UCK.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//

#ifndef BALL_STRUCTURE_UCK_H
#define BALL_STRUCTURE_UCK_H

#ifndef BALL_DATATYPE_STRING_H
  #include <BALL/DATATYPE/string.h>
#endif

#include <vector>

namespace BALL
{
  class Molecule;

  class BALL_EXPORT UCK
  {
    public:

    typedef std::vector<std::pair<Size, Size> > PairVector;
    typedef std::vector<std::vector<Size> >     SizeVector;

    /* default constructor
    */
    UCK();
    
    /* constructor
    */
    UCK(const Molecule& mol, Size d=3);
    
    /* constructor added originally in CADDSuite
     */
    UCK(const Molecule& mol, bool ignore_hydrogens, Size d=3);

    /* copy constructor
    */
    UCK(UCK& uck);
    
    /* destructor
    */
    virtual ~UCK();
    
    /* print Uck to std::out
    */
    void printUCK(std::ostream& outstr);

    Size getDepth();

    const String& getFormula() const;

    const String& getUCK() const;

    const String& getId() const;

    float getWeight();
    
    private:
    
    /* variation of UCK-Algorithm:
    * delete one occurance of the current label from the lambda string
    * this reduces the length of the constructed string
    */
    String eraseDoubleLabels(const Size d, String x, String label);
    
    /* computes the uck
    */
    void makeUCK(const Molecule& m);
    
    /* construct graph-representation of the molecule read
    */
    void getGraph(std::vector<String>& v, PairVector& e, const Molecule& mol);
    
    /* Floyd's Algorithm
    *  find shortest paths between all pairs of nodes
    */
    void makePathMatrix(const PairVector& e, SizeVector& sp, const Size e_size);
    
    /* compute concatenated strings [lambda(a)nlambda(b)] for every pair of nodes
    */
    void makePairs(const std::vector<String>& lambda_map, std::vector<String>& pairs, const std::vector<vector<Size> >& sp);
    
    /* compute lambda-map
    */
    String lambda(String lambda_d, const PairVector& e, const std::vector<String>& v, Size pos, Size d);
    
    /* construct final UCK as follows:
    *  chemical_formula-lexicographically ordered collection of strings pair(a,b)
    */
    void createFinalString(const std::vector<String>& pairs);

    Size depth_;
    String formula_; 
    String uck_str_; 
    String id_;
    float weight_;
    bool ignore_hydrogens_;
  };

}//namespace
#endif // BALL_STRUCTURE_UCK_H