atomTyper.h

// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: atomTyper.h,v 1.1.4.1 2007/03/25 21:25:24 oliver Exp $ 
//

#ifndef BALL_STRUCTURE_ATOMTYPER_H
#define BALL_STRUCTURE_ATOMTYPER_H

#ifndef BALL_DATATYPE_HASHSET_H
# include <BALL/DATATYPE/hashSet.h>
#endif

#ifndef BALL_DATATYPE_STRINGHASHMAP_H
# include <BALL/DATATYPE/stringHashMap.h>
#endif

#include <vector>

namespace BALL 
{
  using std::vector;

  class Molecule;
  class System;
  class Atom;

  class BALL_EXPORT AtomTyper
  {
    public:

    BALL_CREATE(AtomTyper)

    
    AtomTyper();

    AtomTyper(const AtomTyper& t);

    virtual ~AtomTyper() {};

    bool setup(const String& filename);
    
    virtual void assignTo(System& s);
    
    void setAromaticRings(const vector<HashSet<Atom*> >& rings) { aromatic_rings_ = rings;}

    void setRings(const vector<HashSet<Atom*> >& rings) { rings_ = rings;}

    // just for debugging: computational times for the individual SMARTS expressions
    static StringHashMap<float> rule_times;

    protected:
    
    void assignTo(Molecule& mol);

    virtual void assignSpecificValues_(Atom&) {};

    virtual bool specificSetup_() { return true;}

    vector<String>    names_;
    vector<String>    rules_;
    vector<Index>     types_;
    // entries in the file for specificSetup_() :
    vector<vector<String> > fields_;
    // number for fields per line in the config file
    Size                              number_expected_fields_;
    vector<HashSet<Atom*> >           rings_;
    vector<HashSet<Atom*> >           aromatic_rings_;
    StringHashMap<vector<Position> >  element_to_rules_;
    HashSet<Atom*>                    atoms_;
  };

} // namespace BALL

#endif // BALL_STRUCTURE_ATOMTYPER_H

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