extractors.h

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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
// $Id: extractors.h,v 1.2.8.3 2007/03/27 22:41:31 amoll Exp $
//
// Author:
//   Oliver Kohlbacher
//

#ifndef BALL_KERNEL_EXTRACTORS_H
#define BALL_KERNEL_EXTRACTORS_H

#ifndef BALL_COMMON_H
# include <BALL/common.h>
#endif

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

namespace BALL 
{

  class Atom;
  class PDBAtom;
  class Bond;
  class AtomContainer;
  class Fragment;
  class Molecule;
  class Residue;
  class SecondaryStructure;
  class Chain;
  class Protein;
  class Nucleotide;
  class NucleicAcid;


  typedef std::list<Atom*> AtomList;
  typedef std::list<Bond*> BondList;
  typedef std::list<AtomContainer*> AtomContainerList;
  typedef std::list<PDBAtom*> PDBAtomList;
  typedef std::list<Residue*> ResidueList;
  typedef std::list<Fragment*> FragmentList;
  typedef std::list<Molecule*> MoleculeList;
  typedef std::list<Protein*> ProteinList;
  typedef std::list<SecondaryStructure*> SecondaryStructureList;
  typedef std::list<Chain*> ChainList;
  typedef std::list<Nucleotide*> NucleotideList;
  typedef std::list<NucleicAcid*> NucleicAcidList;

   

  BALL_EXPORT AtomList atoms(const AtomContainer& fragment, const String& expression = String());
      
  BALL_EXPORT AtomList atoms(const AtomList& atoms, const String& expression);
      
  BALL_EXPORT PDBAtomList PDBAtoms(const AtomContainer& fragment, const String& expression = String());
      
  BALL_EXPORT BondList bonds(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT BondList bonds(const Atom& atom);

  BALL_EXPORT AtomContainerList atomContainers(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT ResidueList residues(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT FragmentList fragments(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT MoleculeList molecules(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT ProteinList proteins(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT SecondaryStructureList secondaryStructures(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT ChainList chains(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT NucleicAcidList nucleicAcids(const AtomContainer& fragment, bool selected_only = false);

  BALL_EXPORT NucleotideList nucleotides(const AtomContainer& fragment, bool selected_only = false);

  
} // namespace BALL

#endif // BALL_KERNEL_EXTRACTORS_H