Rosetta
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options system initialization routines More...
#include <core/init/init.hh>
#include <core/types.hh>
#include <core/id/bogus.hh>
#include <basic/options/option.hh>
#include <utility/sys_util.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/io/izstream.hh>
#include <basic/Tracer.hh>
#include <basic/prof.hh>
#include <core/chemical/bcl/util.hh>
#include <core/chemical/rdkit/util.hh>
#include <basic/random/init_random_generator.hh>
#include <numeric/random/random.hh>
#include <core/chemical/rotamers/RotamerLibrarySpecificationFactory.hh>
#include <core/pack/palette/PackerPaletteFactory.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryFactory.hh>
#include <core/select/jump_selector/JumpSelectorFactory.hh>
#include <core/select/residue_selector/ResidueSelectorFactory.hh>
#include <basic/resource_manager/ResourceLoaderFactory.hh>
#include <core/init/score_function_corrections.hh>
#include <core/energy_methods/AACompositionEnergyCreator.hh>
#include <core/energy_methods/AARepeatEnergyCreator.hh>
#include <core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/ApproximateBuriedUnsatPenaltyCreator.hh>
#include <core/pack/guidance_scoreterms/buried_unsat_penalty/BuriedUnsatPenaltyCreator.hh>
#include <core/scoring/constraints/ConstraintsEnergyCreator.hh>
#include <core/energy_methods/CentroidDisulfideEnergyCreator.hh>
#include <core/energy_methods/DisulfideMatchingEnergyCreator.hh>
#include <core/energy_methods/FullatomDisulfideEnergyCreator.hh>
#include <core/scoring/etable/EtableEnergyCreator.hh>
#include <core/pack/guidance_scoreterms/hbnet_energy/HBNetEnergyCreator.hh>
#include <core/scoring/hbonds/HBondEnergyCreator.hh>
#include <core/energy_methods/NPDHBondEnergyCreator.hh>
#include <core/scoring/methods/EnergyMethodRegistrator.hh>
#include <core/energy_methods/ArgCationPiEnergyCreator.hh>
#include <core/energy_methods/AspartimidePenaltyEnergyCreator.hh>
#include <core/energy_methods/CenPairEnergyCreator.hh>
#include <core/energy_methods/ChainbreakEnergyCreator.hh>
#include <core/energy_methods/BranchEnergyCreator.hh>
#include <core/energy_methods/ContactOrderEnergyCreator.hh>
#include <core/energy_methods/EnvEnergyCreator.hh>
#include <core/energy_methods/EnvSmoothEnergyCreator.hh>
#include <core/energy_methods/IntermolEnergyCreator.hh>
#include <core/energy_methods/MissingEnergyCreator.hh>
#include <core/scoring/nmer/NMerRefEnergyCreator.hh>
#include <core/scoring/nmer/NMerPSSMEnergyCreator.hh>
#include <core/scoring/nmer/NMerSVMEnergyCreator.hh>
#include <core/energy_methods/OmegaTetherEnergyCreator.hh>
#include <core/energy_methods/OtherPoseEnergyCreator.hh>
#include <core/energy_methods/P_AA_EnergyCreator.hh>
#include <core/energy_methods/P_AA_ss_EnergyCreator.hh>
#include <core/energy_methods/P_AA_pp_EnergyCreator.hh>
#include <core/energy_methods/AbegoEnergyCreator.hh>
#include <core/energy_methods/PackStatEnergyCreator.hh>
#include <core/energy_methods/PairEnergyCreator.hh>
#include <core/energy_methods/PeptideBondEnergyCreator.hh>
#include <core/energy_methods/ProClosureEnergyCreator.hh>
#include <core/energy_methods/BurialEnergyCreator.hh>
#include <core/energy_methods/Burial_v2EnergyCreator.hh>
#include <core/energy_methods/HRF_MSLabelingEnergyCreator.hh>
#include <core/energy_methods/HRFDynamicsEnergyCreator.hh>
#include <core/energy_methods/CCS_IMMSEnergyCreator.hh>
#include <core/energy_methods/CovalentLabelingEnergyCreator.hh>
#include <core/energy_methods/CovalentLabelingFAEnergyCreator.hh>
#include <core/energy_methods/DEPC_MS_EnergyCreator.hh>
#include <core/energy_methods/RG_Energy_FastCreator.hh>
#include <core/energy_methods/RG_LocalEnergyCreator.hh>
#include <core/energy_methods/SA_EnergyCreator.hh>
#include <core/energy_methods/SSElementMotifContactEnergyCreator.hh>
#include <core/energy_methods/D2H_SA_EnergyCreator.hh>
#include <core/energy_methods/ProQ_EnergyCreator.hh>
#include <core/energy_methods/RMS_EnergyCreator.hh>
#include <core/energy_methods/RamaPreProEnergyCreator.hh>
#include <core/energy_methods/RamachandranEnergy2BCreator.hh>
#include <core/energy_methods/RamachandranEnergyCreator.hh>
#include <core/energy_methods/ReferenceEnergyCreator.hh>
#include <core/energy_methods/ReferenceEnergyNoncanonicalCreator.hh>
#include <core/energy_methods/SecondaryStructureEnergyCreator.hh>
#include <core/energy_methods/SugarBackboneEnergyCreator.hh>
#include <core/energy_methods/DFIRE_EnergyCreator.hh>
#include <core/pack/guidance_scoreterms/sap/SapConstraintEnergyCreator.hh>
#include <core/scoring/vdwaals/VDW_EnergyCreator.hh>
#include <core/energy_methods/GoapEnergyCreator.hh>
#include <core/energy_methods/RingClosureEnergyCreator.hh>
#include <core/energy_methods/AromaticBackboneRestraintEnergyCreator.hh>
#include <core/energy_methods/MHCEpitopeEnergyCreator.hh>
#include <core/energy_methods/DumpTrajectoryEnergyCreator.hh>
#include <core/energy_methods/NetChargeEnergyCreator.hh>
#include <core/pack/dunbrack/DunbrackEnergyCreator.hh>
#include <core/pack/dunbrack/cenrot/CenRotDunEnergyCreator.hh>
#include <core/pack/guidance_scoreterms/voids_penalty_energy/VoidsPenaltyEnergyCreator.hh>
#include <core/scoring/carbon_hbonds/CarbonHBondEnergyCreator.hh>
#include <core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergyCreator.hh>
#include <core/energy_methods/CustomAtomPairEnergyCreator.hh>
#include <core/energy_methods/FastDensEnergyCreator.hh>
#include <core/energy_methods/ElecDensCenEnergyCreator.hh>
#include <core/energy_methods/ElecDensAllAtomCenEnergyCreator.hh>
#include <core/energy_methods/ElecDensEnergyCreator.hh>
#include <core/energy_methods/XtalMLEnergyCreator.hh>
#include <core/energy_methods/ElecDensAtomwiseEnergyCreator.hh>
#include <core/energy_methods/ExactOccludedHbondSolEnergyCreator.hh>
#include <core/energy_methods/ContextDependentGeometricSolEnergyCreator.hh>
#include <core/energy_methods/ContextIndependentGeometricSolEnergyCreator.hh>
#include <core/energy_methods/OccludedHbondSolEnergyCreator.hh>
#include <core/energy_methods/OccludedHbondSolEnergy_onebodyCreator.hh>
#include <core/energy_methods/DEEREnergyCreator.hh>
#include <core/scoring/elec/FA_ElecEnergyCreator.hh>
#include <core/energy_methods/ImplicitMembraneElecEnergyCreator.hh>
#include <core/energy_methods/FA_GrpElecEnergyCreator.hh>
#include <core/energy_methods/FA_ElecEnergyAroAroCreator.hh>
#include <core/energy_methods/FA_ElecEnergyAroAllCreator.hh>
#include <core/energy_methods/RNA_FA_ElecEnergyCreator.hh>
#include <core/energy_methods/HackAroEnergyCreator.hh>
#include <core/energy_methods/DNAChiEnergyCreator.hh>
#include <core/energy_methods/DNATorsionEnergyCreator.hh>
#include <core/energy_methods/DNA_BaseEnergyCreator.hh>
#include <core/energy_methods/DNA_DihedralEnergyCreator.hh>
#include <core/energy_methods/DirectReadoutEnergyCreator.hh>
#include <core/energy_methods/DistanceChainbreakEnergyCreator.hh>
#include <core/energy_methods/Fa_MbenvEnergyCreator.hh>
#include <core/energy_methods/Fa_MbsolvEnergyCreator.hh>
#include <core/energy_methods/FreeDOF_EnergyCreator.hh>
#include <core/energy_methods/HybridVDW_EnergyCreator.hh>
#include <core/energy_methods/GenBornEnergyCreator.hh>
#include <core/energy_methods/GenericBondedEnergyCreator.hh>
#include <core/energy_methods/VdWTinkerEnergyCreator.hh>
#include <core/energy_methods/MultipoleElecEnergyCreator.hh>
#include <core/energy_methods/SASAEnergyCreator.hh>
#include <core/energy_methods/FACTSEnergyCreator.hh>
#include <core/energy_methods/LK_PolarNonPolarEnergyCreator.hh>
#include <core/energy_methods/LK_hackCreator.hh>
#include <core/scoring/lkball/LK_BallEnergyCreator.hh>
#include <core/energy_methods/LinearChainbreakEnergyCreator.hh>
#include <core/energy_methods/LinearBranchEnergyCreator.hh>
#include <core/scoring/lkball/LK_DomeEnergyCreator.hh>
#include <core/pack/guidance_scoreterms/lk_dome/LK_DomePackEnergyCreator.hh>
#include <core/scoring/methods/MMBondAngleEnergyCreator.hh>
#include <core/scoring/methods/MMBondLengthEnergyCreator.hh>
#include <core/energy_methods/CartesianBondedEnergyCreator.hh>
#include <core/scoring/methods/MMTorsionEnergyCreator.hh>
#include <core/scoring/methods/MMLJEnergyIntraCreator.hh>
#include <core/scoring/methods/MMLJEnergyInterCreator.hh>
#include <core/energy_methods/MembraneCbetaEnergyCreator.hh>
#include <core/energy_methods/MembraneCenPairEnergyCreator.hh>
#include <core/energy_methods/MembraneEnvEnergyCreator.hh>
#include <core/energy_methods/MembraneEnvPenaltiesCreator.hh>
#include <core/energy_methods/MembraneLipoCreator.hh>
#include <core/energy_methods/MembraneEnvSmoothEnergyCreator.hh>
#include <core/energy_methods/MPPairEnergyCreator.hh>
#include <core/energy_methods/MPEnvEnergyCreator.hh>
#include <core/energy_methods/MPCBetaEnergyCreator.hh>
#include <core/scoring/membrane/MPNonHelixPenaltyCreator.hh>
#include <core/scoring/membrane/MPTerminiPenaltyCreator.hh>
#include <core/scoring/membrane/MPTMProjPenaltyCreator.hh>
#include <core/energy_methods/FaMPEnvEnergyCreator.hh>
#include <core/energy_methods/FaMPSolvEnergyCreator.hh>
#include <core/energy_methods/FaMPEnvSmoothEnergyCreator.hh>
#include <core/energy_methods/FaMPAsymEzCBEnergyCreator.hh>
#include <core/energy_methods/FaMPAsymEzCGEnergyCreator.hh>
#include <core/energy_methods/MPResidueLipophilicityEnergyCreator.hh>
#include <core/energy_methods/MPHelicalityEnergyCreator.hh>
#include <core/energy_methods/MPSpanInsertionEnergyCreator.hh>
#include <core/energy_methods/MPSpanAngleEnergyCreator.hh>
#include <core/energy_methods/pHEnergyCreator.hh>
#include <core/energy_methods/PoissonBoltzmannEnergyCreator.hh>
#include <core/energy_methods/ChemicalShiftAnisotropyEnergyCreator.hh>
#include <core/energy_methods/DipolarCouplingEnergyCreator.hh>
#include <core/energy_methods/ResidualDipolarCouplingEnergyCreator.hh>
#include <core/energy_methods/ResidualDipolarCouplingEnergy_RohlCreator.hh>
#include <core/energy_methods/SmoothCenPairEnergyCreator.hh>
#include <core/energy_methods/SmoothEnvEnergyCreator.hh>
#include <core/energy_methods/CenPairMotifEnergyCreator.hh>
#include <core/energy_methods/CenPairMotifDegreeEnergyCreator.hh>
#include <core/energy_methods/CenRotPairEnergyCreator.hh>
#include <core/energy_methods/CenRotEnvEnergyCreator.hh>
#include <core/energy_methods/CenHBEnergyCreator.hh>
#include <core/energy_methods/MotifDockEnergyCreator.hh>
#include <core/energy_methods/SuckerEnergyCreator.hh>
#include <core/energy_methods/GaussianOverlapEnergyCreator.hh>
#include <core/energy_methods/YHHPlanarityEnergyCreator.hh>
#include <core/energy_methods/HydroxylTorsionEnergyCreator.hh>
#include <core/pack/interaction_graph/SurfaceEnergyCreator.hh>
#include <core/pack/interaction_graph/HPatchEnergyCreator.hh>
#include <core/energy_methods/MgEnergyCreator.hh>
#include <core/energy_methods/RNA_MgPointEnergyCreator.hh>
#include <core/energy_methods/SymmetricLigandEnergyCreator.hh>
#include <core/energy_methods/UnfoldedStateEnergyCreator.hh>
#include <core/energy_methods/SplitUnfoldedTwoBodyEnergyCreator.hh>
#include <core/energy_methods/WaterAdductHBondEnergyCreator.hh>
#include <core/energy_methods/WaterAdductIntraEnergyCreator.hh>
#include <core/energy_methods/WaterSpecificEnergyCreator.hh>
#include <core/scoring/nv/NVscoreCreator.hh>
#include <core/scoring/orbitals/OrbitalsScoreCreator.hh>
#include <core/scoring/interface_/DDPscoreCreator.hh>
#include <core/energy_methods/HolesEnergyCreator.hh>
#include <core/energy_methods/SurfVolEnergyCreator.hh>
#include <core/energy_methods/SurfEnergyCreator.hh>
#include <core/energy_methods/RG_Energy_RNACreator.hh>
#include <core/energy_methods/RNA_BulgeEnergyCreator.hh>
#include <core/energy_methods/RNA_CoarseDistEnergyCreator.hh>
#include <core/energy_methods/RNA_FullAtomStackingEnergyCreator.hh>
#include <core/energy_methods/RNA_JR_SuiteEnergyCreator.hh>
#include <core/energy_methods/RNA_LJ_BaseEnergyCreator.hh>
#include <core/energy_methods/RNA_PairwiseLowResolutionEnergyCreator.hh>
#include <core/energy_methods/RNA_PartitionEnergyCreator.hh>
#include <core/energy_methods/RNP_LowResEnergyCreator.hh>
#include <core/energy_methods/RNP_LowResPairDistEnergyCreator.hh>
#include <core/energy_methods/RNP_LowResStackEnergyCreator.hh>
#include <core/energy_methods/RNA_SugarCloseEnergyCreator.hh>
#include <core/energy_methods/RNA_StubCoordinateEnergyCreator.hh>
#include <core/energy_methods/RNA_SuiteEnergyCreator.hh>
#include <core/energy_methods/TNA_SuiteEnergyCreator.hh>
#include <core/energy_methods/RNA_TorsionEnergyCreator.hh>
#include <core/energy_methods/RNA_VDW_EnergyCreator.hh>
#include <core/energy_methods/RNA_FullAtomVDW_BasePhosphateCreator.hh>
#include <core/energy_methods/StackElecEnergyCreator.hh>
#include <core/energy_methods/RNA_ChemicalShiftEnergyCreator.hh>
#include <core/energy_methods/RNA_ChemicalMappingEnergyCreator.hh>
#include <core/energy_methods/RNA_DataBackboneEnergyCreator.hh>
#include <core/energy_methods/LoopCloseEnergyCreator.hh>
#include <core/scoring/sym_e/symECreator.hh>
#include <core/energy_methods/FastSAXSEnergyCreator.hh>
#include <core/energy_methods/SAXSEnergyCreator.hh>
#include <core/energy_methods/SAXSEnergyCreatorFA.hh>
#include <core/energy_methods/SAXSEnergyCreatorCEN.hh>
#include <core/energy_methods/FiberDiffractionEnergyCreator.hh>
#include <core/energy_methods/FiberDiffractionEnergyDensCreator.hh>
#include <core/energy_methods/PointWaterEnergyCreator.hh>
#include <core/chemical/rotamers/RotamerLibrarySpecificationRegistrator.hh>
#include <core/chemical/rotamers/BasicRotamerLibrarySpecificationCreator.hh>
#include <core/chemical/rotamers/CenrotRotamerLibrarySpecificationCreator.hh>
#include <core/chemical/rotamers/DunbrackRotamerLibrarySpecificationCreator.hh>
#include <core/chemical/rotamers/NCAARotamerLibrarySpecificationCreator.hh>
#include <core/chemical/rotamers/PDBRotamerLibrarySpecificationCreator.hh>
#include <core/pack/dunbrack/SingleResidueDunbrackLibraryCreator.hh>
#include <core/pack/dunbrack/cenrot/SingleResidueCenrotLibraryCreator.hh>
#include <core/pack/rotamers/SingleResidueRotamerLibraryRegistrator.hh>
#include <core/pack/rotamers/SingleBasicRotamerLibraryCreator.hh>
#include <core/pack/rotamers/SingleLigandRotamerLibraryCreator.hh>
#include <core/pack/rotamers/SingleNCAARotamerLibraryCreator.hh>
#include <core/pack/rotamers/StoredRotamerLibraryCreator.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/DesignRestrictionsCreator.hh>
#include <core/pack/task/operation/ClashBasedRepackShellCreator.hh>
#include <core/pack/task/operation/EnableMultiCoolAnnealerCreator.hh>
#include <core/pack/task/operation/EnableSmartAnnealerCreator.hh>
#include <core/pack/task/operation/KeepSequenceSymmetryCreator.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/RestrictInteractionGraphThreadsOperationCreator.hh>
#include <core/select/residue_selector/AsymmetricUnitSelectorCreator.hh>
#include <core/select/residue_selector/BFactorSelectorCreator.hh>
#include <core/select/residue_selector/GlycanLayerSelectorCreator.hh>
#include <core/select/residue_selector/ResidueSelectorCreators.hh>
#include <core/select/residue_selector/ResiduePropertySelectorCreator.hh>
#include <core/select/residue_selector/PrimarySequenceNeighborhoodSelectorCreator.hh>
#include <core/select/residue_selector/SymmetricalResidueSelectorCreator.hh>
#include <core/pack/task/residue_selector/ClashBasedShellSelectorCreator.hh>
#include <core/select/residue_selector/CloseContactResidueSelectorCreator.hh>
#include <core/select/residue_selector/LogicResidueSelectorCreator.hh>
#include <core/select/residue_selector/ResidueSelectorRegistrator.hh>
#include <core/pack/palette/PackerPaletteRegistrator.hh>
#include <core/pack/palette/CustomBaseTypePackerPaletteCreator.hh>
#include <core/pack/palette/DefaultPackerPaletteCreator.hh>
#include <core/pack/palette/NoDesignPackerPaletteCreator.hh>
#include <core/select/jump_selector/AndJumpSelectorCreator.hh>
#include <core/select/jump_selector/ExclusivelySharedJumpSelectorCreator.hh>
#include <core/select/jump_selector/InterchainJumpSelectorCreator.hh>
#include <core/select/jump_selector/JumpForResidueCreator.hh>
#include <core/select/jump_selector/JumpIndexSelectorCreator.hh>
#include <core/select/jump_selector/JumpSelectorRegistrator.hh>
#include <core/select/jump_selector/NotJumpSelectorCreator.hh>
#include <core/select/jump_selector/OrJumpSelectorCreator.hh>
#include <sys/resource.h>
#include <sstream>
#include <string>
#include <cstring>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/testing.OptionKeys.gen.hh>
#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/import_pose/PoseResourceLoaderCreator.hh>
#include <core/init/init.ResourceLocatorCreators.ihh>
#include <core/init/init.ResourceLocatorRegistrators.ihh>
#include <basic/options/keys/LoopModel.OptionKeys.gen.hh>
#include <basic/options/keys/antibody.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/version.hh>
#include <utility/vector1.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/CSI_Sequence.hh>
#include <utility/crash_report.hh>
#include <utility/options/OptionCollection.hh>
Namespaces | |
core | |
A class for reading in the atom type properties. | |
core::init | |
Macros | |
#define | PROCESS_STACK_SIZE (32 * 1024 * 1024) |
Typedefs | |
using | ostringstream_t = std::ostringstream |
Functions | |
static 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_crash_reporter (int argc, char *argv[]) |
Setup crash reporter. 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::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::check_load_fconfig () |
Check if common config file exists and load it/them as flags files. 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
#define PROCESS_STACK_SIZE (32 * 1024 * 1024) |
using ostringstream_t = std::ostringstream |