BALL: addHydrogenProcessor.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 
00005 #ifndef BALL_STRUCTURE_ADDHYDROGENPROCESSOR_H
00006 #define BALL_STRUCTURE_ADDHYDROGENPROCESSOR_H
00007 
00008 #ifndef BALL_CONCEPT_PROCESSOR_H
00009 #include <BALL/CONCEPT/processor.h>
00010 #endif
00011 
00012 #ifndef BALL_MATHS_VECTOR3_H
00013 #include <BALL/MATHS/vector3.h> 
00014 #endif
00015 
00016 #ifndef BALL_KERNEL_ATOM_H
00017 #include <BALL/KERNEL/atom.h>
00018 #endif
00019 
00020 #include <vector>
00021 
00022 namespace BALL
00023 {
00024 
00047   class BALL_EXPORT AddHydrogenProcessor
00048     : public UnaryProcessor<Composite>
00049   {
00050  
00051     public:
00052 
00054     AddHydrogenProcessor();
00055     
00057     virtual ~AddHydrogenProcessor();
00058     
00060     AddHydrogenProcessor(const AddHydrogenProcessor& hbp);
00061 
00062     virtual bool start();
00063     
00065     virtual Processor::Result operator() (Composite &composite);
00066 
00068     Size getConnectivity(Atom& atom);
00069 
00071     void setRings(const vector<vector<Atom*> >& rings);
00072 
00074     Size getNumberOfAddedHydrogens() { return nr_hydrogens_;}
00075     
00076     protected:
00077 
00078     Size countBondOrders(Atom& atom);
00079     void addHydrogen_(Atom& atom, Vector3 position);
00080     inline bool isRingAtom_(Atom& atom);
00081     vector<Atom*> getPartners_(Atom& atom);
00082     Vector3 getNormal_(const Vector3& v);
00083     inline bool normalize_(Vector3& v);
00084     bool hasMultipleBond_(Atom& atom);
00085     // get the ideal bond length for the given element with hydrogen atoms
00086     float getBondLength_(Position element);
00087 
00088     HashSet<Atom*> ring_atoms_;
00089     Position atom_nr_;
00090     Atom*    last_atom_;
00091     Size     nr_hydrogens_;
00092   }; //class AddHydrogenProcessor
00093 
00094 } //namesspace BALL
00095 
00096 #endif // BALL_STRUCTURE_ADDHYDROGENPROCESSOR_H