peptideBuilder.h

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

#ifndef BALL_STRUCTURE_PEPTIDEBUILDER_H
#define BALL_STRUCTURE_PEPTIDEBUILDER_H

#ifndef BALL_STRUCTURE_PEPTIDES_H
# include <BALL/STRUCTURE/peptides.h>
#endif

namespace BALL
{
  class FragmentDB;

  namespace Peptides
  {
    class BALL_EXPORT AminoAcidDescriptor
    {
      public:
     
     AminoAcidDescriptor();
     
     AminoAcidDescriptor(const String& type, const Angle& phi=Angle(-47.,false),
             const Angle& psi=Angle(-58.,false), const Angle& omega=Angle(180.,false));
     
     virtual ~AminoAcidDescriptor();
     
     AminoAcidDescriptor(const AminoAcidDescriptor& aad);

     void setAminoAcidType(const String& type);
     
     void setPhi(const Angle& phi);
     
     void setPsi(const Angle& psi);
     
     void setOmega(const Angle& omega);
     
     const String& getType() const;
     
     const Angle& getPhi() const;
     
     const Angle& getPsi() const;
     
     const Angle& getOmega() const;
     
   protected:
     
     String type_;
     Angle phi_;
     Angle psi_;
     Angle omega_;
   };
       
   class BALL_EXPORT PeptideBuilder
   {
     public:

     PeptideBuilder();
     
     PeptideBuilder(const std::vector<AminoAcidDescriptor>& sequence);

     PeptideBuilder(const String& sequence, const Angle& phi = Angle(-47., false),
                    const Angle& psi = Angle(-58., false), const Angle& omega = Angle(180., false));
     
     PeptideBuilder(const PeptideBuilder& pc);

     virtual ~PeptideBuilder();
     
     void addAminoAcid(const String& type, const Angle& phi=Angle(-47.,false),
           const Angle& psi=Angle(-58.,false), const Angle& omega=Angle(180.,false));
     // Sheet angles ???
     
     void addAminoAcid(const AminoAcidDescriptor& aad);

     void setChainName(const String& name);
    
     const String& getChainName() const;

     void setProteinName(const String& name);
    
     const String& getProteinName() const;

     Protein* construct();

     void setFragmentDB(const FragmentDB* db)
       ;

     const FragmentDB* getFragmentDB() const
       ;
     
   protected:
     std::vector<AminoAcidDescriptor> sequence_;
     String chainname_;
     String proteinname_;
     
     bool is_proline_;
     FragmentDB* fragment_db_;

     Residue* createResidue_(const String& type, const int id);
     void insert_(Residue& resnew, Residue& resold);
     void transform_(const Angle& phi, const Angle& psi, Residue& resold, Residue& resnew);
     void peptide_(Residue& resold, Residue& resnew);
     void setOmega_(Residue& resold, Residue& residue, const Angle& omega);
     PDBAtom* getAtomByName_(Residue& res, const String& name);
   };
       
  } // namespace Peptides

} // namespace BALL

#endif // BALL_STRUCTURE_PEPTIDEBUILDER_H