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GraphScaffold.hh
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1 #ifndef SGM_GRAPHSCAFFOLD_HH_
2 #define SGM_GRAPHSCAFFOLD_HH_
3 
4 
5 #include "sgm/Graph_Interface.hh"
6 #include "sgm/RP_Hanser96.hh"
7 
8 namespace sgm {
9 
10 
11  /*!
12  * Computes the scaffold annotation of each node, ie. whether it is part of
13  * a ring, a ring linker, or a dangling end (side chain).
14  *
15  * See
16  * The Properties of Known Drugs. 1. Molecular Frameworks
17  * Guy W. Bemis and Mark A. Murcko
18  * J. Med. Chem. 1996, 39, 2887-2893
19  *
20  * @author Martin Mann (c) 2013 http://www.bioinf.uni-freiburg.de/~mmann/
21  *
22  */
23  class GraphScaffold : public RP_Hanser96 {
24 
25  public:
26 
27  //! possible scaffold types of graph nodes
28  enum ScaffoldType {
29  GST_UNKNOWN, //!< nodes of this type are not processed yet
30  GST_RING, //!< nodes of this type are part of a ring
31  GST_LINKER, //!< nodes of this type are part of a ring linker
32  GST_DANGLING //!< nodes of this type are part of a dangling end / side chain
33  };
34 
35  //! assignment of scaffold types for each node index
36  typedef std::vector< ScaffoldType > ScaffoldAnnotation;
37 
38  protected:
39 
40  //! the P-graph to be compressed during the ring perception
41  using RP_Hanser96::pGraph;
42 
43  //! the index access for pGraph
44  using RP_Hanser96::pGraphIndex;
45  //! the edge label access for pGraph, i.e. the according RingList
46  using RP_Hanser96::pGraphPath;
47 
48  //! the degree of each node in pGraph
49  using RP_Hanser96::pGraphDegree;
50  //! the nodes to be removed during the ring perception from pGraph
51  using RP_Hanser96::toRemove;
52 
53 
54  public:
55 
56  //! construction
57  GraphScaffold();
58 
59  //! destruction
60  virtual ~GraphScaffold();
61 
62  /*!
63  * Identifies the scaffold type for each node in the graph and returns
64  * the according scaffold annotation.
65  *
66  * @param graph the graph to annotate
67  * @param maxRingSize the maximal size of rings to consider
68  * @return the scaffold type for each node within the graph, ie. the
69  * container has as many entries as the graph nodes.
70  */
71  ScaffoldAnnotation
72  getScaffoldAnnotation( const Graph_Interface & graph
73  , const size_t maxRingSize = std::numeric_limits<size_t>::max() );
74 
75  /*!
76  * Identifies the scaffold type for each node in the graph and returns
77  * the according scaffold annotation.
78  *
79  * @param graph the graph to annotate
80  * @param reporter the ring reporter to forward all rings to
81  * @param maxRingSize the maximal size of rings to consider
82  * @return the scaffold type for each node within the graph, ie. the
83  * container has as many entries as the graph nodes.
84  */
85  ScaffoldAnnotation
86  getScaffoldAnnotation( const Graph_Interface & graph
87  , RingReporter & reporter
88  , const size_t maxRingSize = std::numeric_limits<size_t>::max());
89 
90  protected:
91 
92 
93 
94 
95  /*!
96  * Identifies the scaffold type for each node in the graph and returns
97  * the according scaffold annotation.
98  *
99  * @param graph the graph to annotate
100  * @param reporter the ring reporter to forward all rings to (can be
101  * NULL such that no reporting is done)
102  * @param maxRingSize the maximal size of rings to consider
103  * @return the scaffold type for each node within the graph, ie. the
104  * container has as many entries as the graph nodes.
105  */
106  ScaffoldAnnotation
107  getScaffoldAnnotation( const Graph_Interface & graph
108  , RingReporter * reporter
109  , const size_t maxRingSize );
110 
111 
112  /*!
113  * Ring reporter that stores ring annotations and forwards the
114  * reporting to another ring reporter if given.
115  */
116  class RR_Annotation : public RingReporter {
117 
118  protected:
119 
120  //! the annotation to update with ring information
121  ScaffoldAnnotation & annotation;
122  //! the next reporter to forward the ring information to if not NULL
123  RingReporter * nextReporter;
124 
125  public:
126 
127  /*!
128  * Constructions
129  * @param annotation the annotation to update with ring information
130  * @param nextReporter the next reporter to forward the ring
131  * information to if not NULL
132  */
133  RR_Annotation( ScaffoldAnnotation & annotation
134  , RingReporter * nextReporter = NULL)
135  : annotation(annotation)
136  , nextReporter(nextReporter)
137  {}
138 
139  virtual
140  ~RR_Annotation()
141  {}
142  /*!
143  * Nodes of the reported ring are accordingly annotated and the
144  * ring information is forwarded to the next ring reporter
145  * @param graph the graph that contains the ring
146  * @param ringList the ring to report
147  */
148  virtual
149  void
150  reportRing( const Graph_Interface& graph, const RingList & ringList );
151 
152  };
153 
154  };
155 
156 } // namespace sgm
157 
158 #endif /* SGM_GRAPHSCAFFOLD_HH_ */