EnzdesMovers.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 src/protocols/enzdes/EnzdesMovers.hh
/// @brief a collection of movers that are used at different stages in enzyme design
/// @author Sinisa Bjelic, Florian Richter, floric@u.washington.edu


#ifndef INCLUDED_protocols_enzdes_EnzdesMovers_hh
#define INCLUDED_protocols_enzdes_EnzdesMovers_hh

#include <protocols/enzdes/EnzdesMovers.fwd.hh>
// AUTO-REMOVED #include <protocols/enzdes/EnzdesBaseProtocol.fwd.hh>

// Unit headers
#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/moves/DataMap.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>

// Package headers
#include <core/scoring/constraints/AtomPairConstraint.fwd.hh>
// AUTO-REMOVED #include <core/scoring/constraints/Func.fwd.hh>
#include <core/scoring/constraints/MultiConstraint.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>

// Project headers
// AUTO-REMOVED #include <core/conformation/Residue.fwd.hh>
// AUTO-REMOVED #include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/io/silent/SilentEnergy.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
// AUTO-REMOVED #include <core/scoring/constraints/ConstraintSet.hh>

// Utility Headers
#include <utility/pointer/ReferenceCount.hh>
#include <utility/tag/Tag.fwd.hh>
// AUTO-REMOVED #include <numeric/xyzVector.io.hh>

#include <utility/vector1.hh>


//Utility Headers

// C++ Headers

namespace protocols {
namespace enzdes {

class EnzdesConstraintReporter : public utility::pointer::ReferenceCount
{
public:
  EnzdesConstraintReporter();
  virtual ~EnzdesConstraintReporter();

  EnzdesConstraintReporter( EnzdesConstraintReporter const & );

  /// @brief Recurse through all the constraints in the pose to the ligand,
  /// through all the constraint-container constraints (e.g. Ambiguous constraints
  /// and multi-constraints) to find all the atoms that participate in various constraints
  /// to ligand atoms in the input Pose.
  void
  find_constraints_to_ligand(
    core::pose::Pose const &pose
  );

  /// @brief Read access to the set of atoms that participate in distance constraints
  /// to ligand atoms.
  utility::vector1< core::Size > const & constrained_lig_atoms() const {
    return constrained_lig_atoms_;
  }


  utility::vector1< core::id::AtomID > const & constrained_nonligand_atoms() const {
    return constrained_nonligand_atoms_;
  }

  /// @brief Set the (one) ligand residue index
  void ligand_resno(core::Size res_no) { ligand_seqpos_ = res_no; }

  /// @brief Get the (one) ligand residue index
  core::Size ligand_resno() const { return ligand_seqpos_; }

protected:

  void
  add_constrained_atoms_from_multiconstraint(
    core::scoring::constraints::MultiConstraintCOP real_multi_constraint
  );

  void
  add_constrained_atoms_from_atom_pair_constraint(
    core::scoring::constraints::AtomPairConstraintCOP atom_pair_constraint
  );

  void
  add_constrained_lig_atom(
    core::Size atom_no
  );

  void
  add_constrained_nonligand_atom(
    core::id::AtomID const & atid
  );


private:
  utility::vector1< core::Size   > constrained_lig_atoms_;
  utility::vector1< core::id::AtomID > constrained_nonligand_atoms_;
  core::Size ligand_seqpos_; //Ligand's sequence position


};

class PredesignPerturbMover : public protocols::rigid::RigidBodyPerturbMover
{

public:
  //Deafault constructor
  PredesignPerturbMover();

  //Deafault constructor
  ~PredesignPerturbMover();

  void
  set_docking_pose(
    core::pose::Pose &pose,
    core::pack::task::PackerTaskCOP task );

  void
  reinstate_pose(
    core::pose::Pose &pose,
    core::pose::Pose const &old_Pose );

  //void
  //add_constrained_lig_atoms_from_multiconstraint(
  //  core::scoring::constraints::MultiConstraintCOP real_multi_constraint );

  //void
  //add_constrained_lig_atom(
  //  core::Size atom_no );

  void
  find_constraints_to_ligand(
    core::pose::Pose const &pose );

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

  virtual std::string get_name() const;

  void
  set_ligand(core::Size res_no);

  /// @brief Allow an outside interpretter to the set of atoms for which there are AtomPair constraints to
  /// the ligand.
  utility::vector1< core::Size > const &
  get_constrained_lig_atoms() const
  {
    return constraint_reporter_.constrained_lig_atoms();
  }

  core::Vector
  find_rotation_center( core::pose::Pose const &pose );

  core::Vector
  find_geometric_center_for_constrained_lig_atoms(
    core::pose::Pose const &pose );

//parser functions

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

  protocols::moves::MoverOP clone() const;

  protocols::moves::MoverOP fresh_instance() const;

private:
  EnzdesConstraintReporter constraint_reporter_;
  utility::vector1< core::Size >positions_to_replace_;
  //utility::vector1< core::Size >constrained_lig_atoms_;
  core::Size dock_trials_;
  core::pack::task::TaskFactoryOP task_factory_;
  //core::Size ligand_seqpos_;//Ligand's sequence position
};

/// @brief class that will identify the region around the ligand,
/// remove it, and then do a repack. It can also calculate the following
/// parameters: E diff after the repack, (in essence a crude delta G calc)
/// rmsd of the repacked site after the repack and rmsd of catalytic residues
class RepackLigandSiteWithoutLigandMover : public protocols::moves::Mover
{

public:
  RepackLigandSiteWithoutLigandMover();

  RepackLigandSiteWithoutLigandMover(
    core::scoring::ScoreFunctionCOP sfxn,
    bool calculate_silent_Es
  );

  ~RepackLigandSiteWithoutLigandMover();

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

  virtual std::string get_name() const;

  void
  set_cstio(
    toolbox::match_enzdes_util::EnzConstraintIOCOP enzcst_io );

  void
  set_sfxn(
    core::scoring::ScoreFunctionCOP sfxn );

  void
  set_calculate_silent_Es(
    bool calculate );

  utility::vector1< core::io::silent::SilentEnergy > const &
  silent_Es(){
    return silent_Es_; }

  core::pack::task::PackerTaskCOP get_ptask() const;

private:

  void
  separate_protein_and_ligand( core::pose::Pose & pose ) const;

  core::scoring::ScoreFunctionCOP sfxn_;
  core::Size lig_seqpos_;
  toolbox::match_enzdes_util::EnzConstraintIOCOP enzcst_io_;
  bool calculate_silent_Es_;
  core::pack::task::PackerTaskOP ptask_;
  utility::vector1< core::io::silent::SilentEnergy > silent_Es_;
};


} //enzdes
} //protocols


#endif