RigidBodyMoveRotSetOps.hh

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// 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.
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/// @file   protocols/toolbox/RotamerSetOperations/RigidBodyMoveRotSetOps.hh
/// @brief  classes for rigid body movement during rotamer packing
/// @author Florian Richter, floric@u.washington.edu, sep 2009

#ifndef INCLUDED_protocols_toolbox_rotamer_set_operations_RigidBodyMoveRotSetOps_hh
#define INCLUDED_protocols_toolbox_rotamer_set_operations_RigidBodyMoveRotSetOps_hh

// Unit Headers
#include <protocols/toolbox/rotamer_set_operations/RigidBodyMoveRotSetOps.fwd.hh>
#include <core/pack/rotamer_set/RotamerSetOperation.hh>

//Project headers
#include <core/conformation/Residue.fwd.hh>
#include <core/graph/Graph.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/rotamer_set/BumpSelector.hh>
#include <core/pack/rotamer_set/RotamerSet.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace toolbox {
namespace rotamer_set_operations {

/// @details base class that handles single residue (usually ligand) rigid
/// body movements in the packer. subclass generates a list of alternative rigid body
/// placements. when the alter_rotamer_set function is called, this class
/// superimposes all rotamers in the initial RotamerSet onto every alternative
/// rigid body conformation in the member data list. these superimposed
/// conformations then get added to the rotamer set.
/// this class also handles the increased packer radius necessitated by the
/// rigid body movements. when the increase_packer_residue_radius function
/// is called, the biggest distance between the residue in the initial pose
/// and any of the alternate conformations is returned.
///
/// Generating the alternative rigid body positions:
///
///   Subclasses must implement get_rigid_body_confs.
///
///   Subclasses may implement increase_packer_residue_radius to 
/// optimize this calculation. Default implementation calls get_rigid_body_confs
/// and calculates the maximum nbr_atom delta.
///
class RigidBodyMoveBaseRSO : public core::pack::rotamer_set::RotamerSetOperation
{
  typedef core::pack::rotamer_set::RotamerSetOperation parent;

  protected:
  RigidBodyMoveBaseRSO() :
    parent()
  {}

  RigidBodyMoveBaseRSO(const RigidBodyMoveBaseRSO& other) :
    parent(other),
    bump_selector_(other.bump_selector_)
  {}


  public:
  /// @brief Adds additional rotamers at each rb conf.
  ///
  /// @details
  /// fairly simple: iterate over the rotamers in the rotamer_set, superimpose
  /// each of them onto all the internally stored rigid body confs, and then
  /// add the newly generated rotamers to the rotamer_set
  ///
  /// Recalculates chi-angle expansion via call to RotamerSet::extra_chi_samples
  /// and then generate candidate rotamers from each rb conf via
  /// SingleResidueRotamerLibrary::fill_rotamer_vector if rotamer library is
  /// available for the residue type, else just adds the alternate confs.
  ///
  /// Does not have full safety checks to make sure all the rotamers in the set are
  /// of the same residue type as the internally stored ones, i.e. that no user sets this
  /// position to designing in the task
  virtual
  void
  alter_rotamer_set(
    core::pose::Pose const & pose,
    core::scoring::ScoreFunction const & sfxn,
    core::pack::task::PackerTask const & ptask,
    core::graph::GraphCOP packer_neighbor_graph,
    core::pack::rotamer_set::RotamerSet & rotamer_set
  );

  /// @brief returns the largest possible change in nbr atoms location
  /// 
  /// Default implementation calls determine_larget_nbr_atom_distance with
  /// results of get_rigid_body_confs. Override this function if calculation
  /// can be optimized without call call to get_rigid_body_confs.
  using core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius;
  virtual
  core::Real
  increase_packer_residue_radius(
    core::pose::Pose const & pose,
    core::pack::task::PackerTaskCOP, //the_task
    core::Size residue_index
  );

  /// @brief returns candidate alternate RB conformations
  virtual
  utility::vector1< core::conformation::ResidueCOP >
  get_rigid_body_confs(
    core::pose::Pose const & pose,
    core::pack::task::PackerTask const & ptask,
    core::Size residue_index) = 0;

  /// @brief returns the largest observed distance between the nbr atom
  /// in the target res and the nbr atom in any of the candidate rb confs
  static
  core::Real
  determine_largest_nbr_atom_distance(
    core::conformation::Residue const & target_res,
    utility::vector1< core::conformation::ResidueCOP > alternate_confs);

  private:
    core::pack::rotamer_set::BumpSelector bump_selector_;
};

/// @details
/// Basic implementation of alternate rb conf set operation. 
/// The alternative positions are set externally before packing.
class RigidBodyMoveRSO : public RigidBodyMoveBaseRSO
{
public:
  typedef RigidBodyMoveBaseRSO parent;

  // 'seqpos' could be removed, it can be derived from the input
  // rotamer set. It is left in as a sanity check for this class.
  RigidBodyMoveRSO( core::Size seqpos );
  RigidBodyMoveRSO( RigidBodyMoveRSO const & other );

  virtual
  core::pack::rotamer_set::RotamerSetOperationOP
  clone() const;

  virtual
  utility::vector1< core::conformation::ResidueCOP >
  get_rigid_body_confs(
    core::pose::Pose const & pose,
    core::pack::task::PackerTask const & ptask,
    core::Size residue_index);

  void
  set_rigid_body_confs(
    utility::vector1< core::conformation::ResidueCOP > const & rigid_body_confs
  );

private:

  core::Size seqpos_;
  utility::vector1< core::conformation::ResidueCOP > rigid_body_confs_;
};

} //namespace protocols
} //namespace toolbox
} //namespace rotamer_set_operations

#endif