PDBWriter.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   protocols/match/output/PDBWriter.hh
/// @brief
/// @author Florian Richter (floric@u.washington.edu) june 2009

#ifndef INCLUDED_protocols_match_output_PDBWriter_hh
#define INCLUDED_protocols_match_output_PDBWriter_hh

// Unit headers
#include <protocols/match/output/PDBWriter.fwd.hh>

// Package Headers
#include <core/conformation/Residue.fwd.hh>

// AUTO-REMOVED #include <protocols/match/Hit.hh> // REQUIRED FOR WINDOWS
#include <protocols/match/Hit.fwd.hh>
#include <protocols/match/MatcherTask.fwd.hh>
// AUTO-REMOVED #include <protocols/match/downstream/DownstreamBuilder.hh>
#include <protocols/match/output/MatchGrouper.fwd.hh>
#include <protocols/match/output/OutputWriter.hh>
#include <protocols/match/output/UpstreamHitCacher.fwd.hh>
// AUTO-REMOVED #include <protocols/match/output/WriteUpstreamCoordinateKineamge.fwd.hh>

// Utility headers
#include <utility/pointer/ReferenceCount.hh>

// C++ headers
#include <map>
#include <set>

#include <core/pose/Pose.fwd.hh>
#include <protocols/match/downstream/DownstreamBuilder.fwd.hh>
#include <utility/vector1.hh>
#include <iterator>


namespace protocols {
namespace match {
namespace output {

class PDBWriter : public OutputWriter
{

public:
  typedef std::pair< core::Size, core::Size > SizePair;

  typedef OutputWriter Parent;

public:

  PDBWriter();

  virtual ~PDBWriter();

  virtual
  void
  prepare_for_output_writing();

  virtual
  void
  record_match( match const & m );

  virtual
  void
  record_match( match_dspos1 const & m );

  //core::pose::PoseCOP
  //create_output_pose_from_dspos1_match(
  //  match_dspos1 const & m );

  void
  set_coordinate_cacher( UpstreamHitCacherOP );

  void
  set_prefix( std::string const & prefix );

  void
  initialize_from_matcher_task(
      MatcherTaskCOP mtask
  );

  void
  set_downstream_builder(
    Size geomcst_id,
    downstream::DownstreamBuilderCOP dsbuilder
  );

  void
  assemble_remark_lines(
    core::pose::Pose & outpose,
    utility::vector1< core::conformation::ResidueCOP > const & upstream_matchres,
    std::map< core::Size, core::Size > const & redundant_upstream_res,
    utility::vector1< core::Size > const & ex_geom_ids_for_upstream_res
  ) const;

  core::pose::PoseCOP
  create_output_upstream_pose(
    utility::vector1< core::conformation::ResidueCOP > const & upstream_matchres,
    std::map< core::Size, core::Size > const & redundant_upstream_res,
    utility::vector1< core::Size > const & ex_geom_ids_for_upstream_res
  );

  std::string
  signature_string(
    utility::vector1< core::conformation::ResidueCOP > const & upstream_matchres
  ) const;

  core::Size
  num_geom_cst() const;

  std::string
  scaf_name() const;

  std::string
  cstfile_name() const;

  std::string
  prefix() const;

protected:

  UpstreamHitCacherOP
  coordinate_cacher();

  utility::vector1< downstream::DownstreamBuilderCOP > const &
  dsbuilders();

  std::string
  assemble_outtag(
    utility::vector1< core::conformation::ResidueCOP > const & upstream_matchres
  );


private:

  UpstreamHitCacherOP coordinate_cacher_;

  // whether to write the whole pose or only the matched residues
  bool write_matchres_only_;

  std::string scaf_name_, cstfile_name_, prefix_;

  core::Size num_written_;
  core::Size num_geom_cst_;

  //needed to build the downstream target for pdb writing
  utility::vector1< downstream::DownstreamBuilderCOP > dsbuilders_;

  //
  core::pose::PoseCOP orig_upstream_pose_;
  core::pose::PoseCOP downstream_pose_from_task_;

  //map to keep track of the output names
  std::map< std::string, SizePair > signature_map_;

  //which of the cst res to write separate matches for
  utility::vector1< bool > output_dsgeom_for_geomcst_;

  //info about what the targets are for upstream only matching
  std::map< core::Size, core::Size > upstream_only_geom_cst_;

};

/// @brief an output writer that uses a grouper to group matches and
/// then writes out one pdb file per group, with the different hits
/// from the group in different MODEL sections
class CloudPDBWriter : public PDBWriter
{

public:
  typedef PDBWriter parent;
  typedef utility::vector1< std::set< upstream_hit > > UpstreamHitSets;
  typedef utility::vector1< std::set< downstream_hit > > DownstreamHitSets;

  CloudPDBWriter( MatchGrouperOP grouper );

  virtual ~CloudPDBWriter();

  virtual
  void
  prepare_for_output_writing();

  void
  end_output_writing();

  /// @brief no writing in this function, only saving the hits according
  /// to what group they belong to
  virtual
  void
  record_match( match const & m );

  virtual
  void
  record_match( match_dspos1 const & m );


  /// @brief this is where the actual writing happens
  void
  write_match_groups();

//accessors
public:

  utility::vector1< UpstreamHitSets > const & match_groups_ushits() const;
  utility::vector1< DownstreamHitSets > const &  match_groups_dshits() const;
  utility::vector1< match_dspos1 > const & representative_group_matches() const;

  utility::vector1< std::set< downstream_hit >::const_iterator > const & ds_hitset_its() const;
  utility::vector1< std::set< downstream_hit >::const_iterator > const & ds_hitset_end_its() const;
protected:

  void
  setup_hitset_iterators_for_group(
    core::Size const group );

  void
  clear_match_data();

private:

  MatchGrouperOP grouper_;

  utility::vector1< UpstreamHitSets > match_groups_ushits_;
  utility::vector1< DownstreamHitSets > match_groups_dshits_;
  utility::vector1< std::string > unique_match_names_;
  utility::vector1< match_dspos1 > representative_group_matches_;

  utility::vector1< std::set< upstream_hit >::const_iterator > us_hitset_its_;
  utility::vector1< std::set< upstream_hit >::const_iterator > us_hitset_end_its_;
  utility::vector1< std::set< downstream_hit >::const_iterator > ds_hitset_its_;
  utility::vector1< std::set< downstream_hit >::const_iterator > ds_hitset_end_its_;

};

/// @brief helper class for the MatcherMover that will put a match
/// into a supplied pose
class PoseMatchOutputWriter : public CloudPDBWriter {

public:

  typedef CloudPDBWriter parent;

  PoseMatchOutputWriter( MatchGrouperOP grouper );

  ~PoseMatchOutputWriter();

  void
  insert_match_into_pose(
    core::pose::Pose & pose,
    core::Size match_group
  );

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

  void
  end_output_writing();


};


}
}
}

#endif