Interface.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 Interface - information about the interface between to partners
/// @brief contains the following information:
///   calculate the interface between the two (or other?) partners
///   set the packer task to only pack the interface
/// @author Monica Berrondo


#ifndef INCLUDED_protocols_scoring_Interface_hh
#define INCLUDED_protocols_scoring_Interface_hh

// Unit headers
#include <protocols/scoring/Interface.fwd.hh>

// Package headers
#include <core/types.hh>
#include <core/conformation/Residue.fwd.hh> // replace with .fwd.hh
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pose/Pose.fwd.hh>

// Symmetry headers
// AUTO-REMOVED #include <core/conformation/symmetry/SymmetryInfo.fwd.hh>
// AUTO-REMOVED #include <core/conformation/symmetry/SymmetricConformation.fwd.hh>

// Utility headers
#include <ObjexxFCL/FArray1D.hh>
// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>

#include <utility/vector1.hh>


namespace protocols {
namespace scoring {

class
Interface : public utility::pointer::ReferenceCount {
public:

  typedef core::pack::task::PackerTaskOP PackerTaskOP;
  typedef core::Real Real;


  // default constructor
  Interface() {
    jump_number_ = 1;
    distance_squared_ = 8.0 * 8.0;
    use_input_partners_ = false;
  }

  // constructor with arguments
  Interface(
    Size const jump_number_in
  ) : jump_number_( jump_number_in )
  {
    // set the default distance to 8 Angstrom (for cendist)
    // is this the correct number for a default?
    distance_squared_ = 8.0 * 8.0;
    use_input_partners_ = false;
  }

  Interface(
    ObjexxFCL::FArray1D_bool partner
  )
  {
    partner_ = partner;
    // set the default distance to 8 Angstrom (for cendist)
    // is this the correct number for a default?
    distance_squared_ = 8.0 * 8.0;
    use_input_partners_ = true;
  }

  void jump( Size const jump_number);

  core::Size jump_id() const {
    return jump_number_;
  }

  void calculate( core::pose::Pose const & pose );
  void print( core::pose::Pose const & pose );
  void show( core::pose::Pose const & pose );
  void set_pack( core::pose::Pose const & pose, PackerTaskOP task );

  core::Size closest_interface_residue( core::pose::Pose const & pose, core::Size src_rsd, core::Real & distance );

  void distance( Real const distance_in );

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

  bool is_interface( core::conformation::Residue const & rsd ) const;// { return is_interface_( rsd.seqpos() ); }

  bool is_interface( Size const position ) const;// { return is_interface_(position); }

  /// @brief returns the total number of residues on both sides of the interface for
  /// a given jump
  Size interface_nres();

  /// @brief returns whether the rsd1 and rsd2 are considered a contact pair
  /// based on contact_list_ array
  bool is_pair(
    core::conformation::Residue const & rsd1,
    core::conformation::Residue const & rsd2
  );
  // symmetric interfaces
  void set_symmetric_pack( core::pose::Pose const & pose, PackerTaskOP task );

  /// @brief Get two lists containing the residues on each side of the interface
  ///
  /// You might expect something called pair_list() to output pairs or somehow
  /// relate to the is_pair function, but it does not.
  /// It returns a two element list.
  ///  - The first element is a list of all residues on the lower partner of the
  ///    interface.
  ///  - The second element is a list of all the residues in the interface on the
  ///    upper partner.
  /// Both lists are sorted by residue number, so the indices of one list have
  /// no relationship to the other list.
  /// @todo rename this to something more logical & give it a better return type
  /// @todo make a function that returns a vector1<pair<Size,Size> > containing
  /// all interacting pairs. This would be easy to implement.
  utility::vector1 < utility::vector1_int > pair_list() { return pair_list_; }

  /// @brief The contact_list is pose.total_residue() long, each element
  /// (contact_list_[i]) contains a list of residues from the other partner that
  /// interacts with residue i.  This is calculated in protein_calculate, and
  /// used by Interface.is_pair() function as well as the interchain_vdw,
  /// interchain_env, and interchain_pair scoring components.
  utility::vector1 < utility::vector1_size > contact_list() { return contact_list_; }

private:
  Size jump_number_;
  Real distance_squared_;
  ObjexxFCL::FArray1D_bool partner_;
  ObjexxFCL::FArray1D_bool is_interface_;
  utility::vector1 < utility::vector1_int > pair_list_;
  utility::vector1 < utility::vector1_size > contact_list_;
  //std::vector < bool > is_interface_;
  bool use_input_partners_;

  void protein_calculate( core::pose::Pose const & pose );
  void ligand_calculate( core::pose::Pose const & pose );
  void NA_calculate( core::pose::Pose const & ); //currently set to protein_calculate()
  void symmetric_protein_calculate( core::pose::Pose const & pose );
};

} // namespace scoring
} // namespace protocols

#endif