init.cc File Reference

options system initialization routines More...

#include <time.h>
#include <core/init/init.hh>
#include <core/svn_version.hh>
#include <core/types.hh>
#include <basic/options/option.hh>
#include <utility/basic_sys_util.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/io/izstream.hh>
#include <basic/Tracer.hh>
#include <basic/prof.hh>
#include <core/init/score_function_corrections.hh>
#include <core/scoring/constraints/ConstraintsEnergyCreator.hh>
#include <core/scoring/disulfides/CentroidDisulfideEnergyCreator.hh>
#include <core/scoring/disulfides/DisulfideMatchingEnergyCreator.hh>
#include <core/scoring/disulfides/FullatomDisulfideEnergyCreator.hh>
#include <core/scoring/etable/EtableEnergyCreator.hh>
#include <core/scoring/hbonds/HBondEnergyCreator.hh>
#include <core/scoring/methods/EnergyMethodRegistrator.hh>
#include <core/scoring/methods/CenPairEnergyCreator.hh>
#include <core/scoring/methods/ChainbreakEnergyCreator.hh>
#include <core/scoring/methods/ContactOrderEnergyCreator.hh>
#include <core/scoring/methods/EnvEnergyCreator.hh>
#include <core/scoring/methods/EnvSmoothEnergyCreator.hh>
#include <core/scoring/methods/IntermolEnergyCreator.hh>
#include <core/scoring/methods/MissingEnergyCreator.hh>
#include <core/scoring/methods/FreeResidueBonusEnergyCreator.hh>
#include <core/scoring/methods/NMerRefEnergyCreator.hh>
#include <core/scoring/methods/NMerPSSMEnergyCreator.hh>
#include <core/scoring/methods/NMerSVMEnergyCreator.hh>
#include <core/scoring/methods/OmegaTetherEnergyCreator.hh>
#include <core/scoring/methods/OtherPoseEnergyCreator.hh>
#include <core/scoring/methods/P_AA_EnergyCreator.hh>
#include <core/scoring/methods/P_AA_pp_EnergyCreator.hh>
#include <core/scoring/methods/PackStatEnergyCreator.hh>
#include <core/scoring/methods/PairEnergyCreator.hh>
#include <core/scoring/methods/PeptideBondEnergyCreator.hh>
#include <core/scoring/methods/ProClosureEnergyCreator.hh>
#include <core/scoring/methods/BurialEnergyCreator.hh>
#include <core/scoring/methods/RG_Energy_FastCreator.hh>
#include <core/scoring/methods/RG_LocalEnergyCreator.hh>
#include <core/scoring/methods/SA_EnergyCreator.hh>
#include <core/scoring/methods/D2H_SA_EnergyCreator.hh>
#include <core/scoring/methods/ProQ_EnergyCreator.hh>
#include <core/scoring/methods/RMS_EnergyCreator.hh>
#include <core/scoring/methods/Rama2BOffsetEnergyCreator.hh>
#include <core/scoring/methods/RamachandranEnergy2BCreator.hh>
#include <core/scoring/methods/RamachandranEnergyCreator.hh>
#include <core/scoring/methods/ReferenceEnergyCreator.hh>
#include <core/scoring/methods/ReferenceEnergyNoncanonicalCreator.hh>
#include <core/scoring/methods/SecondaryStructureEnergyCreator.hh>
#include <core/scoring/methods/dfire/DFIRE_EnergyCreator.hh>
#include <core/scoring/vdwaals/VDW_EnergyCreator.hh>
#include <core/scoring/methods/GoapEnergyCreator.hh>
#include <core/pack/dunbrack/DunbrackEnergyCreator.hh>
#include <core/pack/dunbrack/cenrot/CenRotDunEnergyCreator.hh>
#include <core/scoring/carbon_hbonds/CarbonHBondEnergyCreator.hh>
#include <core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergyCreator.hh>
#include <core/scoring/methods/CustomAtomPairEnergyCreator.hh>
#include <core/scoring/electron_density/FastDensEnergyCreator.hh>
#include <core/scoring/electron_density/ElecDensCenEnergyCreator.hh>
#include <core/scoring/electron_density/ElecDensAllAtomCenEnergyCreator.hh>
#include <core/scoring/electron_density/ElecDensEnergyCreator.hh>
#include <core/scoring/electron_density/PattersonCorrEnergyCreator.hh>
#include <core/scoring/cryst/XtalMLEnergyCreator.hh>
#include <core/scoring/electron_density_atomwise/ElecDensAtomwiseEnergyCreator.hh>
#include <core/scoring/geometric_solvation/ExactOccludedHbondSolEnergyCreator.hh>
#include <core/scoring/geometric_solvation/GeometricSolEnergyCreator.hh>
#include <core/scoring/geometric_solvation/ContextIndependentGeometricSolEnergyCreator.hh>
#include <core/scoring/geometric_solvation/OccludedHbondSolEnergyCreator.hh>
#include <core/scoring/geometric_solvation/OccludedHbondSolEnergy_onebodyCreator.hh>
#include <core/scoring/elec/FA_ElecEnergyCreator.hh>
#include <core/scoring/elec/FA_ElecEnergyAroAroCreator.hh>
#include <core/scoring/elec/FA_ElecEnergyAroAllCreator.hh>
#include <core/scoring/elec/RNA_FA_ElecEnergyCreator.hh>
#include <core/scoring/hackaro/HackAroEnergyCreator.hh>
#include <core/scoring/dna/DNAChiEnergyCreator.hh>
#include <core/scoring/dna/DNATorsionEnergyCreator.hh>
#include <core/scoring/methods/DNA_BaseEnergyCreator.hh>
#include <core/scoring/methods/DirectReadoutEnergyCreator.hh>
#include <core/scoring/methods/DistanceChainbreakEnergyCreator.hh>
#include <core/scoring/methods/Fa_MbenvEnergyCreator.hh>
#include <core/scoring/methods/Fa_MbsolvEnergyCreator.hh>
#include <core/scoring/methods/FreeMoietyEnergyCreator.hh>
#include <core/scoring/methods/HybridVDW_EnergyCreator.hh>
#include <core/scoring/methods/GenBornEnergyCreator.hh>
#include <core/scoring/facts/FACTSEnergyCreator.hh>
#include <core/scoring/methods/LK_PolarNonPolarEnergyCreator.hh>
#include <core/scoring/methods/LK_hackCreator.hh>
#include <core/scoring/methods/LK_BallEnergyCreator.hh>
#include <core/scoring/methods/LinearChainbreakEnergyCreator.hh>
#include <core/scoring/methods/MMBondAngleEnergyCreator.hh>
#include <core/scoring/methods/MMBondLengthEnergyCreator.hh>
#include <core/scoring/methods/CartesianBondedEnergyCreator.hh>
#include <core/scoring/methods/MMTorsionEnergyCreator.hh>
#include <core/scoring/methods/MMLJEnergyIntraCreator.hh>
#include <core/scoring/methods/MMLJEnergyInterCreator.hh>
#include <core/scoring/methods/MembraneCbetaEnergyCreator.hh>
#include <core/scoring/methods/MembraneCenPairEnergyCreator.hh>
#include <core/scoring/methods/MembraneEnvEnergyCreator.hh>
#include <core/scoring/methods/MembraneEnvPenaltiesCreator.hh>
#include <core/scoring/methods/MembraneLipoCreator.hh>
#include <core/scoring/methods/MembraneEnvSmoothEnergyCreator.hh>
#include <core/scoring/methods/pHEnergyCreator.hh>
#include <core/scoring/methods/PoissonBoltzmannEnergyCreator.hh>
#include <core/scoring/methods/ChemicalShiftAnisotropyEnergyCreator.hh>
#include <core/scoring/methods/DipolarCouplingEnergyCreator.hh>
#include <core/scoring/methods/ResidualDipolarCouplingEnergyCreator.hh>
#include <core/scoring/methods/ResidualDipolarCouplingEnergy_RohlCreator.hh>
#include <core/scoring/methods/SmoothCenPairEnergyCreator.hh>
#include <core/scoring/methods/SmoothEnvEnergyCreator.hh>
#include <core/scoring/methods/CenRotPairEnergyCreator.hh>
#include <core/scoring/methods/CenRotEnvEnergyCreator.hh>
#include <core/scoring/methods/CenHBEnergyCreator.hh>
#include <core/scoring/methods/SuckerEnergyCreator.hh>
#include <core/scoring/methods/GaussianOverlapEnergyCreator.hh>
#include <core/scoring/methods/YHHPlanarityEnergyCreator.hh>
#include <core/pack/interaction_graph/SurfaceEnergyCreator.hh>
#include <core/pack/interaction_graph/HPatchEnergyCreator.hh>
#include <core/scoring/methods/SymmetricLigandEnergyCreator.hh>
#include <core/scoring/methods/UnfoldedStateEnergyCreator.hh>
#include <core/scoring/methods/WaterAdductHBondEnergyCreator.hh>
#include <core/scoring/methods/WaterAdductIntraEnergyCreator.hh>
#include <core/scoring/nv/NVscoreCreator.hh>
#include <core/scoring/orbitals/OrbitalsScoreCreator.hh>
#include <core/scoring/interface_/DDPscoreCreator.hh>
#include <core/scoring/packing/HolesEnergyCreator.hh>
#include <core/scoring/packing/SurfVolEnergyCreator.hh>
#include <core/scoring/packing/SurfEnergyCreator.hh>
#include <core/scoring/rna/RG_Energy_RNACreator.hh>
#include <core/scoring/rna/RNA_BulgeEnergyCreator.hh>
#include <core/scoring/rna/RNA_DataBackboneEnergyCreator.hh>
#include <core/scoring/rna/RNA_FullAtomStackingEnergyCreator.hh>
#include <core/scoring/rna/RNA_LJ_BaseEnergyCreator.hh>
#include <core/scoring/rna/RNA_PairwiseLowResolutionEnergyCreator.hh>
#include <core/scoring/rna/RNA_SugarCloseEnergyCreator.hh>
#include <core/scoring/rna/RNA_TorsionEnergyCreator.hh>
#include <core/scoring/rna/RNA_VDW_EnergyCreator.hh>
#include <core/scoring/rna/RNA_Mg_EnergyCreator.hh>
#include <core/scoring/rna/RNA_FullAtomVDW_BasePhosphateCreator.hh>
#include <core/scoring/rna/StackElecEnergyCreator.hh>
#include <core/scoring/rna/chemical_shift/RNA_ChemicalShiftEnergyCreator.hh>
#include <core/scoring/loop_graph/LoopCloseEnergyCreator.hh>
#include <core/scoring/sym_e/symECreator.hh>
#include <core/scoring/saxs/FastSAXSEnergyCreator.hh>
#include <core/scoring/saxs/SAXSEnergyCreator.hh>
#include <core/scoring/saxs/SAXSEnergyCreatorFA.hh>
#include <core/scoring/saxs/SAXSEnergyCreatorCEN.hh>
#include <core/scoring/constraints/ConstraintFactory.hh>
#include <core/scoring/constraints/BasicConstraintCreators.hh>
#include <core/pack/dunbrack/DunbrackConstraintCreator.hh>
#include <core/scoring/constraints/SequenceProfileConstraintCreator.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <core/io/silent/BasicSilentStructCreators.hh>
#include <core/import_pose/PDBSilentStructCreator.hh>
#include <core/sequence/SequenceFactory.hh>
#include <core/sequence/BasicSequenceCreators.hh>
#include <core/pack/task/operation/TaskOperationRegistrator.hh>
#include <core/pack/task/operation/TaskOperationCreators.hh>
#include <core/pack/task/operation/OperateOnCertainResiduesCreator.hh>
#include <core/pack/task/operation/OperateOnResidueSubsetCreator.hh>
#include <core/pack/task/operation/NoRepackDisulfidesCreator.hh>
#include <core/pack/task/operation/OptCysHGCreator.hh>
#include <core/pack/task/operation/OptHCreator.hh>
#include <core/pack/task/operation/ResLvlTaskOperationRegistrator.hh>
#include <core/pack/task/operation/ResLvlTaskOperationCreators.hh>
#include <core/pack/task/operation/ResFilterRegistrator.hh>
#include <core/pack/task/operation/ResFilterCreators.hh>
#include <core/pack/task/operation/ReplicateTaskCreator.hh>
#include <core/pack/task/residue_selector/ResidueSelectorCreators.hh>
#include <core/pack/task/residue_selector/ResidueSelectorRegistrator.hh>
#include <platform/types.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <cstring>
#include <fstream>
#include <sstream>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/resource_manager/ResourceLoaderRegistrator.hh>
#include <core/conformation/symmetry/SymmDataLoaderCreator.hh>
#include <core/conformation/symmetry/SymmDataOptionsCreator.hh>
#include <core/io/silent/SilentFileLoaderCreator.hh>
#include <core/io/silent/SilentFileOptionsCreator.hh>
#include <core/import_pose/PoseFromPDBLoaderCreator.hh>
#include <core/import_pose/import_pose_options_creator.hh>
#include <basic/resource_manager/ResourceOptionsRegistrator.hh>
#include <core/scoring/electron_density/ElectronDensityLoaderCreator.hh>
#include <core/scoring/electron_density/ElectronDensityOptionsCreator.hh>
#include <core/chemical/ResidueLoaderCreator.hh>
#include <core/chemical/ResidueLoaderOptionsCreator.hh>
#include <core/membrane/io/SpanFileLoaderCreator.hh>
#include <core/membrane/io/LipoFileLoaderCreator.hh>
#include <core/membrane/io/EmbedSearchParamsLoaderCreator.hh>
#include <core/membrane/io/EmbedDefLoaderCreator.hh>
#include <core/membrane/io/SpanFileOptionsCreator.hh>
#include <core/membrane/io/LipoFileOptionsCreator.hh>
#include <core/membrane/io/EmbedSearchParamsOptionsCreator.hh>
#include <core/membrane/io/EmbedDefOptionsCreator.hh>
#include <basic/options/keys/LoopModel.OptionKeys.gen.hh>
#include <core/pack/task/operation/ResFilterFactory.hh>
#include <core/pack/task/operation/ResLvlTaskOperationFactory.hh>
#include <core/pack/task/operation/TaskOperationFactory.hh>
#include <core/scoring/ScoringManager.hh>
#include <basic/init.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::init

Typedefs
typedef std::ostringstream	ostringstream_t

Functions
void	core::init::init_mpi (int, char **)
void	core::init::init_options (int argc, char *argv[])
	Initialize the option system, which manages command line options. More...
void	core::init::init_tracers ()
	Tracers control output to std::cout and std::cerr. More...
void	core::init::init_source_revision ()
	Choose to output source version control information? More...
void	core::init::init_paths ()
	Setup basic search paths. More...
void	core::init::check_deprecated_flags ()
	Check for deprecated flags specified by the user and output error messages if necessary. More...
void	core::init::report_application_command (int argc, char *argv[])
	Describe the application execution command. More...
void	core::init::init_random_number_generators ()
	Initalize random number generators. More...
void	core::init::init_random_generators (int const start_seed, RND_RunType run_type, std::string const &RGtype)
	Initialize random generator systems (and send debug io to tracer with seed/mode info). More...
void	core::init::random_delay ()
	Choose to randomly delay execution to desyncronize parallel execution. More...
void	core::init::locate_rosetta_database ()
	Locate rosetta_database. More...
void	core::init::init_profiling ()
	Profiling measures execution performance. More...
void	core::init::init (int argc, char *argv[])
	Init basic core systems: options system, random system. More...
void	core::init::init (utility::vector1< std::string > const &args)
	wrapper for core system Init More...

Variables
static EnergyMethodRegistrator < scoring::constraints::ConstraintsEnergyCreator >	core::init::ConstraintsEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::disulfides::CentroidDisulfideEnergyCreator >	core::init::CentroidDisulfideEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::disulfides::DisulfideMatchingEnergyCreator >	core::init::DisulfideMatchingEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::disulfides::FullatomDisulfideEnergyCreator >	core::init::FullatomDisulfideEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::etable::EtableEnergyCreator >	core::init::EtableEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::hbonds::HBondEnergyCreator >	core::init::HBondEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ChainbreakEnergyCreator >	core::init::ChainbreakEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::CenPairEnergyCreator >	core::init::CenPairEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ContactOrderEnergyCreator >	core::init::ContactOrderEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::IntermolEnergyCreator >	core::init::IntermolEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MissingEnergyCreator >	core::init::MissingEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::EnvEnergyCreator >	core::init::EnvEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::EnvSmoothEnergyCreator >	core::init::EnvSmoothEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::OmegaTetherEnergyCreator >	core::init::OmegaTetherEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::OtherPoseEnergyCreator >	core::init::OtherPoseEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::NMerRefEnergyCreator >	core::init::NMerRefEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::NMerPSSMEnergyCreator >	core::init::NMerPSSMEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::NMerSVMEnergyCreator >	core::init::NMerSVMEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::P_AA_EnergyCreator >	core::init::P_AA_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::P_AA_pp_EnergyCreator >	core::init::P_AA_pp_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::PackStatEnergyCreator >	core::init::PackStatEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::PairEnergyCreator >	core::init::PairEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::PeptideBondEnergyCreator >	core::init::PeptideBondEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ProClosureEnergyCreator >	core::init::ProClosureEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::BurialEnergyCreator >	core::init::BurialCreator_registrator
static EnergyMethodRegistrator < scoring::methods::RG_Energy_FastCreator >	core::init::RG_Energy_FastCreator_registrator
static EnergyMethodRegistrator < scoring::methods::RG_LocalEnergyCreator >	core::init::RG_LocalEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::SA_EnergyCreator >	core::init::SA_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::D2H_SA_EnergyCreator >	core::init::D2H_SA_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ProQ_EnergyCreator >	core::init::ProQ_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::RMS_EnergyCreator >	core::init::RMS_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::Rama2BOffsetEnergyCreator >	core::init::Ramac2BOffsetEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::RamachandranEnergy2BCreator >	core::init::RamachandranEnergy2BCreator_registrator
static EnergyMethodRegistrator < scoring::methods::RamachandranEnergyCreator >	core::init::RamachandranEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ReferenceEnergyCreator >	core::init::ReferenceEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ReferenceEnergyNoncanonicalCreator >	core::init::ReferenceEnergyNoncanonicalCreator_registrator
static EnergyMethodRegistrator < scoring::methods::SecondaryStructureEnergyCreator >	core::init::SecondaryStructureEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::dfire::DFIRE_EnergyCreator >	core::init::DFIRE_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::vdwaals::VDW_EnergyCreator >	core::init::VDW_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::GoapEnergyCreator >	core::init::GoapEnergyCreator_registrator
static EnergyMethodRegistrator < pack::dunbrack::DunbrackEnergyCreator >	core::init::DunbrackEnergyCreator_registrator
static EnergyMethodRegistrator < pack::dunbrack::cenrot::CenRotDunEnergyCreator >	core::init::CenRotDunEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::nv::NVscoreCreator >	core::init::NVscoreCreator_registrator
static EnergyMethodRegistrator < scoring::orbitals::OrbitalsScoreCreator >	core::init::OrbitalsScoreCreator_registrator
static EnergyMethodRegistrator < scoring::interface_::DDPscoreCreator >	core::init::DDPscoreCreator_registrator
static EnergyMethodRegistrator < scoring::carbon_hbonds::CarbonHBondEnergyCreator >	core::init::CarbonHBondEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::custom_pair_distance::FullatomCustomPairDistanceEnergyCreator >	core::init::FullatomCustomPairDistanceEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::CustomAtomPairEnergyCreator >	core::init::CustomAtomPairEnergy_registrator
static EnergyMethodRegistrator < scoring::electron_density::FastDensEnergyCreator >	core::init::FastDensEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::electron_density::ElecDensCenEnergyCreator >	core::init::ElecDensCenEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::electron_density::ElecDensAllAtomCenEnergyCreator >	core::init::ElecDensAllAtomCenEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::electron_density::ElecDensEnergyCreator >	core::init::ElecDensEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::electron_density::PattersonCorrEnergyCreator >	core::init::PattersonCorrEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::cryst::XtalMLEnergyCreator >	core::init::XtalMLEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::electron_density_atomwise::ElecDensAtomwiseEnergyCreator >	core::init::ElecDensAtomwiseEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::geometric_solvation::ExactOccludedHbondSolEnergyCreator >	core::init::ExactOccludedHbondSolEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::geometric_solvation::GeometricSolEnergyCreator >	core::init::GeometricSolEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::geometric_solvation::ContextIndependentGeometricSolEnergyCreator >	core::init::ContextIndependentGeometricSolEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::geometric_solvation::OccludedHbondSolEnergyCreator >	core::init::OccludedHbondSolEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::geometric_solvation::OccludedHbondSolEnergy_onebodyCreator >	core::init::OccludedHbondSolEnergy_onebodyCreator_registrator
static EnergyMethodRegistrator < scoring::elec::FA_ElecEnergyCreator >	core::init::FA_ElecEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::elec::RNA_FA_ElecEnergyCreator >	core::init::RNA_FA_ElecEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::elec::FA_ElecEnergyAroAroCreator >	core::init::FA_ElecEnergyAroAroCreator_registrator
static EnergyMethodRegistrator < scoring::elec::FA_ElecEnergyAroAllCreator >	core::init::FA_ElecEnergyAroAllCreator_registrator
static EnergyMethodRegistrator < scoring::hackaro::HackAroEnergyCreator >	core::init::HackAroEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::dna::DNAChiEnergyCreator >	core::init::DNAChiEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::dna::DNATorsionEnergyCreator >	core::init::DNATorsionEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::loop_graph::LoopCloseEnergyCreator >	core::init::LoopCloseEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::DNA_BaseEnergyCreator >	core::init::DNA_BaseEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::DirectReadoutEnergyCreator >	core::init::DirectReadoutEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::DistanceChainbreakEnergyCreator >	core::init::DistanceChainbreakEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::Fa_MbenvEnergyCreator >	core::init::Fa_MbenvEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::Fa_MbsolvEnergyCreator >	core::init::Fa_MbsolvEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::FreeMoietyEnergyCreator >	core::init::FreeMoietyEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::GenBornEnergyCreator >	core::init::GenBornEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::FACTSEnergyCreator >	core::init::FACTSEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::HybridVDW_EnergyCreator >	core::init::HybridVDW_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::LK_PolarNonPolarEnergyCreator >	core::init::LK_PolarNonPolarEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::LK_hackCreator >	core::init::LK_hackCreator_registrator
static EnergyMethodRegistrator < scoring::methods::LK_BallEnergyCreator >	core::init::LK_BallEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::LinearChainbreakEnergyCreator >	core::init::LinearChainbreakEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MMBondAngleEnergyCreator >	core::init::MMBondAngleEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::CartesianBondedEnergyCreator >	core::init::CartesianBondedEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MMBondLengthEnergyCreator >	core::init::MMBondLengthEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MMTorsionEnergyCreator >	core::init::MMTorsionEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MMLJEnergyInterCreator >	core::init::MMLJEnergyInterCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MMLJEnergyIntraCreator >	core::init::MMLJEnergyIntraCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MembraneCbetaEnergyCreator >	core::init::MembraneCbetaEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MembraneCenPairEnergyCreator >	core::init::MembraneCenPairEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MembraneEnvEnergyCreator >	core::init::MembraneEnvEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MembraneEnvPenaltiesCreator >	core::init::MembraneEnvPenaltiesCreator_registrator
static EnergyMethodRegistrator < scoring::methods::SmoothCenPairEnergyCreator >	core::init::SmoothCenPairEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::SmoothEnvEnergyCreator >	core::init::SmoothEnvEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::CenRotPairEnergyCreator >	core::init::CenRotPairEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::CenRotEnvEnergyCreator >	core::init::CenRotEnvEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::CenHBEnergyCreator >	core::init::CenHBEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MembraneLipoCreator >	core::init::MembraneLipoCreator_registrator
static EnergyMethodRegistrator < scoring::methods::MembraneEnvSmoothEnergyCreator >	core::init::MembraneEnvSmoothEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::pHEnergyCreator >	core::init::pHEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ChemicalShiftAnisotropyEnergyCreator >	core::init::ChemicalShiftAnisotropyEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::DipolarCouplingEnergyCreator >	core::init::DipolarCouplingEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ResidualDipolarCouplingEnergyCreator >	core::init::ResidualDipolarCouplingEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::ResidualDipolarCouplingEnergy_RohlCreator >	core::init::ResidualDipolarCouplingEnergy_RohlCreator_registrator
static EnergyMethodRegistrator < scoring::methods::SuckerEnergyCreator >	core::init::SuckerEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::GaussianOverlapEnergyCreator >	core::init::GaussianOverlapEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::YHHPlanarityEnergyCreator >	core::init::YYHPlanarityEnergyCreator_registrator
static EnergyMethodRegistrator < pack::interaction_graph::SurfaceEnergyCreator >	core::init::SurfaceEnergyCreator_registrator
static EnergyMethodRegistrator < pack::interaction_graph::HPatchEnergyCreator >	core::init::HPatchEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::SymmetricLigandEnergyCreator >	core::init::SymmetricLigandEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::UnfoldedStateEnergyCreator >	core::init::UnfoldedStateEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::WaterAdductHBondEnergyCreator >	core::init::WaterAdductHBondEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::methods::WaterAdductIntraEnergyCreator >	core::init::WaterAdductIntraEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::packing::HolesEnergyCreator >	core::init::HolesEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::packing::SurfVolEnergyCreator >	core::init::SurfVolEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::packing::SurfEnergyCreator >	core::init::SurfEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RG_Energy_RNACreator >	core::init::RG_Energy_RNACreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_BulgeEnergyCreator >	core::init::RNA_BulgeEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_DataBackboneEnergyCreator >	core::init::RNA_DataBackboneEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_FullAtomStackingEnergyCreator >	core::init::RNA_FullAtomStackingEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_LJ_BaseEnergyCreator >	core::init::RNA_LJ_BaseEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_PairwiseLowResolutionEnergyCreator >	core::init::RNA_PairwiseLowResolutionEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_SugarCloseEnergyCreator >	core::init::RNA_SugarCloseEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_TorsionEnergyCreator >	core::init::RNA_TorsionEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_VDW_EnergyCreator >	core::init::RNA_VDW_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_Mg_EnergyCreator >	core::init::RNA_Mg_EnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::RNA_FullAtomVDW_BasePhosphateCreator >	core::init::RNA_FullAtomVDW_BasePhosphateCreator_registrator
static EnergyMethodRegistrator < scoring::rna::StackElecEnergyCreator >	core::init::StackElecEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::rna::chemical_shift::RNA_ChemicalShiftEnergyCreator >	core::init::NA_ChemicalShiftEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::sym_e::symECreator >	core::init::symECreator_registrator
static EnergyMethodRegistrator < scoring::methods::PoissonBoltzmannEnergyCreator >	core::init::PoissonBoltzmannEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::saxs::FastSAXSEnergyCreator >	core::init::FastSAXSEnergyCreator_registrator
static EnergyMethodRegistrator < scoring::saxs::SAXSEnergyCreatorCEN >	core::init::SAXSEnergyCreatorCEN_registrator
static EnergyMethodRegistrator < scoring::saxs::SAXSEnergyCreatorFA >	core::init::SAXSEnergyCreatorFA_registrator
static EnergyMethodRegistrator < scoring::saxs::SAXSEnergyCreator >	core::init::SAXSEnergyCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::AmbiguousConstraintCreator >	core::init::AmbiguousConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::AmbiguousNMRConstraintCreator >	core::init::AmbiguousNMRConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::AmbiguousNMRDistanceConstraintCreator >	core::init::AmbiguousNMRDistanceConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::AngleConstraintCreator >	core::init::AngleConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::AtomPairConstraintCreator >	core::init::AtomPairConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::BigBinConstraintCreator >	core::init::BigBinConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::CoordinateConstraintCreator >	core::init::CoordinateConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::DihedralConstraintCreator >	core::init::DihedralConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::DihedralPairConstraintCreator >	core::init::DihedralPairConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::KofNConstraintCreator >	core::init::KofNConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::LocalCoordinateConstraintCreator >	core::init::LocalCoordinateConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::MultiConstraintCreator >	core::init::MultiConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::FabConstraintCreator >	core::init::FabConstraintCreator_registrator
static ConstraintRegistrator < core::pack::dunbrack::DunbrackConstraintCreator >	core::init::DunbrackConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::SiteConstraintCreator >	core::init::SiteConstraintCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::SiteConstraintResiduesCreator >	core::init::SiteConstraintResiduesCreator_registrator
static ConstraintRegistrator < core::scoring::constraints::SequenceProfileConstraintCreator >	core::init::SequenceProfileConstraintCreator_registrator
static SilentStructRegistrator < core::io::silent::ProteinSilentStructCreator >	core::init::ProteinSilentStructCreator_registrator
static SilentStructRegistrator < core::io::silent::ProteinSilentStruct_SinglePrecCreator >	core::init::ProteinSilentStruct_SinglePrecCreator_registrator
static SilentStructRegistrator < core::io::silent::RNA_SilentStructCreator >	core::init::RNA_SilentStructCreator_registrator
static SilentStructRegistrator < core::import_pose::PDBSilentStructCreator >	core::init::PDBSilentStructCreator_registrator
static SilentStructRegistrator < core::io::silent::BinarySilentStructCreator >	core::init::BinarySilentStructCreator_registrator
static SilentStructRegistrator < core::io::silent::ScoreFileSilentStructCreator >	core::init::ScoreFileSilentStructCreator_registrator
static SilentStructRegistrator < core::io::silent::ScoreJumpFileSilentStructCreator >	core::init::ScoreJumpFileSilentStructCreator_registrator
static SequenceRegistrator < core::sequence::SimpleSequenceCreator >	core::init::SimpleSequenceCreator_registrator
static SequenceRegistrator < core::sequence::SequenceProfileCreator >	core::init::SequenceProfileCreator_registrator
static SequenceRegistrator < core::sequence::SequenceCouplingCreator >	core::init::SequenceCouplingCreator_registrator
static SequenceRegistrator < core::sequence::CompositeSequenceCreator >	core::init::CompositeSequenceCreator_registrator
static TaskOperationRegistrator < RestrictYSDesignCreator >	core::init::RestrictYSDesignCreator_registrator
static TaskOperationRegistrator < PreventRepackingCreator >	core::init::PreventRepackingCreator_registrator
static TaskOperationRegistrator < PreserveCBetaCreator >	core::init::PreserveCBetaCreator_registrator
static TaskOperationRegistrator < AppendRotamerSetCreator >	core::init::AppendRotamerSetCreator_registrator
static TaskOperationRegistrator < AppendRotamerCreator >	core::init::AppendRotamerCreator_registrator
static TaskOperationRegistrator < ExtraRotamersCreator >	core::init::ExtraRotamersCreator_registrator
static TaskOperationRegistrator < ExtraChiCutoffCreator >	core::init::ExtraChiCutoffCreator_registrator
static TaskOperationRegistrator < SetRotamerCouplingsCreator >	core::init::SetRotamerCouplingsCreator_registrator
static TaskOperationRegistrator < SetRotamerLinksCreator >	core::init::SetRotamerLinksCreator_registrator
static TaskOperationRegistrator < ReadResfileCreator >	core::init::ReadResfileCreator_registrator
static TaskOperationRegistrator < ReadResfileAndObeyLengthEventsCreator >	core::init::ReadResfileAndObeyLengthEventsCreator_registrator
static TaskOperationRegistrator < IncludeCurrentCreator >	core::init::IncludeCurrentCreator_registrator
static TaskOperationRegistrator < InitializeExtraRotsFromCommandlineCreator >	core::init::InitializeExtraRotsFromCommandlineCreator_registrator
static TaskOperationRegistrator < InitializeFromCommandlineCreator >	core::init::InitializeFromCommandlineCreator_registrator
static TaskOperationRegistrator < ExtraRotamersGenericCreator >	core::init::ExtraRotamersGenericCreator_registrator
static TaskOperationRegistrator < RotamerExplosionCreator >	core::init::RotamerExplosionCreator_registrator
static TaskOperationRegistrator < RestrictAbsentCanonicalAASCreator >	core::init::RestrictAbsentCanonicalAASCreator_registrator
static TaskOperationRegistrator < DisallowIfNonnativeCreator >	core::init::DisallowIfNonnativeCreator_registrator
static TaskOperationRegistrator < RestrictResidueToRepackingCreator >	core::init::RestrictResidueToRepackingCreator_registrator
static TaskOperationRegistrator < RestrictToRepackingCreator >	core::init::RestrictToRepackingCreator_registrator
static TaskOperationRegistrator < OperateOnCertainResiduesCreator >	core::init::OperateOnCertainResiduesCreator_registrator
static TaskOperationRegistrator < OperateOnResidueSubsetCreator >	core::init::OperateOnResidueSubsetCreator_registrator
static TaskOperationRegistrator < NoRepackDisulfidesCreator >	core::init::NoRepackDisulfidesCreator_registrator
static TaskOperationRegistrator < ReplicateTaskCreator >	core::init::ReplicateTaskCreator_registrator
static TaskOperationRegistrator < OptCysHGCreator >	core::init::OptCysHGCreator_registrator
static TaskOperationRegistrator < OptHCreator >	core::init::OptHCreator_registrator
static ResLvlTaskOperationRegistrator < RestrictToRepackingRLTCreator >	core::init::RestrictToRepackingRLTCreator_registrator
static ResLvlTaskOperationRegistrator < RestrictAbsentCanonicalAASRLTCreator >	core::init::RestrictAbsentCanonicalAASRLTCreator_registrator
static ResLvlTaskOperationRegistrator < DisallowIfNonnativeRLTCreator >	core::init::DisallowIfNonnativeRLTCreator_registrator
static ResLvlTaskOperationRegistrator < PreventRepackingRLTCreator >	core::init::PreventRepackingRLTCreator_registrator
static ResLvlTaskOperationRegistrator < AddBehaviorRLTCreator >	core::init::AddBehaviorRLTCreator_registrator
static ResFilterRegistrator < ResidueHasPropertyCreator >	core::init::ResidueHasPropertyCreator_registrator
static ResFilterRegistrator < ResiduePDBInfoHasLabelCreator >	core::init::ResiduePDBInfoHasLabelCreator_registrator
static ResFilterRegistrator < ResidueLacksPropertyCreator >	core::init::ResidueLacksPropertyCreator_registrator
static ResFilterRegistrator < ResidueName3IsCreator >	core::init::ResidueName3IsCreator_registrator
static ResFilterRegistrator < ResidueName3IsntCreator >	core::init::ResidueName3IsntCreator_registrator
static ResFilterRegistrator < ResidueIndexIsCreator >	core::init::ResidueIndexIsCreator_registrator
static ResFilterRegistrator < ResidueIndexIsntCreator >	core::init::ResidueIndexIsntCreator_registrator
static ResFilterRegistrator < ResiduePDBIndexIsCreator >	core::init::ResiduePDBIndexIsCreator_registrator
static ResFilterRegistrator < ResiduePDBIndexIsntCreator >	core::init::ResiduePDBIndexIsntCreator_registrator
static ResFilterRegistrator < ChainIsCreator >	core::init::ChainIsCreator_registrator
static ResFilterRegistrator < ChainIsntCreator >	core::init::ChainIsntCreator_registrator
static ResFilterRegistrator < AnyResFilterCreator >	core::init::AnyResFilterCreator_registrator
static ResFilterRegistrator < AllResFilterCreator >	core::init::AllResFilterCreator_registrator
static ResFilterRegistrator < NoResFilterCreator >	core::init::NoResFilterCreator_registrator
static ResFilterRegistrator < ResidueTypeFilterCreator >	core::init::ResidueTypeResFilterCreator_registrator
static ResidueSelectorRegistrator < AndResidueSelectorCreator >	core::init::reg_AndResidueSelectorCreator
static ResidueSelectorRegistrator < ChainSelectorCreator >	core::init::reg_ChainSelectorCreator
static ResidueSelectorRegistrator < InterGroupInterfaceByVectorSelectorCreator >	core::init::reg_InterGroupInterfaceByVectorSelectorCreator
static ResidueSelectorRegistrator < JumpDownstreamSelectorCreator >	core::init::reg_JumpDownstreamSelectorCreator
static ResidueSelectorRegistrator < JumpUpstreamSelectorCreator >	core::init::reg_JumpUpstreamSelectorCreator
static ResidueSelectorRegistrator < NeighborhoodResidueSelectorCreator >	core::init::reg_NeighborhoodResidueSelectorCreator
static ResidueSelectorRegistrator < NotResidueSelectorCreator >	core::init::reg_NotResidueSelectorCreator
static ResidueSelectorRegistrator < NumNeighborsSelectorCreator >	core::init::reg_NumNeighborsSelectorCreator
static ResidueSelectorRegistrator < OrResidueSelectorCreator >	core::init::reg_OrResidueSelectorCreator
static ResidueSelectorRegistrator < ResidueIndexSelectorCreator >	core::init::reg_ResidueIndexSelectorCreator
static ResourceLoaderRegistrator < core::conformation::symmetry::SymmDataLoaderCreator >	core::init::SymmDataLoaderCreator_registrator
static ResourceLoaderRegistrator < core::io::silent::SilentFileLoaderCreator >	core::init::SilentFileLoaderCreator_registrator
static ResourceLoaderRegistrator < core::import_pose::PoseFromPDBLoaderCreator >	core::init::PoseFromPDBLoaderCreator_registrator
static ResourceLoaderRegistrator < core::scoring::electron_density::ElectronDensityLoaderCreator >	core::init::ElectronDensityLoaderCreator_registrator
static ResourceLoaderRegistrator < core::chemical::ResidueLoaderCreator >	core::init::ResidueLoaderCreator_registrator
static ResourceLoaderRegistrator < core::membrane::io::EmbedSearchParamsLoaderCreator >	core::init::EmbedSearchParamsLoaderCreator_registrator
static ResourceLoaderRegistrator < core::membrane::io::SpanFileLoaderCreator >	core::init::SpanFileLoaderCreator_registrator
static ResourceLoaderRegistrator < core::membrane::io::LipoFileLoaderCreator >	core::init::LipOFileLoaderCreator_registrator
static ResourceLoaderRegistrator < core::membrane::io::EmbedDefLoaderCreator >	core::init::EmbedDefLoaderCreator_registrator
static ResourceOptionsRegistrator < core::conformation::symmetry::SymmDataOptionsCreator >	core::init::SymmDataOptionsCreator_registrator
static ResourceOptionsRegistrator < core::import_pose::ImportPoseOptionsCreator >	core::init::ImportPoseOptionsCreator_registrator
static ResourceOptionsRegistrator < core::io::silent::SilentFileOptionsCreator >	core::init::SilentFileOptionsCreator_registrator
static ResourceOptionsRegistrator < core::scoring::electron_density::ElectronDensityOptionsCreator >	core::init::ElectronDensityOptionsCreator_registrator
static ResourceOptionsRegistrator < core::chemical::ResidueLoaderOptionsCreator >	core::init::ResiudeLoaderOptionsCreator_registrator
static ResourceOptionsRegistrator < core::membrane::io::EmbedSearchParamsOptionsCreator >	core::init::EmbedSearchParamsOptionsCreator_registrator
static ResourceOptionsRegistrator < core::membrane::io::SpanFileOptionsCreator >	core::init::SpanFileOptionsCreator_registrator
static ResourceOptionsRegistrator < core::membrane::io::LipoFileOptionsCreator >	core::init::LipoFileLoaderCreator_registrator
static ResourceOptionsRegistrator < core::membrane::io::EmbedDefOptionsCreator >	core::init::EmbedDefOptionsCreator_registrator
static basic::Tracer	core::init::TR ("core.init")

Detailed Description

options system initialization routines

Author

Sergey Lyskov

Typedef Documentation

typedef std::ostringstream ostringstream_t