IterativeBase.cc File Reference

#include <protocols/abinitio/IterativeBase.hh>
#include <protocols/jd2/archive/ArchiveManager.hh>
#include <protocols/noesy_assign/NoesyModule.hh>
#include <protocols/noesy_assign/NoesyModule.impl.hh>
#include <protocols/topology_broker/TopologyBroker.hh>
#include <protocols/topology_broker/ConstraintClaimer.hh>
#include <protocols/topology_broker/ConstraintEvaluatorWrapper.hh>
#include <protocols/topology_broker/util.hh>
#include <basic/options/keys/broker.OptionKeys.gen.hh>
#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ResidualDipolarCoupling.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/util.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <protocols/toolbox/DecoySetEvaluation.hh>
#include <protocols/toolbox/DecoySetEvaluation.impl.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <protocols/abinitio/PairingStatistics.hh>
#include <protocols/simple_filters/JumpEvaluator.hh>
#include <protocols/simple_filters/RmsdEvaluator.hh>
#include <protocols/simple_filters/ScoreEvaluator.hh>
#include <protocols/simple_filters/RDC_Evaluator.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/LoopsFileIO.hh>
#include <basic/Tracer.hh>
#include <basic/MemTracer.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/file/FileName.hh>
#include <utility/file/file_sys_util.hh>
#include <numeric/random/random.hh>
#include <utility/DereferenceIterator.hh>
#include <utility/options/OptionCollection.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/jumps.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/cluster.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <cstdlib>
#include <string>
#include <vector>
#include <basic/options/option_macros.hh>
#include <numeric/random/random_permutation.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <protocols/noesy_assign/CrossPeakList.impl.hh>
#include <utility/vector1.hh>
#include <protocols/abinitio/HedgeArchive.hh>
#include <core/scoring/ScoreFunction.hh>
#include <basic/prof.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::abinitio

Macros
#define	OBSOLETE(key)

Functions
static basic::Tracer	tr ("protocols.iterative")
std::string const	NOESY_CST_FILE_NAME ("noe_auto_assign.cst")
void	warn_obsolete_flags ()
void	protocols::abinitio::fix_chainbreak_patch (scoring::ScoreFunctionOP scorefxn, std::string const &patch_name)
bool	protocols::abinitio::decide_on_beta_jumping_from_frags ()
void	protocols::abinitio::get_core (toolbox::DecoySetEvaluation &eval, core::Real cutoff, loops::Loops &rigid)

Variables
static basic::MemTracer	mem_tr

Macro Definition Documentation

OBSOLETE

#define OBSOLETE

(

key

)

Value:

  if ( option[ key ].user() ) {                 \
    tr.Warning << "Option "<< #key<< " is deprecated!" << std::endl; \
  }

Function Documentation

NOESY_CST_FILE_NAME()

std::string const NOESY_CST_FILE_NAME

(

"noe_auto_assign.cst"

)

Referenced by protocols::abinitio::IterativeBase::reassign_noesy_data().

tr()

static basic::Tracer tr ( "protocols.iterative"  )

static

Referenced by protocols::abinitio::IterativeBase::add_structure(), protocols::abinitio::IterativeBase::collect_hedgeing_decoys_from_batches(), protocols::abinitio::IterativeBase::compute_cores(), protocols::abinitio::decide_on_beta_jumping_from_frags(), protocols::abinitio::IterativeBase::do_dynamic_patching(), protocols::abinitio::fix_chainbreak_patch(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), protocols::abinitio::IterativeBase::gen_enumerate_pairings(), protocols::abinitio::IterativeBase::gen_evaluation_output(), protocols::abinitio::IterativeBase::gen_noe_assignments(), protocols::abinitio::IterativeBase::gen_resample_stage2(), protocols::abinitio::IterativeBase::gen_resample_topologies(), protocols::abinitio::IterativeBase::generate_batch(), protocols::abinitio::get_core(), protocols::abinitio::IterativeBase::guess_pairings_from_secondary_structure(), protocols::abinitio::IterativeBase::idle(), protocols::abinitio::IterativeBase::increment_stage(), protocols::abinitio::IterativeBase::init_from_decoy_set(), protocols::abinitio::IterativeBase::initialize(), protocols::abinitio::IterativeBase::IterativeBase(), protocols::abinitio::IterativeBase::read_structures(), protocols::abinitio::IterativeBase::reassign_noesy_data(), protocols::abinitio::IterativeBase::replace_noesy_filter_constraints(), protocols::abinitio::IterativeBase::rescore_nonlocal_archive(), protocols::abinitio::IterativeBase::restore_status(), protocols::abinitio::IterativeBase::setup_autoNOE(), protocols::abinitio::IterativeBase::setup_filter_cst(), protocols::abinitio::IterativeBase::test_broker_settings(), protocols::abinitio::IterativeBase::test_for_stage_end(), and protocols::abinitio::IterativeBase::update_noesy_filter_files().

warn_obsolete_flags()

void warn_obsolete_flags

(

)

References OBSOLETE.

Referenced by protocols::abinitio::IterativeBase::IterativeBase().

Variable Documentation

mem_tr

basic::MemTracer mem_tr

static

Referenced by protocols::abinitio::decide_on_beta_jumping_from_frags(), protocols::abinitio::IterativeBase::gen_noe_assignments(), protocols::abinitio::IterativeBase::gen_resample_fragments(), protocols::abinitio::IterativeBase::gen_resample_stage2(), protocols::abinitio::IterativeBase::generate_batch(), protocols::abinitio::IterativeBase::initialize(), protocols::abinitio::IterativeBase::IterativeBase(), and protocols::abinitio::IterativeBase::reassign_noesy_data().