StarTreeBuilder.hh

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
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/// @file protocols/nonlocal/StarTreeBuilder.hh
/// @author Christopher Miles (cmiles@uw.edu)

#ifndef INCLUDED_PROTOCOLS_NONLOCAL_STARTREEBUILDER_HH
#define INCLUDED_PROTOCOLS_NONLOCAL_STARTREEBUILDER_HH

// Unit headers
#include <protocols/nonlocal/StarTreeBuilder.fwd.hh>

// C/C++ headers
#include <string>

// Project headers
#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <protocols/loops/Loop.fwd.hh>
#include <protocols/loops/Loops.fwd.hh>

// Package headers
#include <protocols/nonlocal/TreeBuilder.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace nonlocal {

class StarTreeBuilder : public TreeBuilder {
 protected:
  static const std::string PREFIX_INITIAL;
  static const std::string PREFIX_FINAL;

 public:
  StarTreeBuilder();

  /// @brief Constructs a star fold tree by placing a virtual residue at
  /// <chunks> center of mass and adding jumps from it to a stochastically
  /// chosen anchor residue in each chunk. Cutpoints are added on chunk
  /// boundaries.
  ///
  /// Important: chunks must be sorted in increasing order of start position.
  /// The simplest way to achieve this is a call to Loops::sequential_order().
  ///
  /// Additionally, every residue in pose must belong to one and only one chunk.
  void set_up(const protocols::loops::Loops& chunks, core::pose::Pose* pose);

  /// @brief Removes the virtual residue added to <pose> in calls to set_up()
  void tear_down(core::pose::Pose* pose);

 protected:
  /// @brief Stochastically selects an anchor position
  core::Size choose_anchor_position(const protocols::loops::Loop& chunk) const;

  /// @brief When native is available, computes rmsd of jump residues, storing
  /// the results as comments in silent file output. If specified, prefix string
  /// will precede the result in the silent file output.
  void do_compute_jump_rmsd(core::pose::Pose* model, const std::string& prefix = "") const;

 private:
  /// @brief Index of the virtual residue we added to the pose in set_up()
  int virtual_res_;
};

}  // namespace nonlocal
}  // namespace protocols

#endif  // PROTOCOLS_NONLOCAL_STARTREEBUILDER_HH_