MotifDnaPacker.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 MotifDnaPacker.hh
/// @author sthyme
/// @brief
/// @details

#ifndef INCLUDED_protocols_motifs_MotifDnaPacker_hh
#define INCLUDED_protocols_motifs_MotifDnaPacker_hh

// Unit Headers
#include <protocols/motifs/MotifDnaPacker.fwd.hh>

// Project Headers
#include <core/pack/rotamer_set/RotamerSet.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/dna/DnaInterfacePacker.fwd.hh>
#include <protocols/dna/DnaDesignDef.fwd.hh>
#include <protocols/dna/PDBOutput.fwd.hh>
#include <protocols/motifs/MotifSearch.fwd.hh>

#include <list>
#include <map>
#include <set>

#include <utility/vector1.hh>

namespace protocols {
namespace motifs {

class MotifDnaPacker : public protocols::moves::Mover {

public:
  MotifDnaPacker();

  MotifDnaPacker(
    core::scoring::ScoreFunctionOP,
    bool minimize = false,
    std::string filename_root = "dnapacker"
  );

  virtual ~MotifDnaPacker(); // important for properly "releasing" owning pointer data

  virtual protocols::moves::MoverOP fresh_instance() const;
  virtual protocols::moves::MoverOP clone() const;
  virtual std::string get_name() const;

  virtual void apply( core::pose::Pose & );

  //void minimize_dna( core::pose::Pose & );

private:
  void init_standard( core::pose::Pose & );
  void init_options();

  void
  run_motifs(
    core::pose::Pose & pose,
    utility::vector1< core::Size > & design_positions,
    std::set< core::Size > & src_pos,
    std::map< core::Size, core::pack::rotamer_set::Rotamers > & rotamer_map,
    std::map< core::Size, std::set< std::string > > & types_map,
    std::list< std::string > & info_lines,
    core::pack::task::TaskFactoryOP taskfactory
  );

  // aromatic_motifs and expand_motifs could likely be combined at some point
  // if an input type list was added that defaults to all 20 amino acids
  void
  expand_motifs(
    core::pose::Pose & pose,
    utility::vector1< core::Size > & design_positions,
    std::set< core::Size > & src_pos,
    std::map< core::Size, core::pack::rotamer_set::Rotamers > & rotamer_map,
    std::map< core::Size, std::set< std::string > > & types_map,
    std::list< std::string > & info_lines,
    core::pack::task::TaskFactoryOP taskfactory
  );

  void
  aromatic_motifs(
    core::pose::Pose & pose,
    utility::vector1< core::Size > & design_positions,
    std::set< core::Size > & src_pos,
    std::map< core::Size, core::pack::rotamer_set::Rotamers > & rotamer_map,
    std::map< core::Size, std::set< std::string > > & types_map,
    std::list< std::string > & info_lines,
    core::pack::task::TaskFactoryOP taskfactory
  );

private:
  protocols::dna::DnaInterfacePackerOP dna_packer_;
  protocols::motifs::MotifSearchOP motif_search_;
  core::scoring::ScoreFunctionOP scorefxn_;
  protocols::dna::PDBOutputOP pdboutput_;
  core::pose::PoseCOP starting_pose_;
  protocols::dna::DnaDesignDefOPs targeted_dna_;

  // user defined options
  bool run_motifs_;
  bool expand_motifs_;
  bool aromatic_motifs_;
  bool minimize_dna_;
  core::Real special_rotweight_;
  core::Real num_repacks_;
  bool flex_dna_sugar_;
  std::string filename_root_;
  bool dna_design_;

};

} // namespace motifs
} // namespace protocols

#endif