBondIdx[i] = -1;
67 */
68 for (size_t i = 0; i < VisitedTargetBonds.size(); i++)
69 VisitedTargetBonds[i] = false;
70 for (size_t i = 0; i < VisitedTargetAtoms.size(); i++)
71 VisitedTargetAtoms[i] = false;
72
73 MatchedAtomSize = match.size();
74 for (match_V_t::const_iterator mit = match.begin(); mit != match.end();
75 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 =
82 seed.MoleculeFragment.Bonds.begin();
83 bond != seed.MoleculeFragment.Bonds.end(); bond++) {
84 unsigned i = (*bond)->getBeginAtomIdx();
85 unsigned j = (*bond)->getEndAtomIdx();
86 unsigned ti = TargetAtomIdx[i];
87 unsigned tj = TargetAtomIdx[j];
88 const Bond* tb = target.Molecule->getBondBetweenAtoms(ti, tj);
89 if (tb) {
90 MatchedBondSize++;
91 TargetBondIdx[(*bond)->getIdx()] = tb->getIdx(); // add
92 VisitedTargetBonds[tb->getIdx()] = true;
93 }
94 }
95 Empty = false;
96 }
97 };
98 }
99 }
RDKit::FMCS::TargetMatch::TargetBondIdx
std::vector< unsigned > TargetBondIdx
Definition: TargetMatch.h:22
RDKit::FMCS::Target::Molecule
const ROMol * Molecule
Definition: Target.h:21
RDKit::FMCS::Seed
Definition: Seed.h:60
FMCS.h
RDKit::FMCS::TargetMatch::init
void init(const Seed &seed, const match_V_t &match, const ROMol &query, const Target &target)
Definition: TargetMatch.h:53
RDKit::FMCS::TargetMatch::TargetAtomIdx
std::vector< unsigned > TargetAtomIdx
Definition: TargetMatch.h:21
RDKit::ROMol::getNumAtoms
unsigned int getNumAtoms(bool onlyExplicit=1) const
returns our number of atoms
RDKit::FMCS::TargetMatch::VisitedTargetAtoms
std::vector< bool > VisitedTargetAtoms
Definition: TargetMatch.h:24
RDKit::ROMol
ROMol is a molecule class that is intended to have a fixed topology.
Definition: ROMol.h:102
RDKit::FMCS::TargetMatch::TargetMatch
TargetMatch(const TargetMatch &src)
Definition: TargetMatch.h:27
RDKit::FMCS::TargetMatch::clear
void clear()
Definition: TargetMatch.h:45
RDKit::ROMol::getBondBetweenAtoms
Bond * getBondBetweenAtoms(unsigned int idx1, unsigned int idx2)
returns a pointer to the bond between two atoms, Null on failure
RDKit::FMCS::TargetMatch::TargetMatch
TargetMatch()
Definition: TargetMatch.h:26
RDKit::FMCS::TargetMatch::Empty
bool Empty
Definition: TargetMatch.h:18
RDKit::ROMol::getNumBonds
unsigned int getNumBonds(bool onlyHeavy=1) const
returns our number of Bonds
RDKit::FMCS::TargetMatch::VisitedTargetBonds
std::vector< bool > VisitedTargetBonds
Definition: TargetMatch.h:23
RDKit
Includes a bunch of functionality for handling Atom and Bond queries.
Definition: Atom.h:28
RDKit::FMCS::TargetMatch::operator=
TargetMatch & operator=(const TargetMatch &src)
Definition: TargetMatch.h:28
RDKit::FMCS::TargetMatch::MatchedAtomSize
size_t MatchedAtomSize
Definition: TargetMatch.h:19
RDKit::FMCS::TargetMatch::MatchedBondSize
size_t MatchedBondSize
Definition: TargetMatch.h:20
RDKit::FMCS::Target
Definition: Target.h:20
RDKit::Bond
class for representing a bond
Definition: Bond.h:46
RDKit::FMCS::match_V_t
std::vector< std::pair< FMCS::Graph::vertex_descriptor, FMCS::Graph::vertex_descriptor > > match_V_t
Definition: SubstructMatchCustom.h:19
RDKit::FMCS::Seed::MoleculeFragment
MolFragment MoleculeFragment
Definition: Seed.h:69
RDKit::FMCS::MolFragment::Bonds
std::vector< const Bond * > Bonds
Definition: Seed.h:25
MatchTable.h
RDKit::Bond::getIdx
unsigned int getIdx() const
returns our index within the ROMol
Definition: Bond.h:158
RDKit::FMCS::TargetMatch
Definition: TargetMatch.h:17
RDKit::FMCS::MolFragment::AtomsIdx
std::vector< unsigned > AtomsIdx
Definition: Seed.h:26
RDKit::FMCS::TargetMatch::empty
bool empty() const
Definition: TargetMatch.h:44