Generated on Wed Apr 29 2015 11:51:40 for GGL-4.1.2 by doxygen 1.8.3.1
GS_MolCheck.hh
Go to the documentation of this file.
1 #ifndef GGL_CHEM_GS_MOLCHECK_HH_
2 #define GGL_CHEM_GS_MOLCHECK_HH_
3 
4 #include <iostream>
5 
6 #include "ggl/chem/GS_chem.hh"
7 #include "ggl/chem/Molecule.hh"
8 #include "ggl/chem/AromaticityPerception.hh"
9 
10 namespace ggl {
11 namespace chem {
12 
13 
14  ////////////////////////////////////////////////////////////////////////////
15 
16  /*! @brief Molecule correction graph storage
17  *
18  * A graph storage that checks each reported molecule graph to consistency
19  * and does needed corrections.
20  *
21  * Applied corrections are e.g.
22  * - aromaticity perception and relabeling
23  *
24  * The corrected molecule is than reported to the given successive graph
25  * storage.
26  *
27  * @author Martin Mann (c) 2011 http://www.bioinf.uni-freiburg.de/~mmann/
28  *
29  */
30  class GS_MolCheck : public GS_chem {
31 
32  protected:
33 
34  //! the graph storage to which checked molecules are forwarded to
35  GS_chem* nextGS;
36 
37  //! aromaticity perception handler to relabel aromatic and non-aromatic
38  //! rings
39  AromaticityPerception * aromaticityPerception;
40 
41  //! whether or not exceptions are to be ignored or forwarded
42  bool ignoreExceptions;
43 
44  public:
45 
46  /*!
47  * Construction.
48  *
49  * @param gs the graph storage to report the checked and relabeled
50  * molecules to
51  * @param aromaticityPerception the aromaticity perception instance
52  * to be used to perform the aromaticity relabeling;
53  * @param ignoreExceptions if true: exceptions raised during molecule
54  * check are ignored; otherwise the exception is forwarded
55  */
56  GS_MolCheck( GS_chem & gs
57  , const AromaticityPerception & aromaticityPerception
58  , const bool ignoreExceptions = true );
59 
60  /*!
61  * Copy construction
62  * @param toCopy the instance to make this object a copy of
63  */
64  GS_MolCheck( const GS_MolCheck & toCopy );
65 
66 
67  /*!
68  * Assignment operator
69  * @param toCopy the instance to make this object a copy of
70  * @return the altered object *this
71  */
72  GS_MolCheck &
73  operator=( const GS_MolCheck & toCopy );
74 
75 
76  //! destruction
77  virtual ~GS_MolCheck();
78 
79  /*!
80  * Checks a given molecule graph for inconsistent labeling and
81  * corrects it accordingly. The corrected molecule is than forwarded
82  * to the successive graph storage.
83  *
84  * Note: errors during the aromaticity rewrites etc. will also result
85  * in the disposal of the molecule without further notification!
86  *
87  * @param mol the molecule graph object to check and add.
88  *
89  * @throw std::runtime_error in case the molecule correction fails
90  * and ignoreExceptions is set to false; otherwise no
91  * exception is thrown
92  */
93  virtual
94  void
95  addMolecule( const Molecule & mol );
96  };
97 
98  ////////////////////////////////////////////////////////////////////////////
99 
100 
101 }} // namespace ggl
102 
103 #include "ggl/chem/GS_MolCheck.icc"
104 
105 #endif /*GGL_CHEM_GS_MOLCHECK_HH_*/