stage/include/ost/mol/chain_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_CHAIN_HANDLE_HS
#define OST_CHAIN_HANDLE_HS

#include <vector>

#include <ost/mol/module_config.hh>

#include <ost/geom/geom.hh>

#include "chain_base.hh"

#include "query.hh"
#include "view_type_fw.hh"
#include "handle_type_fw.hh"
#include "residue_prop.hh"
#include "entity_visitor_fw.hh"
#include "sec_structure.hh"

namespace ost { namespace mol {

class DLLEXPORT_OST_MOL ChainHandle : public ChainBase {

public:
  ChainHandle();

  ChainHandle(const impl::ChainImplPtr& impl);
  

  EntityHandle GetEntity() const;

  void Apply(EntityVisitor& visitor);

  
  ResidueHandle GetPrev(const ResidueHandle& rh);
  ResidueHandle GetNext(const ResidueHandle& rh);






  ResidueHandle FindResidue(const ResNum& num) const;

  AtomHandle FindAtom(const ResNum& num, 
                      const String& atom_name) const;
  ResidueHandle GetResidueByIndex(int index) const;
  
  //
  // To count all atoms of the entity the chain belongs to, use 
  // \c EntityHandle::GetAtomCount(). For count of specific residues, use
  // \c ResidueHandle::GetResidueCount().
  int GetAtomCount() const;

  int GetBondCount() const;
  
  int GetResidueCount() const;
  
  
  
  AtomHandleList GetAtomList() const;
  
  ResidueHandleList GetResidueList() const;

  Real GetMass() const;
  
  geom::Vec3 GetCenterOfMass() const;
  
  geom::Vec3 GetCenterOfAtoms() const;
  
  geom::AlignedCuboid GetBounds() const;  
  void AssignSecondaryStructure(SecStructure ss, 
                                const ResNum& start, 
                                const ResNum& end);

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

  EntityView Select(const String& query_string, QueryFlags flags=0) const;

  ChainHandle GetHandle() const;
  bool InSequence() const;
  bool operator==(const ChainHandle& ref) const;
  bool operator!=(const ChainHandle& ref) const;

  void SetInSequence(const int index);
};

}} // ns

#endif // OST_CHAIN_HANDLE_HH

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