PeakAssignmentResidueMap.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 CrossPeakList.hh
/// @author Oliver Lange

#ifndef INCLUDED_protocols_noesy_assign_PeakAssignmentResidueMap_HH
#define INCLUDED_protocols_noesy_assign_PeakAssignmentResidueMap_HH


// Unit Headers
#include <protocols/noesy_assign/PeakAssignmentResidueMap.fwd.hh>
#include <protocols/noesy_assign/CrossPeakList.fwd.hh>
// AUTO-REMOVED #include <protocols/noesy_assign/ResonanceList.hh>
#include <core/types.hh>

// Package Headers
#include <protocols/noesy_assign/PeakAssignment.fwd.hh>
#include <core/id/NamedAtomID.fwd.hh>

// Project Headers

// Utility headers
// AUTO-REMOVED #include <utility/exit.hh>
// #include <utility/excn/Exceptions.hh>
#include <utility/vector1.hh>
#include <utility/pointer/ReferenceCount.hh>
// #include <numeric/numeric.functions.hh>
// #include <core/util/prof.hh>
//#include <core/util/Tracer.hh>
// #include <core/options/option.hh>
// #include <core/options/keys/abinitio.OptionKeys.gen.hh>
// #include <core/options/keys/run.OptionKeys.gen.hh>
//#include <core/options/keys/templates.OptionKeys.gen.hh>

//// C++ headers
// AUTO-REMOVED #include <cstdlib>
// AUTO-REMOVED #include <string>
#include <list>
#include <set>
#include <map>

#include <protocols/noesy_assign/ResonanceList.fwd.hh>


namespace protocols {
namespace noesy_assign {



///@brief fast access to assignments by residue number
class PeakAssignmentResidueMap : public utility::pointer::ReferenceCount {
public:
  typedef std::list< PeakAssignmentOP > PeakAssignments;
  typedef std::map< core::Size, PeakAssignments > PeakAssignmentMap;
  typedef utility::vector1< PeakAssignmentMap > ResidueList;

  PeakAssignmentResidueMap();
  virtual ~PeakAssignmentResidueMap();

  ///@brief add all PeakAssignments in all Crosspeaks of list
  void add( CrossPeakList const& );

  ///@brief add individual PeakAssignment
  void add( PeakAssignmentOP const& );


  ///@brief add all resonances for backward compatibility in covalent-part of network-analysis
  void add_all_atoms( ResonanceList const& );

  ///@brief remove individual PeakAssignment
  void remove( PeakAssignment const& );

  ///@brief invalidate non symmetric peaks
  void check_for_symmetric_peaks( CrossPeakList&, bool accumulate_symmetry );

  ///@brief remove all ambiguous assignments to i,i+1 CrossPeaks.

  //commented out 9/10/12 because the only relevant action within the subroutine is commented out already
  //void invalidate_competitors_to_sequential_NOE( CrossPeakList& );

  void network_analysis( Size n_total_assignments );
  void network_analysis2( ResonanceList const& resonances );
  ///@brief get list of PeakAssignments for pair of residues --- throws Exception
  PeakAssignments const& assignments( core::Size resi, core::Size resj ) const;
  PeakAssignments& assignments( core::Size resi, core::Size resj );

  ///@brief add assignments found between resi and resj to collector
  void assignments( core::Size resi, core::Size resj, PeakAssignments& collector ) const;

  ///@brief has some (valid or invalid) assignments between residue pair
  bool has( core::Size resi, core::Size resj );

  core::Size total_residue() const {
    return residues_.size();
  }

private:
  ///@brief same as "assignments()" but returns BOGUS_ASSIGNMENTS if not found
  PeakAssignments const& _assignments( core::Size resi, core::Size resj ) const;
  PeakAssignments& _assignments( core::Size resi, core::Size resj );

  ///@brief subroutine to compute Nk for alpha->gamma->beta path.
  core::Real compute_Nk(
     PeakAssignment const&  alpha_beta,
     core::id::NamedAtomID const& gamma_atom,
     bool connect_in_i,
     bool connect_in_j,
     bool sequential,
     PeakAssignments const& close_to_i_assignments,
     PeakAssignments const& close_to_j_assignments,
     core::Real longrange_peak_volume
     /*either the a-g or g-b peak_volume (corresponding to the "false" in one of the connect_in_i/j */
  ) const;

  ///@brief subroutine to collect putative gammas that need to be queried due to covalent structure
  void fill_covalent_gammas( Size, std::map< core::id::NamedAtomID, bool >& collector ) const;


  //find out if we have an initial assignment to gamma
  /// map with resid of atom(2) as search key.
  ///per residue - a PeakAssignmentMap --- all residues that are connected by an initial assignment
  ResidueList residues_;
  PeakAssignments BOGUS_ASSIGNMENTS; //emtpy list

  // a little redundancy in the residue number
  // but saves lot of time later we can just reference these objects.
  typedef std::set< core::id::NamedAtomID > AtomList;
  typedef utility::vector1< AtomList > AtomByResList;

  //for reach residue list of NamedAtomIDs
  AtomByResList atoms_;
};

}
}

#endif