AbrelaxApplication.cc File Reference

#include <utility/io/izstream.hh>
#include <protocols/jobdist/JobDistributors.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/abinitio/AbrelaxApplication.hh>
#include <protocols/abinitio/util.hh>
#include <protocols/constraints_additional/AdditionalConstraintCreators.hh>
#include <protocols/loops/util.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/loop_mover/refine/LoopMover_KIC.hh>
#include <protocols/loops/loops_main.hh>
#include <core/kinematics/util.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/abinitio/ClassicAbinitio.hh>
#include <protocols/abinitio/MembraneAbinitio.hh>
#include <protocols/abinitio/FoldConstraints.hh>
#include <protocols/abinitio/LoopJumpFoldCst.hh>
#include <protocols/abinitio/DoubleLayerKinematicAbinitio.hh>
#include <protocols/abinitio/Templates.hh>
#include <protocols/abinitio/TemplateJumpSetup.hh>
#include <protocols/abinitio/PairingStatistics.hh>
#include <protocols/abinitio/StrandConstraints.hh>
#include <protocols/simple_moves/FragmentMover.fwd.hh>
#include <protocols/abinitio/Protocol.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <protocols/jumping/SheetBuilder.hh>
#include <protocols/jumping/RandomSheetBuilder.hh>
#include <protocols/jumping/JumpSetup.hh>
#include <core/scoring/dssp/PairingsList.hh>
#include <protocols/jumping/ResiduePairJumpSetup.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <core/scoring/dssp/StrandPairing.hh>
#include <protocols/jumping/util.hh>
#include <protocols/jumping/MembraneJump.hh>
#include <protocols/evaluation/PoseEvaluator.hh>
#include <protocols/evaluation/EvaluatorFactory.hh>
#include <protocols/evaluation/PCA.hh>
#include <protocols/moves/PyMOLMover.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <core/scoring/SS_Killhairpins_Info.hh>
#include <core/energy_methods/ContactOrderEnergy.hh>
#include <core/types.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <basic/MetricValue.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/constraints.OptionKeys.gen.hh>
#include <basic/options/keys/filters.OptionKeys.gen.hh>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/jumps.OptionKeys.gen.hh>
#include <basic/options/keys/loopfcst.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/templates.OptionKeys.gen.hh>
#include <basic/options/keys/relax.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/trRosetta.OptionKeys.gen.hh>
#include <basic/tensorflow_manager/util.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/constraints/ConstraintFactory.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <core/scoring/constraints/util.hh>
#include <protocols/pose_metric_calculators/ClashCountCalculator.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/SilentFileOptions.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/io/raw_data/DisulfideFile.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/ScoreType.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/func/Func.fwd.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/MembraneTopology.hh>
#include <core/sequence/util.hh>
#include <core/sequence/Sequence.hh>
#include <protocols/simple_filters/RmsdEvaluator.hh>
#include <protocols/simple_filters/JumpEvaluator.hh>
#include <protocols/evaluation/TimeEvaluator.hh>
#include <protocols/constraints_additional/ConstraintEvaluator.hh>
#include <protocols/simple_filters/PoseMetricEvaluator.hh>
#include <protocols/loops/loop_closure/ccd/SlidingWindowLoopClosure.hh>
#include <protocols/loops/loop_closure/ccd/WidthFirstSlidingWindowLoopClosure.hh>
#include <protocols/relax/loop_closure/FASelectSlidingWindowLoopClosure.hh>
#include <protocols/loops/Exceptions.hh>
#include <protocols/simple_filters/RGFilter.hh>
#include <protocols/simple_filters/COFilter.hh>
#include <protocols/simple_filters/SheetFilter.hh>
#include <protocols/simple_filters/PDDFScoreFilter.hh>
#include <protocols/simple_filters/SAXSScoreFilter.hh>
#include <protocols/moves/MoverStatus.hh>
#include <protocols/simple_moves/RepulsiveOnlyMover.hh>
#include <protocols/trRosetta_protocols/constraint_generators/trRosettaConstraintGenerator.hh>
#include <numeric/random/random.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <utility/io/util.hh>
#include <utility/exit.hh>
#include <basic/citation_manager/CitationManager.hh>
#include <basic/citation_manager/CitationCollection.hh>
#include <string>
#include <utility>
#include <vector>
#include <core/fragment/FragData.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/fragment/FrameList.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/scoring/func/FuncFactory.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <protocols/abinitio/KinematicAbinitio.hh>
#include <protocols/relax/ClassicRelax.hh>
#include <protocols/relax/FastRelax.hh>
#include <protocols/relax/util.hh>
#include <ObjexxFCL/format.hh>
#include <core/scoring/ScoreFunction.hh>
#include <protocols/abinitio/ResolutionSwitcher.hh>

Classes
class	protocols::abinitio::PcaEvaluator
class	protocols::abinitio::ShowViolation
class	protocols::abinitio::ComputeTotalDistCst
class	protocols::abinitio::Stage1Sampler

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

Typedefs
typedef std::pair< core::pose::Pose, core::Real >	protocols::abinitio::PoseWithScore

Functions
static basic::Tracer	tr ("protocols.abinitio.AbrelaxApplication")
bool	protocols::abinitio::sort_PoseWithScore (const PoseWithScore &left, const PoseWithScore &right)

Function Documentation

tr()

static basic::Tracer tr ( "protocols.abinitio.AbrelaxApplication"  )

static

Referenced by protocols::abinitio::AbrelaxApplication::add_constraints(), protocols::abinitio::AbrelaxApplication::check_filters(), protocols::abinitio::AbrelaxApplication::copy_native_structure(), protocols::abinitio::AbrelaxApplication::copy_structure(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::do_rerun(), protocols::abinitio::AbrelaxApplication::fold(), protocols::abinitio::AbrelaxApplication::initialize_constraint_forest(), protocols::abinitio::AbrelaxApplication::process_decoy(), protocols::abinitio::AbrelaxApplication::relax(), protocols::abinitio::AbrelaxApplication::setup(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::abinitio::AbrelaxApplication::setup_fragments(), protocols::abinitio::AbrelaxApplication::setup_jumps(), and protocols::abinitio::AbrelaxApplication::setup_templates().