ModifyStoredLigandRBConfsMovers.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 .hh file for movers that mess around with additional ligand rigid body conformations
/// stored in the enzdes cacheable observer
/// @brief
/// @author Florian Richter, floric@u.washington.edu, oct 09

#ifndef INCLUDED_protocols_enzdes_ModifyStoredLigandRBConfsMovers_hh
#define INCLUDED_protocols_enzdes_ModifyStoredLigandRBConfsMovers_hh

//unit headers
#include <protocols/enzdes/ModifyStoredLigandRBConfsMovers.fwd.hh>
#include <protocols/moves/Mover.hh>
//#include <protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.fwd.hh>
//#include <core/pose/datacache/CacheableObserver.hh>

//package headers
#include <core/conformation/Residue.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/types.hh>

#include <utility/vector1.hh>



namespace protocols {
namespace enzdes {


/// @pure virtual base class that has some common functionality
class ModifyStoredRBConfs : public protocols::moves::Mover {

public:
  typedef core::Size Size;
  typedef core::Real Real;
  typedef protocols::moves::Mover parent;
  typedef utility::vector1< utility::vector1< core::conformation::ResidueCOP > > RBConfLists;

public:

  ModifyStoredRBConfs( std::string const name );
  ~ModifyStoredRBConfs();

  virtual
  void
  apply( core::pose::Pose & pose ) = 0;

  virtual std::string get_name() const;

  /// @brief helper function to exchange coordinates in a pose
  /// this function doesn't actually exchange the residues,
  /// but sets all the coords of pose.residue( rescoords.seqpos() )
  /// to what is in rescoords and vice versa
  void
  swap_coordinates_in_pose(
    core::pose::Pose & pose,
    core::conformation::Residue & rescoords
  ) const;

  /// @brief calculates the closest orient atom (i.e. atoms used in rotamer placement
  /// msd between every conf and the confs coming before it in the pose or in the vector
  utility::vector1< Real >
  closest_orient_atoms_msd(
    core::pose::Pose const & pose,
    utility::vector1< core::conformation::ResidueCOP > const & confs
  ) const;

protected:

  /// @brief this function is the function that all derived classes
  /// should call to get access to pose stored additional rb confs.
  /// right now it only returns the confs in the proper format,
  /// but in the future some logic might be added as to for which seqpos
  /// to return the stored confs
  RBConfLists
  get_rigid_body_confs( core::pose::Pose const & pose ) const;

  /// @brief same as for above function. all derived classes
  /// should use this function to communicate new/changed rigid
  /// body confs back to the pose/enzdes cacheable observer
  void
  set_rigid_body_confs( RBConfLists rbs, core::pose::Pose & pose ) const;

  /// @brief see comments for set_rigid_body_confs
  void
  set_rigid_body_confs_for_seqpos(
    core::Size seqpos,
    utility::vector1< core::conformation::ResidueCOP > & confs,
    core::pose::Pose & pose
  ) const;

};

/// @brief generates random rbconfs until a total of num_total_rbconfs_
/// are present in the cacheable observer. The diversifier is used to
/// ensure that all newly generated confs are different.
/// note: no scorefunction used
class GenerateStoredRBConfs : public ModifyStoredRBConfs {

public:
  typedef ModifyStoredRBConfs parent;

public:

  GenerateStoredRBConfs(
    Size num_total_rbconfs,
    bool include_metals );

  ~GenerateStoredRBConfs();

  void
  apply( core::pose::Pose & pose );
  virtual std::string get_name() const;

private:

  Size num_total_rbconfs_;
  bool include_metals_;

};

/// @brief for every ligand that has additional stored rb conformations
/// in the enzdes cacheable observer, the one currently in the pose gets
/// exchanged with a random stored one
class ApplyRandomStoredRBConf : public ModifyStoredRBConfs {

public:
  typedef ModifyStoredRBConfs parent;

public:

  ApplyRandomStoredRBConf();
  ~ApplyRandomStoredRBConf();

  void
  apply( core::pose::Pose & pose );
  virtual std::string get_name() const;

};

/// @brief rotamer trials/minimizes each of the ligand conformations stored in the enzdes
/// cacheable observer and overwrites them with the minimized position.
/// if the new, minimized position is too close to one that already exists,
///  a random small perturbation is applied to ensure diversity
/// note: only jump minimization
class MinimizeStoredRBConfs : public ModifyStoredRBConfs {

public:
  typedef ModifyStoredRBConfs parent;

public:

  MinimizeStoredRBConfs( core::scoring::ScoreFunctionCOP sfxn );
  ~MinimizeStoredRBConfs();

  void
  apply( core::pose::Pose & pose );
  virtual std::string get_name() const;

  void
  rb_minimize_all_confs(
    core::pose::Pose const & pose,
    utility::vector1< core::conformation::ResidueCOP > & confs
  ) const;

private:

  core::scoring::ScoreFunctionCOP sfxn_;
  Real min_rms_;

};


/// @brief uses a docking mover to diversiy the stored confs
/// until they're all min_rms_ away from each other
/// note: no scorefunction used here
class DiversifyStoredRBConfs : public ModifyStoredRBConfs {

public:
  typedef ModifyStoredRBConfs parent;

public:

  DiversifyStoredRBConfs(
    Real min_rms );

  ~DiversifyStoredRBConfs();

  void
  apply( core::pose::Pose & pose );
  virtual std::string get_name() const;

  void
  diversify_all_confs(
    core::pose::Pose const & pose,
    utility::vector1< core::conformation::ResidueCOP > & confs
  ) const;

private:
  Real min_rms_;
  Size max_trials_;

};



} // enzdes
} //protocols


#endif