![]() |
Rosetta Core
2015.09
|
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/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/ContextDependentGeometricSolEnergyCreator.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_GrpElecEnergyCreator.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/FreeDOF_EnergyCreator.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/membrane/MPPairEnergyCreator.hh>
#include <core/scoring/membrane/MPEnvEnergyCreator.hh>
#include <core/scoring/membrane/MPCBetaEnergyCreator.hh>
#include <core/scoring/membrane/MPNonHelixPenaltyCreator.hh>
#include <core/scoring/membrane/MPTerminiPenaltyCreator.hh>
#include <core/scoring/membrane/MPTMProjPenaltyCreator.hh>
#include <core/scoring/membrane/FaMPEnvEnergyCreator.hh>
#include <core/scoring/membrane/FaMPSolvEnergyCreator.hh>
#include <core/scoring/membrane/FaMPEnvSmoothEnergyCreator.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_FullAtomStackingEnergyCreator.hh>
#include <core/scoring/rna/RNA_JR_SuiteEnergyCreator.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_SuiteEnergyCreator.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/rna/data/RNA_ChemicalMappingEnergyCreator.hh>
#include <core/scoring/rna/data/RNA_DataBackboneEnergyCreator.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/fiber_diffraction/FiberDiffractionEnergyCreator.hh>
#include <core/scoring/fiber_diffraction/FiberDiffractionEnergyDensCreator.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/scoring/fiber_diffraction/FiberDiffractionLoaderCreator.hh>
#include <core/scoring/fiber_diffraction/FiberDiffractionOptionsCreator.hh>
#include <core/chemical/ResidueLoaderCreator.hh>
#include <core/chemical/ResidueLoaderOptionsCreator.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 reading in the atom type properties. | |
core::init | |
Typedefs | |
typedef std::ostringstream | ostringstream_t |
Functions | |
static thread_local basic::Tracer | core::init::TR ("core.init") |
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_complex_options () |
After the tracers have been initialized, now go back and modify some of the values in the options system based on (hard coded) inter-flag relationships. Some of these relationships are set in the basic::options::process() function, some of them are handled in this .cc file. 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, 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_resources () |
Set up system resources. 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... | |
options system initialization routines
typedef std::ostringstream ostringstream_t |