import_pose_options.hh

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// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
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/// @file   core/import_pose/import_pose_options.hh
///
/// @brief
/// @author Brian D. Weitzner brian.weitzner@gmail.com

#ifndef INCLUDED_core_import_pose_import_pose_options_HH
#define INCLUDED_core_import_pose_import_pose_options_HH


// Unit headers
#include <core/import_pose/import_pose_options.fwd.hh>
#include <core/io/pdb/pdb_dynamic_reader_options.hh>

// C++ headers
#include <string>


namespace core {
namespace import_pose {

/// @brief This class contains all of the data which is used in
/// the process of reading a PDB into a Pose.  There is actually
/// a substantial amount of data!
class ImportPoseOptions : public io::pdb::PDB_DReaderOptions
{
public:
  ImportPoseOptions();
  
  virtual ~ImportPoseOptions();
  
  virtual
  void parse_my_tag( utility::tag::TagPtr tag );
  
  virtual
  std::string type() const;
  
  // accessors
  bool centroid() const;
  bool fold_tree_io() const;
  bool no_optH() const;
  bool pack_missing_sidechains() const;
  bool read_fold_tree() const;
  bool rna() const;
  bool skip_set_reasonable_fold_tree() const;
  std::string const & residue_type_set() const;

  // mutators
  void set_centroid( bool centroid );
  void set_fold_tree_io( bool fold_tree_io );
  void set_no_optH( bool no_optH );
  void set_pack_missing_sidechains( bool pack_missing_sidechains );
  void set_read_fold_tree( bool read_fold_tree );
  void set_rna( bool rna );
  void set_skip_set_reasonable_fold_tree_( bool skip_set_reasonable_fold_tree );
  void set_residue_type_set( std::string const & residue_type_set );

private:
  /// @brief Assigns user specified values to primitive members using command line options
  void init_from_options();

private:
  bool centroid_;
  bool fold_tree_io_;
  bool no_optH_;
  bool pack_missing_sidechains_;
  bool read_fold_tree_;
  bool rna_;
  bool skip_set_reasonable_fold_tree_;
  
  std::string residue_type_set_;
  
};

} // namespace import_pose
} // namespace core

#endif // INCLUDED_core_import_pose_import_pose_options_HH