libball1.4-dev 1.4.3~beta1-4 / usr / include / BALL / QSAR / ringPerceptionProcessor.h

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: ringPerceptionProcessor.h,v 1.17.4.2 2007/04/03 13:29:45 bertsch Exp $
//

#ifndef BALL_QSAR_RINGPERCEPTIONPROCESSOR_H
#define BALL_QSAR_RINGPERCEPTIONPROCESSOR_H

#ifndef BALL_KERNEL_ATOMCONTAINER_H
	#include <BALL/KERNEL/atomContainer.h>
#endif

#ifndef BALL_STRUCTURE_SIMPLEMOLECULARGRAPH_H
	#include <BALL/STRUCTURE/simpleMolecularGraph.h>
#endif

#ifndef BALL_DATATYPE_OPTIONS_H
	#include <BALL/DATATYPE/options.h>
#endif

#include <stack>
#include <vector>

namespace BALL
{
	/**	Processor, which marks all atoms and bonds in a ring structure with the
	    Composite Property "InRing".
			calculateSSSR() can also compute the number of rings found.
			
			The processor is an implementation of Figueras algorithm, described in:
			J. Figueras, J. Chem. Inf. Comput. Sci., 1996, 36(5), 986-991

			and the Balducci Pearlman algorithm described in:
			Renzo Balducci, Robert S. Pearlman, J. Chem. Inf. Comput. Sci., 34:822-831, 1994
	*/
	class BALL_EXPORT RingPerceptionProcessor
		:	public UnaryProcessor<AtomContainer>
	{
		public:

			/** @name Constants and Definitions
			*/
			//@{
			/// Option names
			struct Option
			{
				/** The name of the algorithm which sould be used 
				 *	for the ring perception. At the moment this can be 
				 *	either Figueras algorithm or as default the Balducci/
				 *	Pearlman algorithm. \par
				 *	Valid values are <b> Figueras <b> for the Figueras and
				 *	<b> Balducci <b> for the Balducci Pearlman algorithm (default)
				 */
				static const char* ALGORITHM_NAME;
			};

			/// default options for the ring perception
			struct Default
			{
				/** Default name of the algorithm. This is set to the
				 *	provable correct Balducci/Pearlman algorithm,
				 *	<b> Balducci <b>
				 */
				static const char* ALGORITHM_NAME;
			};


			BALL_CREATE(RingPerceptionProcessor)
	
			/** @name Constrcutors and Destructors
			*/
			//@{
			/** Default constructor
			*/
			RingPerceptionProcessor();

			/** Copy constructor
			*/
			RingPerceptionProcessor(const RingPerceptionProcessor& rp);

			/** Destructor
			*/
			virtual ~RingPerceptionProcessor();

			//@}
			/** @name Assignment
			*/
			//@{

			/** Assignment operator
			*/
			RingPerceptionProcessor& operator = (const RingPerceptionProcessor& rp);

			//@}
			/** @name Accessors
			*/
			//@{

			/** Method to get a smallest set of smallest rings (SSSR) from a molecule.
					@param SSSR, vector of rings, where the rings are stored in vector<Atom*>
					@param AtomContiner, from which AtomContainer the rings are to be percepted
			*/
			Size calculateSSSR(vector<vector<Atom*> >& sssr, AtomContainer& ac);
			//@}

			/** Getter which returns all the 3 - 6 membered rings, calculateSSSR with
			 *  the Balducci-Pearlman Algorithm (defalt) is needed prior this call.
			 */
			const vector<vector<Atom*> >& getAllSmallRings() const;
			
			/** @name Processor-related methods
			*/
			//@{
			Processor::Result operator () (AtomContainer& ac);
			//@}
	
			/** Method that finds all biconnected components, the algorithm is freely
					adapted from a standard bcc (binary connected components) algorithm. 
					Returns the number of bccs found.
			*/
			Size findAllBCC(std::vector<SimpleMolecularGraph*>& bcc, SimpleMolecularGraph& graph);

			/*_ Options for the ring perception
			*/
			Options options;									

			/** sets the default options of this processor
			*/
			void setDefaultOptions();

		protected:
	
			/*_ @name Accessors
			*/
			//@{
			/*_ Implementation of the Figueras algorithm. This algorithm has some build
					in bugs, and should not be used any more. Hence as default the provable
					correct Balducci/Pearlman algorithm is used.
			*/
			Size FiguerasAlgorithm_(vector<vector<Atom*> >& sssr, AtomContainer& ac);

			/*_ Method that return the smallest ring which atom n participates
					@param atom from which the search is started
					@param ring set in which the found ring is stored (if any)
			*/
			Size getRing_(Atom* n, HashSet<Atom*>& ring_set);

			/*_ A bond, which when deleted leads to the smallest ring
					is deleted. 
					@param ring_set atoms to test
					@param ac the atom container the algorithm works on
			*/
			void checkEdges_(HashSet<Atom*>& ring_set, AtomContainer& ac);
	
			/*_ Method that finds all biconnected components, the algorithm is freely 
					adapted from a standard bcc algorithm.
			*/
			Size findAllBCC_(std::vector<SimpleMolecularGraph*>& bcc, SimpleMolecularGraph& graph);
	
			/*_ recursive function that finds bccs
			*/
			void DFSBCC_( std::vector<SimpleMolecularGraph*>& bccs, Size dfbi, 
										HashMap<NodeItem<Index, Index>*, Size> DFBIndex, 
										NodeItem<Index, Index>* v);
																		
			HashSet<NodeItem<Index, Index>* > visited_;
			HashSet<EdgeItem<Index, Index>* > visited_bonds_;
			HashMap<NodeItem<Index, Index>* , Size> P_;
			HashMap<NodeItem<Index, Index>*, NodeItem<Index, Index>* > parents_;
			std::stack<EdgeItem<Index, Index>* > BCC_;
	
	
			// Balducci and Pearlman algorithm
			struct PathMessage_;
			
			/*_ The tnode structure described in the paper
			*/
			struct TNode_
			{
				/// method to process the messages in the recieve buffer
				void recieve();
				
				/// method to process the messages in the send buffer
				void send();
	
				/// the recieve buffer, where messages are stored in
				std::vector<PathMessage_> recieve_buffer;
	
				/// the send buffer, where messages are stored in
				std::vector<PathMessage_> send_buffer;
			};
		
			/*_ The pathMsg structure described in the paper
			*/
			struct PathMessage_
			{
				void push(EdgeItem<Index, Index>* bond, TNode_* node);
		
				// path of the message
				BitVector beep;
				
				/// pointer to the first node this message was sent from
				TNode_* nfirst;
			
				// pointer to the last node of the messages' path
				TNode_* nlast;

				/// pointer to the first edge of the message path
				EdgeItem<Index, Index>* efirst;
			};

			/// mapping for internal TNode structure and the nodes of the molecular graph
			static HashMap<TNode_*, NodeItem<Index, Index>* > tnode_to_atom_;
			static HashMap<NodeItem<Index, Index>* , TNode_*> atom_to_tnode_;
			
			/// mapping for the path representation as bitvectors
			static HashMap<EdgeItem<Index, Index>*, Size> bond_to_index_;
			static HashMap<Size, EdgeItem<Index, Index>*> index_to_bond_;
			
			/// the SSSR detected by the algorithm
			static std::vector<BitVector> rings_;
			
			/// the matrix for the independency tests
			static std::vector<BitVector> matrix_;
			
			/// the rings of the ith phase, which are to be forwarded to the ring selector
			static std::vector<BitVector> forwarded_rings_;
			
			/// rings (beer) which have already been tested
			static std::vector<BitVector> tested_beers_;

			/// contains all 3 to 6 membered rings after the procedure of the Balducci-Pearlman algorithm
			static std::vector<std::vector<Atom*> > all_small_rings_;

			/// contains all 3 to 6 membered rings as beers
			static std::vector<BitVector> all_small_beers_;
			
			/*_ function that gets a binary edge-encoded ring as a BitVector
					and adds it to the ringset if its linearly independend
			*/
			static void BalducciPearlmanRingSelector_(BitVector bit_vector);
	
			/*_ Implementation of the Balducci/Pearlman algorithm 
			*/
			Size BalducciPearlmanAlgorithm_(std::vector<std::vector<Atom*> >& sssr, SimpleMolecularGraph& graph);
	};
} // namespace BALL

#endif // BALL_QSAR_RINGPERCEPTIONPROCESSOR_H