DnaInterfaceFinder.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.

/// @brief
/// @author ashworth

#ifndef INCLUDED_protocols_dna_DnaInterfaceFinder_hh
#define INCLUDED_protocols_dna_DnaInterfaceFinder_hh

#include <protocols/dna/DnaInterfaceFinder.fwd.hh>

#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>

#include <utility/pointer/ReferenceCount.hh>
#include <utility/vector1.fwd.hh>

#include <map>

#include <utility/vector1.hh>


namespace protocols {
namespace dna {

class DnaNeighbor {
public:
  DnaNeighbor() : close_(false), contact_(false) {}
  void close( bool val ) { close_ |= val; }
  void contact( bool val ) { contact_ |= val; }
  bool close() const { return close_; }
  bool contact() const { return contact_; }
private:
  bool close_, contact_;
};

typedef std::map< core::Size, DnaNeighbor > DnaNeighbors;

class DnaInterfaceFinder : public utility::pointer::ReferenceCount {
public:

  DnaInterfaceFinder(
    core::Real close_threshold = 10 * 10,
    core::Real contact_threshold = 3.7 * 3.7,
    core::Real z_cutoff = 10.,
    bool base_only = false
  ) : utility::pointer::ReferenceCount(),
      close_threshold_( close_threshold ),
      contact_threshold_( contact_threshold ),
      z_cutoff_( z_cutoff ),
      base_only_( base_only ),
      initialized_( false )
  {}

  virtual ~DnaInterfaceFinder(){}

  DnaInterfaceFinderOP clone() const { return new DnaInterfaceFinder(*this); }

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

  void
  determine_interface(
    core::pose::Pose const & pose,
    utility::vector1< core::Size > const & protein_positions,
    utility::vector1< core::Size > const & dna_positions
  );

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

  void
  determine_protein_interface(
    core::pose::Pose const & pose,
    utility::vector1< core::Size > const & protein_positions,
    utility::vector1< core::Size > const & dna_positions
  );

  void
  determine_dna_interface(
    core::pose::Pose const & pose,
    utility::vector1< core::Size > const & protein_positions,
    utility::vector1< core::Size > const & dna_positions
  );

  bool initialized() const { return initialized_; }

  DnaNeighbors const & protein_neighbors() const;
  DnaNeighbors const & dna_neighbors() const;

private:
  core::Real close_threshold_, contact_threshold_, z_cutoff_;
  bool base_only_;
  bool initialized_;
  DnaNeighbors protein_neighbors_;
  DnaNeighbors dna_neighbors_;

};

} // namespace dna
} // namespace protocols

#endif