NormalizedEvaluatedArchive.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:
//
// This file is part of the Rosetta software suite and is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// (C) 199x-2009 Rosetta Commons participating institutions and developers.
// For more information, see http://www.rosettacommons.org/.

/// @file   protocols/jd2/MPIWorkPoolJobDistributor.hh
/// @brief  header for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs  that spawn new jobs based on a pool/archive of
///         structures
/// @author Oliver Lange olange@u.washington.edu

#ifndef INCLUDED_protocols_jd2_archive_NormalizedEvaluatedArchive_hh
#define INCLUDED_protocols_jd2_archive_NormalizedEvaluatedArchive_hh

// Unit headers
#include <protocols/jd2/archive/ArchiveManager.fwd.hh>
#include <protocols/jd2/archive/EvaluatedArchive.hh>
#include <protocols/jd2/archive/VarianceStatisticsArchive.fwd.hh>
//#include <protocols/jd2/archive/NormalizedEvaluatedArchive.fwd.hh>
// AUTO-REMOVED #include <core/scoring/constraints/ConstraintSet.hh>

// Package headers
#include <core/io/silent/silent.fwd.hh>
#include <core/pose/Pose.fwd.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunction.hh>

// AUTO-REMOVED #include <protocols/evaluation/PoseEvaluator.hh>

// Utility headers
#include <core/types.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/exit.hh>

// C++ headers
#include <string>
#include <list>

#include <core/scoring/ResidualDipolarCoupling.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <protocols/evaluation/PoseEvaluator.fwd.hh>
#include <utility/vector1.hh>


namespace protocols {
namespace jd2 {
namespace archive {
//class ArchiveManager;



///@brief Tags used to tag messeges sent by MPI functions used to decide whether a slave is requesting a new job id or
///flagging as job as being a bad input

///@details This job distributor is meant for running jobs where the machine you are using has a large number of
///processors, the number of jobs is much greater than the number of processors, or the runtimes of the individual jobs
///could vary greatly. It dedicates the head node (whichever processor gets processor rank #0) to handling job requests
///from the slave nodes (all nonzero ranks). Unlike the MPIWorkPartitionJobDistributor, this JD will not work at all
///without MPI and the implementations of all but the interface functions have been put inside of ifdef directives.
///Generally each function has a master and slave version, and the interface functions call one or the other depending
///on processor rank.

class NormalizedEvaluatedArchive : public EvaluatedArchive {
  typedef EvaluatedArchive Parent;
public:

  ///@brief Constructor  and Destructor
  NormalizedEvaluatedArchive( ArchiveManagerAP ptr );
  NormalizedEvaluatedArchive();
  ~NormalizedEvaluatedArchive();

  ///@brief Archive specific options
  static void register_options();

  void init_from_options();

  virtual void initialize();

  ///@brief add decoy to Archive
  ///@detail evaluate decoy and call add_evaluated_structure
  virtual bool add_evaluated_structure( core::io::silent::SilentStructOP from_batch, Batch const& );

  ///@brief overloaded that we can sort the pool after reading
  virtual bool restore_from_file();

  ///@brief determine variation of scores (those that are non-zeros in select_weights_ )
  bool determine_score_variations() const;

  ///overloaded to save / restore the variance_archive_
  virtual void save_to_file( std::string suffix = "" );

  ///@brief recompute all score-values of all decoys and re-order the archive by (new) select_score
  void rescore();

  virtual WeightMap const& score_variations() const;

  virtual core::Real score_variation( std::string const& col ) const;


protected:

  virtual void invalidate_score_variations() {
    score_variations_are_clean_ = false;
  }

private:
  bool is_start_zero_score( std::string const& ) const;

  mutable WeightMap score_variations_;
  mutable bool score_variations_are_clean_;
  VarianceStatisticsArchiveOP variance_archive_;

  //option settings
  core::Size min_decoys_for_statistics_;
  core::Size nstruct_for_statistics_;
  bool keep_adding_to_statistics_;
  bool use_variance_archive_;
  core::Real insertion_prob_;
  bool activated_;
  bool lower_quartile_;
  //for these scores we compute the variance as 0...Q3 instead of Q1..Q3
  utility::vector1< std::string > positive_scores_;
  ///@brief keep track whether our options have been registered at start up
  static bool options_registered_;
};


}//archive
}//jd2
}//protocols


#endif //INCLUDED_protocols_jd2_Archive_HH