EnzConstraintParameters.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 IO-functionality for enzyme Constraints
/// @brief
/// @author Florian Richter, floric@u.washington.edu


#ifndef INCLUDED_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_hh
#define INCLUDED_protocols_toolbox_match_enzdes_util_EnzConstraintParameters_hh


// Unit headers
#include <protocols/toolbox/match_enzdes_util/EnzConstraintIO.fwd.hh>

// Package headers
#include <core/scoring/constraints/Func.fwd.hh>

#include <core/scoring/ScoreFunction.fwd.hh>

// Project headers
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/pose/Pose.fwd.hh>


// Utility Headers
#include <utility/pointer/ReferenceCount.hh>
#include <set>

#include <core/types.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <core/scoring/constraints/Constraint.fwd.hh>
#include <protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.fwd.hh>
#include <utility/vector1.hh>
#include <iostream>



//Utility Headers

// C++ Headers

namespace protocols {
namespace toolbox {
namespace match_enzdes_util {


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

/// @brief helper class to allow for removal of covalent constraints
class CovalentConnectionReplaceInfo : public utility::pointer::ReferenceCount {

public:

  CovalentConnectionReplaceInfo(
    std::string resA_base_in,
      std::string resB_base_in,
      std::string resA_var_in,
      std::string resB_var_in,
      core::Size Apos_in,
      core::Size Bpos_in,
      core::chemical::ResidueTypeSetCAP restype_set_in
    );

  CovalentConnectionReplaceInfo( CovalentConnectionReplaceInfo const & other );

  virtual ~CovalentConnectionReplaceInfo();

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

  void
  remap_resid( core::id::SequenceMapping const & smap );

private:

  std::string resA_basename_, resB_basename_;
  std::string resA_varname_, resB_varname_;
  std::string resA_modname_, resB_modname_;

  core::Size resA_seqpos_, resB_seqpos_;
  core::chemical::ResidueTypeSetCAP restype_set_;

}; //class CovalentConnection


/// @brief class that holds all the parameters for one specific constraint
class EnzConstraintParameters : public utility::pointer::ReferenceCount {


public:

  void
  set_mcfi(
    toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi );

  EnzConstraintParameters();

  EnzConstraintParameters(
    core::Size cst_block,
    core::chemical::ResidueTypeSetCAP src_restype_set,
    EnzConstraintIOCAP src_enz_io);

  EnzConstraintParameters( EnzConstraintParameters const & other );

  virtual ~EnzConstraintParameters();

  void
  show_definitions() const;

  void
  generate_pose_specific_data(
    core::pose::Pose & pose,
    core::scoring::ScoreFunctionCOP scofx
  ) const;

  bool
  is_empty() const {
    return empty_;
  }

  bool
  is_covalent() const {
    return is_covalent_;
  }

  bool
  missing_in_pose( core::pose::Pose const & pose) const;

  /// @brief function that takes all rotamers for the ResidueType(s)
  /// of the residue that's missing in the pose and places them
  /// according to the geometry specified in the mcfi
  //utility::vector1< core::conformation::ResidueCOP >
  //inverse_rotamers_for_residue_missing_in_pose(
  //  core::pose::Pose const & pose ) const;

  core::Size
  cst_block() const {
    return cst_block_;}

  void
  set_cst_block( core::Size cst_block ){ cst_block_ = cst_block;}

  /// @brief updates the pdb remarks according to what is in the
  /// EnzCstTemplateRes member data. returns false in case any
  /// error occured
  bool
  update_pdb_remarks(
    core::pose::Pose & pose
  ) const;


  EnzConstraintIOCAP
  enz_io() const{
    return enz_io_; }

  EnzCstTemplateResOP
  nonconst_resA();

  EnzCstTemplateResOP
  nonconst_resB();

  EnzCstTemplateResCOP
  resA() const;

  EnzCstTemplateResCOP
  resB() const;

  EnzCstTemplateResCOP
  get_missing_template_res( core::pose::Pose const & pose ) const;

  EnzCstTemplateResCOP
  get_missing_template_other_res( core::pose::Pose const & pose ) const;

  /// @brief all residue names specified in the cstfile
  /// returns an empty set if the constraints don't apply
  /// to the specifed position
  std::set< std::string >
  allowed_res_name3_at_position( core::pose::Pose const & pose, core::Size seqpos ) const;

  void
  set_external_position_for_resA( core::Size pos );

  void
  set_external_position_for_resB( core::Size pos );

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

  void
  remap_resid( core::id::SequenceMapping const & smap );

  static
  core::scoring::constraints::FuncOP
  convert_GeomSampleInfo_to_FuncOP(
    toolbox::match_enzdes_util::GeomSampleInfoCOP gsi,
    core::Real & ideal_val);

private:

  void
  generate_active_pose_constraints(
    core::pose::Pose & pose,
    core::scoring::ScoreFunctionCOP scofx
  ) const;

  void
  make_constraint_covalent(
    core::pose::Pose & pose,
    Size resA_pos,
    Size resB_pos,
    Size resA_At,
    Size resB_At
  ) const;

  void
  make_constraint_covalent_helper(
    core::pose::Pose & pose,
    EnzCstTemplateResOP template_res,
    core::Size res_pos,
    core::Size Atpos,
    core::Real itorsion,
    core::Real iangle,
    core::Real idis,
    std::string & res_varname
  ) const;

  core::Size
  determine_best_constraint(
    core::pose::Pose const & pose,
    core::scoring::ScoreFunctionCOP scofx,
    utility::vector1< core::scoring::constraints::ConstraintCOP > candidate_csts
  ) const;


private: //data

  EnzCstTemplateResOP resA_, resB_;

  toolbox::match_enzdes_util::MatchConstraintFileInfoCOP mcfi_;

  core::scoring::constraints::FuncOP disAB_, angleA_, angleB_, torsionA_, torsionB_, torsionAB_;

  core::Real ndisAB_, nangleA_, nangleB_, ntorsionA_, ntorsionB_, ntorsionAB_;

  bool is_covalent_;

  mutable bool empty_; //safeguard if someone reads in a cstfile with all force constants set to 0
  core::chemical::ResidueTypeSetCAP restype_set_;

  EnzConstraintIOCAP enz_io_; //the EnzConstraintIO object that this template res belongs to
  core::Size cst_block_; //the block in the cst file that corresponds to this residue

}; // class EnzConstraintParameters


}
} //enzdes
} //protocols


#endif