InputStreamWithResidueInfo.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 InputStreamWithResidueInfo.hh
/// @brief
/// @detailed
///
/// @author Rhiju Das


#ifndef INCLUDED_protocols_swa_InputStreamWithResidueInfo_HH
#define INCLUDED_protocols_swa_InputStreamWithResidueInfo_HH

#include <protocols/swa/InputStreamWithResidueInfo.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/options/StringVectorOption.fwd.hh>

#include <map>

namespace protocols {
namespace swa {

  void
  initialize_input_streams(   utility::vector1< protocols::swa::InputStreamWithResidueInfoOP > & input_streams );

  void
  initialize_input_streams_with_residue_info( utility::vector1< InputStreamWithResidueInfoOP > & input_streams_with_residue_info,
                                              utility::vector1< std::string > const & pdb_tags,
                                              utility::vector1< std::string > const & silent_files_in,
                                              utility::vector1< core::Size > const & input_res,
                                              utility::vector1< core::Size > const & input_res2
                                              );

  core::import_pose::pose_stream::PoseInputStreamOP
  setup_pose_input_stream(
                          utility::options::StringVectorOption const & option_s1,
                          utility::options::StringVectorOption const & option_silent1,
                          utility::options::StringVectorOption const & option_tags1 );


  //////////////////////////////////////////////////////////////////////////////////////////////////
  //////////////////////////////////////////////////////////////////////////////////////////////////
  class InputStreamWithResidueInfo:public utility::pointer::ReferenceCount {
  public:

    InputStreamWithResidueInfo( core::import_pose::pose_stream::PoseInputStreamOP pose_input_stream,
                                utility::vector1< Size > const & input_res,
                                utility::vector1< Size > const & slice_res );

    InputStreamWithResidueInfo( core::import_pose::pose_stream::PoseInputStreamOP pose_input_stream,
                                utility::vector1< Size > const & input_res);

    virtual ~InputStreamWithResidueInfo();

    core::import_pose::pose_stream::PoseInputStreamOP & pose_input_stream();
    utility::vector1< Size > const & input_res();
    utility::vector1< Size > const & slice_res();
    std::map< Size, Size > & full_to_sub();

    void set_slice_res(   utility::vector1< Size > const & slice_res );
    void set_full_to_sub( std::map< Size, Size > const & full_to_sub );
    void set_rsd_set( core::chemical::ResidueTypeSetCAP & rsd_set );

    void reset();

    bool has_another_pose() const;

    void copy_next_pose_segment( core::pose::Pose & pose );

    void copy_next_pose_segment( core::pose::Pose & pose,
                                 core::pose::Pose & import_pose,
                                 bool const check_sequence_matches,
                                 bool const align_pose_to_import_pose = false );

    void set_backbone_only( bool const setting );

  private:

    void
    initialize_defaults();

    void cleanup_pose( core::pose::Pose & import_pose ) const;

    void check_sequence( core::pose::Pose const & pose, core::pose::Pose const & import_pose );


  private:

    core::import_pose::pose_stream::PoseInputStreamOP pose_input_stream_;
    utility::vector1< Size > input_res_;
    utility::vector1< Size > slice_res_;
    std::map< Size, Size > full_to_sub_;
    core::chemical::ResidueTypeSetCAP rsd_set_;
    bool backbone_only_;
  };


} //swa
} // protocols

#endif