Rosetta  2020.46
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Macros | Functions | Variables
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/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ResidualDipolarCoupling.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/util.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/evaluation/util.hh>
#include <protocols/loops/util.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/LoopsFileIO.hh>
#include <basic/Tracer.hh>
#include <basic/MemTracer.hh>
#include <protocols/cluster/cluster.hh>
#include <protocols/toolbox/Cluster.hh>
#include <protocols/toolbox/Cluster.impl.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 <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/vector0.hh>
#include <utility/vector1.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

#define OBSOLETE (   key)
Value:
if ( option[ key ].user() ) { \
tr.Warning << "Option "<< #key<< " is deprecated!" << std::endl; \
}
static basic::Tracer tr("protocols.iterative")

Referenced by warn_obsolete_flags().

Function Documentation

std::string const NOESY_CST_FILE_NAME ( "noe_auto_assign.cst"  )
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().

void warn_obsolete_flags ( )

Variable Documentation

basic::MemTracer mem_tr
static