flexibleMolecule.h

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// ----------------------------------------------------
// $Maintainer: Marc Röttig $
// $Authors: Marc Röttig, Marcel Schumann $
// ----------------------------------------------------

#ifndef BALL_DOCKING_COMMON_FLEXIBLEMOLECULE_H
#define BALL_DOCKING_COMMON_FLEXIBLEMOLECULE_H

#include <BALL/KERNEL/molecule.h>
#include <BALL/KERNEL/forEach.h>
#include <BALL/DATATYPE/hashMap.h>
#include <BALL/DOCKING/COMMON/conformation.h>
#include <BALL/COMMON/exception.h>
#include <iostream>

namespace BALL
{
    class BALL_EXPORT FlexibleMolecule
    {
      public:

        /* Constructor.
         */
        FlexibleMolecule(Molecule* mol);

        FlexibleMolecule(const FlexibleMolecule& flexmol);

        virtual ~FlexibleMolecule();

        virtual void addConformation(Conformation* conf);

        void clearConformations();

        static void generateTopologyHash(const AtomContainer* mol, String& hash, bool ignore_hydrogen = false);


        Size getNumberOfConformations();

        const vector < Conformation* > & getConformations() const;

        String getConformationId(Position i);

        Conformation*  getConformation(Position i);

        Molecule* getConformer(Position i);

        Molecule* getConformerById(String id);

        Conformation* getConformationById(String id);

        bool hasConformation(String id);

        Molecule* getParent();

        String  getId() const;

        void setId(String id);

        void removeMoleculeOwnership();

      protected:
        String id;
        bool checkCompatibility(Conformation* conf);
        Molecule* molecule;
        vector < Conformation* > conformations;
        HashMap < String, Conformation* > conf_ids_;
        bool molecule_ownership_;

      private:
        static void calculatePseudoSmile(const Atom* atom, String& smile, HashSet<const Atom*>& visited_atoms, bool ignore_hydrogen);
    };

    typedef FlexibleMolecule Ligand;
}

#endif /* BALL_DOCKING_COMMON_FLEXIBLEMOLECULE_H */