modeller.hh

#ifndef OST_MMMODELLER_HH
#define OST_MMMODELLER_HH


#include <vector>
#include <set>

#include <ost/platform.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/mol/entity_handle.hh>
#include <ost/mol/residue_handle.hh>
#include <ost/mol/atom_handle.hh>
#include <ost/geom/vec3.hh>
#include <ost/geom/composite.hh>
#include <ost/geom/transform.hh>
#include <ost/mol/xcs_editor.hh>
#include <ost/mol/bond_handle.hh>
#include <ost/message.hh>
//#include <ost/mol/mm/gromacs_data.hh>
#include <ost/mol/bounding_box.hh>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mm/forcefield.hh>
#include <ost/mol/mm/mm_settings.hh>
#include <ost/mol/mm/index.hh>
#include <ost/mol/mm/topology.hh>
#include <ost/conop/heuristic.hh>
#include <ost/mol/spatial_organizer.hh>


namespace ost { namespace mol{ namespace mm{

class Modeller{
public:

  static void GenerateDisulfidBonds(ost::mol::EntityHandle& handle);

  static void GenerateCYSHEMEBonds(ost::mol::EntityHandle& handle);

  static void GenerateHISHEMEBonds(ost::mol::EntityHandle& handle);

  static void GenerateMETHEMEBonds(ost::mol::EntityHandle& handle);

  //may sound pretty stupid...
  //But this is necessary if we want to compare our energies with
  //the energies calculated by gromacs. When ost writes and entity
  //down to disk, it uses 3 digits precision.
  //If we feed this into gromacs, it also produces a topology
  //with three digits precision. The problem is, that gromacs
  //uses nm, therefore the precision gets lowered tenfold.
  //To take care of that it is necessary to lower our precision...
  static void LowerPrecision(ost::mol::EntityHandle& handle);

  static void AssignPDBNaming(ost::mol::EntityHandle& handle);

  static void AssignGromacsNaming(ost::mol::EntityHandle& handle);
};


}}}

#endif