stage/include/ost/mol/entity_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_ENTITY_HANDLE_HH
#define OST_ENTITY_HANDLE_HH

#include <ost/mol/module_config.hh>

#include "impl/entity_impl_fw.hh"
#include "entity_visitor_fw.hh"
#include "query.hh"
#include "entity_observer_fw.hh"
#include "residue_prop.hh"
#include "entity_view.hh"
#include "chain_handle.hh"
#include "handle_type_fw.hh"


#include "editor_type_fw.hh"

namespace ost { namespace mol {

DLLEXPORT_OST_MOL EntityHandle CreateEntity();

class DLLEXPORT_OST_MOL EntityHandle : public EntityBase {
public:
  friend class XCSEditor;
  friend class ICSEditor;
  
  EntityHandle(const impl::EntityImplPtr&);

  EntityHandle();
  




  EntityHandle Copy() const;
  







  geom::Vec3 GetCenterOfAtoms() const;
  
  Real GetMass() const;
  
  geom::Vec3 GetCenterOfMass() const;  

  geom::AlignedCuboid GetBounds() const;
  
  void Swap(EntityHandle& eh);

  void DeepSwap(EntityHandle& eh);



  void AttachObserver(const EntityObserverPtr&);
  
  
  void DetachObserver(const EntityObserverPtr&);


  void Apply(EntityVisitor& v);


  TorsionHandle FindTorsion(const AtomHandle& a1, const AtomHandle& a2,
                            const AtomHandle& a3, const AtomHandle& a4) const;

  ChainHandleList GetChainList() const;








  ChainHandle FindChain(const String& name) const;

  ResidueHandle FindResidue(const String& chain_name,
                            const ResNum& number) const;

  AtomHandle FindAtom(const String& chain_name,
                      const ResNum& number,
                      const String& atom_name) const;

  AtomHandleList FindWithin(const geom::Vec3& pos, Real radius) const;

  void SetDefaultQueryFlags(QueryFlags flags);

  QueryFlags GetDefaultQueryFlags() const;

  EntityView Select(const Query& q) const;

  EntityView Select(const String& query_string) const;

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

  EntityView Select(const String& query_string, QueryFlags flags) const;

  EntityView CreateFullView() const;

  EntityView CreateEmptyView() const;

  int GetAtomCount() const;

  int GetResidueCount() const;

  int GetChainCount() const;

  int GetBondCount() const;

  mol::BondHandleList GetBondList() const;


  Real GetAngle(const AtomHandle& a1, const AtomHandle& a2,
                const AtomHandle& a3) const;

  Real GetAngle(const AtomView& a1, const AtomView& a2,
                const AtomView& a3) const;

  geom::Mat4 GetTransformationMatrix() const;
  geom::Mat4 GetInvTransformationMatrix() const;
  bool IsTransformationIdentity() const;

  geom::Transform GetTransform() const;
  void SetTransform(const geom::Transform& t);
  bool HasTransform() const;
  void ClearTransform();
  void FixTransform();

  ResidueHandleList GetResidueList() const;
  
  AtomHandleList GetAtomList() const;
  
  geom::Vec3List GetAtomPosList(bool ordered_by_index = false) const;
  
  XCSEditor EditXCS(EditMode mode=UNBUFFERED_EDIT) const;
  
  ICSEditor EditICS(EditMode mode=UNBUFFERED_EDIT) const;  
  
  EntityHandle GetHandle() const;
  bool operator==(const EntityHandle& ref) const;
  bool operator!=(const EntityHandle& ref) const;
};

}}

#endif // OST_ENTITY_HANDLE_HH

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