MinimizeBackbone.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   core/pack/task/ResfileReader.hh
/// @brief  header of classes for resfile options
/// @author Gordon Lemmon

#ifndef INCLUDED_protocols_ligand_docking_MinimizeBackbone_hh
#define INCLUDED_protocols_ligand_docking_MinimizeBackbone_hh

// Unit Headers
#include <protocols/ligand_docking/MinimizeBackbone.fwd.hh>
#include <protocols/ligand_docking/ligand_options/Interface.fwd.hh>
#include <protocols/ligand_docking/InterfaceBuilder.fwd.hh>

// Package Headers
#include <core/kinematics/FoldTree.fwd.hh> 
#include <core/kinematics/Edge.fwd.hh>
// AUTO-REMOVED #include <core/id/AtomID.hh>

//// Project Headers
#include <protocols/moves/Mover.hh>

//// Scripter Headers
#include <utility/tag/Tag.fwd.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>

#include <core/id/AtomID.fwd.hh>
#include <protocols/loops/Loop.fwd.hh>
#include <utility/vector1.hh>

///////////////////////////////////////////////////////////////////////

namespace protocols {
namespace ligand_docking {

///@brief
class MinimizeBackbone : public protocols::moves::Mover
{
public:
  MinimizeBackbone();
  MinimizeBackbone(InterfaceBuilderOP interface_builder);
  virtual ~MinimizeBackbone();
  MinimizeBackbone(MinimizeBackbone const & that);

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

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

  void parse_my_tag(
    utility::tag::TagPtr const tag,
    protocols::moves::DataMap &,
    protocols::filters::Filters_map const &,
    protocols::moves::Movers_map const &,
    core::pose::Pose const &
  );

private:
  // map of ligand chains to minimize backbone around and how much minimization around each chain
  // Real is the Size of one standard deviation.  For restraints placed on C-alphas
  InterfaceBuilderOP interface_builder_;

  void reorder_foldtree_around_mobile_regions(
    ligand_options::Interface const & interface,
    core::pose::Pose & pose
  );

  core::kinematics::FoldTreeOP
  create_fold_tree_with_ligand_jumps_from_attach_pts(
    core::kinematics::FoldTreeCAP,
    ligand_options::Interface const & interface,
    core::pose::Pose & pose
  )const;

  core::kinematics::FoldTreeOP
  create_fold_tree_with_cutpoints(
    core::kinematics::FoldTreeCOP f,
    ligand_options::Interface const & interface,
    core::pose::Pose & pose
  );

  utility::vector1< protocols::loops::Loop >
  add_cut_points(
    core::kinematics::Edge const & edge,
    ligand_options::Interface const & interface,
    core::pose::Pose & pose
  );

  std::map<core::Size, core::Size> find_attach_pts(
    const ligand_options::Interface interface,
    core::pose::Pose const & pose
  ) const;

  void
  restrain_protein_Calphas(
    ligand_options::Interface const & interface,
    core::pose::Pose & pose
  );
  void restrain_protein_Calpha(
      ligand_options::Interface const & interface,
      core::pose::Pose & pose,
      core::Size residue_id,
      core::id::AtomID const & fixed_pt
  );
};

void restrict_to_protein_residues(
  ligand_options::Interface & interface,
  core::pose::Pose const & pose
);

void reorder_with_first_non_mobile_as_root(
  core::kinematics::FoldTreeOP f,
  const ligand_options::Interface & interface,
  core::pose::Pose & pose
);

core::Size find_attach_pt(
  core::Size const jump_id,
  ligand_options::Interface const interface,
  core::pose::Pose const & pose
);

core::Size
find_peptide_attach_pt(
  int const & start,
  int const & stop,
  std::map<core::Size, core::Size > const jump_to_attach
);


} //namespace ligand_docking
} //namespace protocols

#endif