stage/include/ost/mol/residue_handle.hh

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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
//------------------------------------------------------------------------------
#ifndef OST_RESIDUE_HANDLE_HU
#define OST_RESIDUE_HANDLE_HU

#include <ost/geom/vec3.hh>
#include <ost/geom/aligned_cuboid.hh>

#include <ost/mol/query.hh>
#include <ost/mol/module_config.hh>
#include <ost/mol/residue_base.hh>
#include <ost/mol/entity_visitor_fw.hh>

namespace ost { namespace mol {

class DLLEXPORT_OST_MOL ResidueHandle : public ResidueBase {
public:
  ResidueHandle();

  ResidueHandle(const impl::ResidueImplPtr& impl)
    : ResidueBase(impl) {}
  EntityHandle GetEntity() const;

  double GetMass() const;
  
  geom::Vec3 GetCenterOfMass() const;
  
  geom::Vec3 GetCenterOfAtoms() const;
  
  geom::AlignedCuboid GetBounds() const;
  
  ChainHandle GetChain() const;

  ResidueHandle GetPrev() const;

  ResidueHandle GetNext() const;

  AtomHandle FindAtom(const String& aname) const;

  void Apply(EntityVisitor& visitor);

  AtomHandleList GetAtomList() const;

  int GetAtomCount() const;

  int GetBondCount() const;

  TorsionHandle FindTorsion(const String& torsion_name) const;

  TorsionHandleList GetTorsionList() const;

  int GetIndex() const;




  bool HasAltAtomGroup(const String& group) const;

  const String& GetCurrentAltGroupName() const;
  
  std::vector<String> GetAltAtomGroupNames() const;

  bool HasAltAtoms() const;
  
  geom::Vec3 GetAltAtomPos(const AtomHandle& atom, const String& group) const;
  
  bool SwitchAtomPos(const String& group);

  ResidueHandle GetHandle() const;
  unsigned long GetHashCode() const;

  EntityView Select(const Query& q, QueryFlags flags=0) const;

  EntityView Select(const String& query_string, QueryFlags flags=0) const;
    
  bool operator==(const ResidueHandle& ref) const;
  bool operator!=(const ResidueHandle& ref) const;
  
  

};

bool DLLEXPORT_OST_MOL InSequence(const ResidueHandle& residue_one,
                                  const ResidueHandle& residue_two);
                                       

}} //ns

#endif // OST_RESIDUE_HANDLE_HH

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