FlexPepDockingPoseMetrics.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) 199x-2008 Hebrew University, Jerusalem
//
// (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   FlexPepDockingPoseMetrics.hh
///
/// @brief metrics calculations specific for FlexPepDock (at least for now)
/// @date March 29th, 2009
/// @author Barak Raveh / Nir London

#ifndef INCLUDED_protocols_flexpep_docking_FlexPepDockingPoseMetrics_hh
#define INCLUDED_protocols_flexpep_docking_FlexPepDockingPoseMetrics_hh

#include <protocols/flexpep_docking/FlexPepDockingFlags.hh>
#include <protocols/flexpep_docking/FlexPepDockingPoseMetrics.fwd.hh>

// ObjexxFCL headers
#include <ObjexxFCL/FArray1D.fwd.hh>

#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace flexpep_docking {

using namespace core::pose;
using namespace core;

class FlexPepDockingPoseMetrics
{
public:
  typedef bool (*t_predicate_func)(Pose const &, Pose const &, core::Size, core::Size);


  FlexPepDockingPoseMetrics(FlexPepDockingFlagsCOP flags)
    : flags_(flags)
  {} // TODO: move to .cc

  core::Real calc_frac_native_contacts ( Pose const& native,
    Pose const& final,
    core::Real threashold ) const;

  /////////////////////////////////////////////////////////////////////////////
  /// @begin calculate fractions of atoms that are at the same location as native
  ///
  /// @brief calculate fractions of atoms that are at the same location as native
  ///
  //  @detailed
  //  Calculate fraction of atoms that are less than k Angstroms between native and
  //  final pose, using only residues marked in res_subset, and only atoms qualifying to
  //  predicate function (see core/scoring/rms_utils.hh for definitions of predicates)
  //
  //  @param
  //  pose1 - the first structure to be assessed
  //  pose2 - the second structure to be assessed
  //  predicate - a predicate on atoms included in the assesment (e.g., CA atoms only)
  //  k - threshold in angstroms of atoms to be included in the assesment
  //  ngood [output] - absolute number of atoms that are less than k Angstroms
  //
  // @return
  // fraction of atoms that are less than k Angstroms between poses
  ////////////////////////////////////////////////////////////////////////////
  core::Real calc_frac_atoms_kA_to_native(
    Pose const& pose1, Pose const& pose2,
    ObjexxFCL::FArray1D_bool const & res_subset,
    t_predicate_func predicate,
    double k,
    core::Size& ngood
  ) const;


  // check all sequential Kmers in the peptide, and output the best RMS Kmer
  core::Real best_Kmer_rms(
    Pose const& pose1,
    Pose const& pose2,
    t_predicate_func predicate,
    core::Size k
  ) const;

  /////////////////////////////////////////////////////////////////////////////
  /// @begin calculate phi/psi torsion-RMSD over peptide
  ///
  //  @detailed
  //  Calculate the RMSD in phi.psi angle over peptide between pose1 and pose2
  //
  //  @param
  //  pose1 - the first structure to be assessed
  //  pose2 - the second structure to be assessed
  //
  // @return
  // phi/psi torsion-RMSD between peptide backbones
  ////////////////////////////////////////////////////////////////////////////
  core::Real calc_phipsi_RMSD(
    Pose const& pose1,
    Pose const& pose2,
    ObjexxFCL::FArray1D_bool const & res_subset
  ) const;


  //calculaer different metrics for the interface of the given pose;
  std::map < std::string, core::Real >
  calc_interface_metrics
  (core::pose::Pose & pose, Size rb_jump, core::scoring::ScoreFunctionOP scorefxn);

  /////////////////////////////////////////
  // Calculate peptide score with and w/o
  // fa_ref sequence reference energy
  /////////////////////////////////////////
  void
  calc_pep_scores
  ( core::pose::Pose const & pose, Real& pepScore, Real& pepScore_noref ) const;

  // ======== Accessor Methods ========

  void set_flags(FlexPepDockingFlagsCOP flags){
    flags_ = flags;
  }



private:
  FlexPepDockingFlagsCOP flags_;

  // helper method to check if two given residues are within "threashold" of each other
  bool isInContact ( core::conformation::Residue const res1,
                       core::conformation::Residue const res2,
                       core::Real threashold ) const;


}; // end class FlexPepDockingPoseMetrics

} // end namespace flexPepDocking
} // end namespace protocols

#endif