RDKit: Rings.h Source File

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Rings.h
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1//
2// Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
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
11//! \file Rings.h
12//! \brief utility functionality for working with ring systems
13
14#include <RDGeneral/export.h>
15#ifndef _RDRINGS_H_
16#define _RDRINGS_H_
17
18#include <vector>
19#include <map>
20#include <boost/dynamic_bitset_fwd.hpp>
21
22namespace RDKit {
23class ROMol;
24};
25
26 namespace RingUtils {
27 typedef std::vector<int> INT_VECT;
28 typedef std::vector<std::vector<int>> VECT_INT_VECT;
29 typedef std::map<int, std::vector<int>> INT_INT_VECT_MAP;
30
31//! Pick a set of rings that are fused together and contain a specified ring
32/*!
33
34 \param curr the ID for the irng that should be in the fused system
35 \param neighMap adjacency lists for for all rings in the molecule.
36 See documentation for makeNeighMap
37 \param res used to return the results: a list of rings that are fused
38 with curr in them
39 \param done a bit vector recording the rings that are already dealt with
40 this also can be used to avoid any rings that should not be included
41 in
42 the fused system
43 \param depth used to track recursion depth
44
45*/
46 RDKIT_GRAPHMOL_EXPORT void pickFusedRings(int curr,
47 const INT_INT_VECT_MAP &neighMap,
48 INT_VECT &res,
49 boost::dynamic_bitset<> &done,
50 int depth = 0);
51
52//! \brief For each ring in bring compute and store the ring that are fused
53//! (share at least one bond with it).
54/*!
55 Useful both for the keulization stuff and aromaticity perception.
56
57 \param brings list of rings - each ring is specified as a list of bond IDs
58 \param neighMap an STL map into which the results are stored. Each entry in
59 the
60 map is indexed by the ring ID and the contents are the list
61 rings (rather their IDs) that are fused with this ring
62 \param maxSize if this is >0, rings that are larger than the threshold
63 will not be considered as candidates to be neighbors
64 \param maxOverlapSize if this is >0, rings that overlap by more bonds than
65 this will not be considered to be neighbors
66
67*/
68 RDKIT_GRAPHMOL_EXPORT void makeRingNeighborMap(const VECT_INT_VECT &brings,
69 INT_INT_VECT_MAP &neighMap,
70 unsigned int maxSize = 0,
71 unsigned int maxOverlapSize = 0);
72
73//! converts a list of atom indices into a list of bond indices
74/*!
75
76 \param res list of ring - each ring is a list of atom ids
77 \param brings reference to a list of rings to the write the results to
78 each ring here is list of bonds ids
79 \param mol the molecule of interest
80
81 <b>Assumptions:</b>
82 - each list of atom ids in "res" form a legitimate ring
83 - each of these list of ordered such that a ring can be traversed
84*/
85 RDKIT_GRAPHMOL_EXPORT void convertToBonds(const VECT_INT_VECT &res,
86 VECT_INT_VECT &brings,
87 const RDKit::ROMol &mol);
88}; // namespace RingUtils
89
90#endif
RDKit::ROMol
Definition ROMol.h:199
export.h
RDKIT_GRAPHMOL_EXPORT
#define RDKIT_GRAPHMOL_EXPORT
Definition export.h:249
RDKit
Std stuff.
Definition Abbreviations.h:19
RingUtils
Definition Rings.h:26
RingUtils::INT_VECT
std::vector< int > INT_VECT
Definition Rings.h:27
RingUtils::makeRingNeighborMap
RDKIT_GRAPHMOL_EXPORT void makeRingNeighborMap(const VECT_INT_VECT &brings, INT_INT_VECT_MAP &neighMap, unsigned int maxSize=0, unsigned int maxOverlapSize=0)
For each ring in bring compute and store the ring that are fused (share at least one bond with it).
RingUtils::convertToBonds
RDKIT_GRAPHMOL_EXPORT void convertToBonds(const VECT_INT_VECT &res, VECT_INT_VECT &brings, const RDKit::ROMol &mol)
converts a list of atom indices into a list of bond indices
RingUtils::pickFusedRings
RDKIT_GRAPHMOL_EXPORT void pickFusedRings(int curr, const INT_INT_VECT_MAP &neighMap, INT_VECT &res, boost::dynamic_bitset<> &done, int depth=0)
Pick a set of rings that are fused together and contain a specified ring.
RingUtils::VECT_INT_VECT
std::vector< std::vector< int > > VECT_INT_VECT
Definition Rings.h:28
RingUtils::INT_INT_VECT_MAP
std::map< int, std::vector< int > > INT_INT_VECT_MAP
Definition Rings.h:29