JointSequenceOperation.hh

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (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
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file protocols/toolbox/task_operations/JointSequenceOperation.hh
/// @brief set every position to be designable to residues observed in a set of structures
/// @author Rocco Moretti, rmoretti@u.washington.edu

#ifndef INCLUDED_protocols_toolbox_task_operations_JointSequenceOperation_hh
#define INCLUDED_protocols_toolbox_task_operations_JointSequenceOperation_hh

// unit headers
#include <protocols/toolbox/task_operations/JointSequenceOperation.fwd.hh>

//package headers
#include <core/pack/task/operation/TaskOperation.hh>
// AUTO-REMOVED #include <core/pack/rotamer_set/UnboundRotamersOperation.hh>

//project headers
// AUTO-REMOVED #include <core/chemical/AA.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/sequence/Sequence.fwd.hh>
#include <core/types.hh>
// AUTO-REMOVED #include <protocols/ddg/ddGData.fwd.hh>

// Utility Headers
#include <utility/tag/Tag.fwd.hh>
#include <utility/vector1.hh>

// AUTO-REMOVED #include <iostream>

#include <core/pack/rotamer_set/UnboundRotamersOperation.fwd.hh>


using namespace core::pack::task;

namespace protocols{
namespace toolbox{
namespace task_operations{

class JointSequenceOperation : public core::pack::task::operation::TaskOperation {
public:

  typedef std::string String;
  typedef core::Real Real;
  typedef core::pose::Pose Pose;
  typedef core::pack::task::PackerTask PackerTask;
  typedef core::pack::task::operation::TaskOperation TaskOperation;
  typedef core::pack::task::operation::TaskOperationOP TaskOperationOP;
  typedef TaskOperation parent;
  typedef utility::tag::TagPtr TagPtr;

public:

  /// @brief default constructor
  JointSequenceOperation();

  /// @brief destructor
   ~JointSequenceOperation();

  /// @brief make clone
  virtual TaskOperationOP clone() const;

public:

  void parse_tag( TagPtr tag );
  void parse_def( utility::lua::LuaObject const & def );

  /// @brief apply
  virtual void apply( Pose const & pose, PackerTask & task ) const;

  /// @brief Add the sequence from the given filename to the set of allowed aas.
  void add_pdb( std::string filename );

  /// @brief Add the sequence from the given pose to the set of allowed aas.
  void add_pose( Pose const & pose );

  /// @brief Add the sequence from the given filename to the set of allowed aas
  /// and add the rotamers to the set of possible rotamers
  void add_native_pdb( std::string filename );

  /// @brief Add the sequence from the given pose to the set of allowed aas
  /// and add the rotamers to the set of possible rotamers
  void add_native_pose( core::pose::PoseCOP posecop );

  /// @brief Should the current pose (pose supplied to apply) be used in addition to the other ones?
  void use_current_pose( bool ucp );

  /// @brief Should the rotamers for the native poses be used?
  void use_natro( bool unr );

  /// @brief Return which chain to operate on with 0 meaning all
  void set_chain(core::Size chain);

  /// @brief Add the sequence from the given fasta filename to the set of allowed aas
  void add_native_fasta( std::string fasta_file );

private:

  bool use_current_pose_;
  bool use_natro_; // set only with use_natro(), bookkeeping of ubr_
  bool use_fasta_;                                                                                                                 
  core::pack::rotamer_set::UnboundRotamersOperationOP ubr_;
  std::vector<core::sequence::SequenceOP> sequences_;
  /// @brief Which chain to operate on
  core::Size chain_;
};


} // TaskOperations
} // toolbox
} // protocols
#endif