editor_base.hh

Go to the documentation of this file.

//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 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_EDITOR_BASE_HS
#define OST_EDITOR_BASE_HS
/*
  Author: Marco Biasini
 */
 
#include <ost/mol/module_config.hh>
 
#include <ost/geom/geom.hh>
 
#include "entity_handle.hh"
#include "residue_prop.hh"
#include "editor_type_fw.hh"
 
namespace ost { namespace mol {
 
class DLLEXPORT_OST_MOL EditorBase {
public:
  ChainHandle InsertChain(const String& chain_name);
 
  ChainHandle InsertChain(const String& chain_name, ChainHandle chain, bool deep=false);
 
  ResidueHandle AppendResidue(ChainHandle chain, const ResidueKey& k);
  
  ResidueHandle AppendResidue(ChainHandle chain, const ResidueKey& k, 
                              const ResNum& num); 
 
 
  ResidueHandle AppendResidue(ChainHandle chain, ResidueHandle residue, bool deep=false);
 
  ResidueHandle InsertResidueBefore(ChainHandle chain, int index, 
                                    const ResNum& num,
                                    const ResidueKey& k);
 
  ResidueHandle InsertResidueAfter(ChainHandle chain, int index,
                                   const ResNum& num,
                                   const ResidueKey& k);
  
 
  AtomHandle InsertAtom(ResidueHandle residue, const String& name,
                        const geom::Vec3& pos, const String& ele="",
                        Real occupancy=1.0, Real b_factor=0.0, 
                        bool is_hetatm=false);
 
 
  AtomHandle InsertAtom(ResidueHandle residue, AtomHandle atom);
 
  AtomHandle InsertAltAtom(ResidueHandle residue, const String& name, 
                           const String& alt_group, const geom::Vec3& pos,
                           const String& ele="", Real occ=1.0,
                           Real b_factor=0.0);
 
 
  AtomHandle InsertAltAtom(ResidueHandle residue, AtomHandle atom,
                           const String& alt_group);
 
 
  void AddAltAtomPos(const String& group, const AtomHandle& atom, 
                     const geom::Vec3& position, Real occ=1.0,
                     Real b_factor=0.0);
  //\}
  
  BondHandle Connect(const AtomHandle& first, const AtomHandle& second);
  BondHandle Connect(const AtomHandle& first, const AtomHandle& second,
                     unsigned char bond_order);
  BondHandle Connect(const AtomHandle& first, const AtomHandle& second,
                     Real len, Real theta, Real phi);
  BondHandle Connect(const AtomHandle& first, const AtomHandle& second,
                     Real len, Real theta, Real phi,
                     unsigned char bond_order);
 
  void RenameResidue(ResidueHandle res, const String& new_name);
  
  void SetResidueNumber(ResidueHandle res, const ResNum& num);
   
  void RenameChain(ChainHandle chain, const String& new_name);
 
  void SetChainType(ChainHandle chain, const ChainType type);
 
  void SetChainDescription(ChainHandle chain, const String desc);
 
  void DeleteAllAtoms(ResidueHandle res);
  
  void DeleteAtom(const AtomHandle& atom);
  void DeleteAtoms(const AtomHandleList& atoms);
 
  void DeleteBond(const BondHandle& bond);
 
  void DeleteBonds(const BondHandleList& bonds);
  
  TorsionHandle AddTorsion(const String& name, const AtomHandle& a1,
                           const AtomHandle& a2, const AtomHandle& a3,
                           const AtomHandle& a4);  
  void DeleteChain(const ChainHandle& chain);
 
  void DeleteResidue(const ResidueHandle& residue_handle);
 
  void ReorderResidues(const ChainHandle& chain);
 
  void ReorderAllResidues();
 
  void RenumberAllResidues(int start, bool keep_spacing);
 
 
  void RenumberChain(ChainHandle chain, const ResNumList& new_numbers);
 
  void RenumberChain(const ChainHandle& chain, int start, bool keep_spacing);
    
  EditMode GetMode() const {return mode_;}
  
  EntityHandle GetEntity() const {return ent_;}
 
  void RenameAtom(AtomHandle atom, const String& new_name);
 
  void Prune(); 
 
protected:
  EditorBase(const EntityHandle& ent, EditMode mode);
  void UpdateTrace();
  EntityHandle     ent_;
  EditMode         mode_;
};
 
}} //ns
 
#endif