Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
protocols::rosetta_scripts Namespace Reference

Classes

class  AdditionalOutputWrapper
 
class  AdditionalOutputWrapperCreator
 
class  MultipleOutputWrapper
 
class  MultipleOutputWrapperCreator
 
class  MultiplePoseMover
 
class  MultiplePoseMoverCreator
 
class  ParsedProtocol
 
class  ParsedProtocolCreator
 
class  PosePropertyReporter
 
class  PosePropertyReporterCreator
 Abstract base class for a PosePropertyReporter factory; the Creator class is responsible for creating a particular PosePropertyReporter class. More...
 
class  PosePropertyReporterFactory
 
class  PosePropertyReporterRegistrator
 This templated class will register an instance of an PosePropertyReporterCreator (class T) with the PosePropertyReporterFactory. It will ensure that no PosePropertyReporterCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  PoseSelector
 
class  PoseSelectorCreator
 Abstract base class for a PoseSelector factory; the Creator class is responsible for creating a particular PoseSelector class. More...
 
class  PoseSelectorFactory
 
class  PoseSelectorRegistrator
 This templated class will register an instance of an PoseSelectorCreator (class T) with the PoseSelectorFactory. It will ensure that no PoseSelectorCreator is registered twice, and, centralizes this registration logic so that thread safety issues can be handled in one place. More...
 
class  RosettaScriptsParser
 Reading the xml file and generating the mover. More...
 
class  SavePoseMover
 mover that can be used to save or restore a pose at an arbitrary point during a rosetta scripts protocol. other movers or filters can be set up to access poses saved by this mover during their apply calls. More...
 
class  SavePoseMoverCreator
 

Typedefs

typedef
utility::pointer::owning_ptr
< MultiplePoseMover
MultiplePoseMoverOP
 
typedef
utility::pointer::owning_ptr
< MultiplePoseMover const > 
MultiplePoseMoverCOP
 
typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef
utility::pointer::owning_ptr
< ParsedProtocol
ParsedProtocolOP
 
typedef
utility::pointer::owning_ptr
< ParsedProtocol const > 
ParsedProtocolCOP
 
typedef
utility::pointer::owning_ptr
< PosePropertyReporter
PosePropertyReporterOP
 
typedef
utility::pointer::owning_ptr
< PosePropertyReporter const > 
PosePropertyReporterCOP
 
typedef
utility::pointer::owning_ptr
< PosePropertyReporterCreator
PosePropertyReporterCreatorOP
 
typedef
utility::pointer::owning_ptr
< PosePropertyReporterCreator
const > 
PosePropertyReporterCreatorCOP
 
typedef
utility::pointer::owning_ptr
< PosePropertyReporterFactory
PosePropertyReporterFactoryOP
 
typedef
utility::pointer::owning_ptr
< PosePropertyReporterFactory
const > 
PosePropertyReporterFactoryCOP
 
typedef
utility::pointer::owning_ptr
< PoseSelector
PoseSelectorOP
 
typedef
utility::pointer::owning_ptr
< PoseSelector const > 
PoseSelectorCOP
 
typedef
utility::pointer::owning_ptr
< PoseSelectorCreator
PoseSelectorCreatorOP
 
typedef
utility::pointer::owning_ptr
< PoseSelectorCreator const > 
PoseSelectorCreatorCOP
 
typedef
utility::pointer::owning_ptr
< PoseSelectorFactory
PoseSelectorFactoryOP
 
typedef
utility::pointer::owning_ptr
< PoseSelectorFactory const > 
PoseSelectorFactoryCOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef utility::tag::TagOP TagOP
 
typedef
utility::pointer::owning_ptr
< SavePoseMover
SavePoseMoverOP
 
typedef
utility::pointer::owning_ptr
< SavePoseMover const > 
SavePoseMoverCOP
 

Enumerations

enum  PoseSelectorFlags { PSF_NONE = 0, PSF_NEED_FULL_POSE_SET = (1 << 0) }
 

Functions

std::pair< moves::MoverOP,
std::string
parse_mover_subtag (utility::tag::TagCOP const tag_ptr, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 
core::pack::task::TaskFactoryOP parse_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
 
core::pack::task::TaskFactoryOP parse_task_operations (std::string const task_list, basic::datacache::DataMap const &data)
 
core::pack::task::TaskFactoryOP parse_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap &data, core::pack::task::TaskFactoryOP &task_factory)
 option to add or refer to a Taskfactory through the datamap, similar to how to add/refer to movemap OPs (EMS) More...
 
utility::vector1
< core::pack::task::operation::TaskOperationOP
get_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
 
core::scoring::ScoreFunctionOP parse_score_function (utility::tag::TagCOP tag, std::string const &option_name, basic::datacache::DataMap const &data, std::string const dflt_key="talaris2013")
 Look up the score function defined in the <SCOREFXNS> through the given option. Default to 'talaris2013' by default. More...
 
core::scoring::ScoreFunctionOP parse_score_function (utility::tag::TagCOP tag, basic::datacache::DataMap const &data, std::string const dflt_key="talaris2013")
 Look up the score function defined in the <SCOREFXNS> through the option 'scorefxn='. Default to 'talaris2013' by default. More...
 
std::string get_score_function_name (utility::tag::TagCOP tag, std::string const &option_name)
 Look up the name of assigned score function to the given option. Use this to prevent hard coding default score functions into protocols. More...
 
std::string get_score_function_name (utility::tag::TagCOP tag)
 Look up the name of assigned score function to the 'scorefxn=' option. Use this to prevent hard coding default score functions into protocols. More...
 
core::pose::PoseOP saved_reference_pose (utility::tag::TagCOP in_tag, basic::datacache::DataMap &data_map, std::string const tag_str="reference_name")
 convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable More...
 
void foreach_movemap_tag (utility::tag::TagCOP const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP mm)
 utility function for parse_movemap which goes over each of the tags in a movemap section More...
 
void parse_movemap (utility::tag::TagCOP const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP &mm, basic::datacache::DataMap &data, bool const reset_map)
 variant of parse_movemap that takes in a datamap and searches it for already existing movemaps More...
 
void parse_movemap (utility::tag::TagCOP const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP mm, bool const reset_movemap)
 
void add_movemaps_to_datamap (utility::tag::TagCOP in_tag, core::pose::Pose const &pose, basic::datacache::DataMap &data, bool initialize_mm_as_true=false)
 Parses in_tag, adding any MoveMaps specified in branches with names to the datamap for use after. Skips any mm names that are already loaded. This should allow multiple MoveMaps to be specified and loaded in a mover. More...
 
bool has_branch (utility::tag::TagCOP in_tag, std::string const branch_name)
 Does the tag have a branch of the given name. More...
 
protocols::filters::FilterOP parse_filter (std::string const filter_name, protocols::filters::Filters_map const &filters)
 
protocols::moves::MoverOP parse_mover (std::string const mover_name, protocols::moves::Movers_map const &movers)
 
numeric::xyzVector< core::Realparse_xyz_vector (utility::tag::TagCOP const xyz_vector_tag)
 utility function for parsing xyzVector More...
 
core::Size find_nearest_res (core::pose::Pose const &source, core::pose::Pose const &target, core::Size const res, core::Size const chain)
 Return the number of the residue on source that is nearest to res on target. If the distance is greater than 2.0 returns 0 to indicate error. More...
 
void find_nearest_res (core::pose::Pose const &source, core::pose::Pose const &target, core::Size const res, core::Size &target_res, core::Real &dist, core::Size const chain=0)
 find nearest residue and also return the distance More...
 
utility::vector1< core::Sizeresidue_packer_states (core::pose::Pose const &pose, core::pack::task::TaskFactoryCOP tf, bool const designable, bool const packable)
 returns a vector containing all the residues with a given packer state according to the TF More...
 
core::Size find_nearest_disulfide (core::pose::Pose const &pose, core::Size const res)
 finds the nearest disulife to given residue on pose by searching both up and down stream to the given postion More...
 
void parse_bogus_res_tag (utility::tag::TagCOP tag, std::string const prefix)
 Access res_num/pdb_num tag with prefix. This is to allow parsing at apply time (pdb_num) instead of at parse_my_tag. This allows one to use SavePoseMovers within a protocol with the correct residue from pdb_num. This function is to prevent unused variable crash. More...
 

Variables

static basic::Tracer TR ("protocols.rosetta_scripts.AdditionalOutputWrapper")
 
static basic::Tracer TR ("protocols.rosetta_scripts.MultipleOutputWrapper")
 
static basic::Tracer TR ("protocols.rosetta_scripts.MultiplePoseMover")
 
static basic::Tracer TR ("protocols.rosetta_scripts.ParsedProtocol")
 
static basic::Tracer TR_call_order ("protocols.rosetta_scripts.ParsedProtocol_call_order")
 
static basic::Tracer TR_report ("protocols.rosetta_scripts.ParsedProtocol.REPORT")
 
static
numeric::random::RandomGenerator 
RG (48569)
 
static basic::Tracer TR ("protocols.rosetta_scripts.PosePropertyReporterFactory")
 
static basic::Tracer TR ("protocols.rosetta_scripts.PoseSelectorFactory")
 
static basic::Tracer TR ("protocols.rosetta_scripts.RosettaScriptsParser")
 

Typedef Documentation

typedef core::Real protocols::rosetta_scripts::Real

Enumeration Type Documentation

Enumerator
PSF_NONE 
PSF_NEED_FULL_POSE_SET 

Function Documentation

void protocols::rosetta_scripts::add_movemaps_to_datamap ( utility::tag::TagCOP  in_tag,
core::pose::Pose const &  pose,
basic::datacache::DataMap data,
bool  initialize_mm_as_true 
)

Parses in_tag, adding any MoveMaps specified in branches with names to the datamap for use after. Skips any mm names that are already loaded. This should allow multiple MoveMaps to be specified and loaded in a mover.

References basic::datacache::DataMap::add(), foreach_movemap_tag(), basic::datacache::DataMap::has(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

Referenced by protocols::grafting::AnchoredGraftMover::parse_my_tag().

core::Size protocols::rosetta_scripts::find_nearest_disulfide ( core::pose::Pose const &  pose,
core::Size const  res 
)

finds the nearest disulife to given residue on pose by searching both up and down stream to the given postion

References core::chemical::DISULFIDE, core::conformation::Residue::has_variant_type(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and utility_exit_with_message.

core::Size protocols::rosetta_scripts::find_nearest_res ( core::pose::Pose const &  source,
core::pose::Pose const &  target,
core::Size const  res,
core::Size const  chain 
)
void protocols::rosetta_scripts::find_nearest_res ( core::pose::Pose const &  source,
core::pose::Pose const &  target,
core::Size const  res,
core::Size target_res,
core::Real target_dist,
core::Size const  chain 
)
void protocols::rosetta_scripts::foreach_movemap_tag ( utility::tag::TagCOP const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP  mm 
)
std::string protocols::rosetta_scripts::get_score_function_name ( utility::tag::TagCOP  tag,
std::string const &  option_name 
)
std::string protocols::rosetta_scripts::get_score_function_name ( utility::tag::TagCOP  tag)

Look up the name of assigned score function to the 'scorefxn=' option. Use this to prevent hard coding default score functions into protocols.

References get_score_function_name().

utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::rosetta_scripts::get_task_operations ( utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  data 
)
bool protocols::rosetta_scripts::has_branch ( utility::tag::TagCOP  in_tag,
std::string const  branch_name 
)

Does the tag have a branch of the given name.

Referenced by protocols::grafting::AnchoredGraftMover::parse_my_tag().

void protocols::rosetta_scripts::parse_bogus_res_tag ( utility::tag::TagCOP  tag,
std::string const  prefix 
)

Access res_num/pdb_num tag with prefix. This is to allow parsing at apply time (pdb_num) instead of at parse_my_tag. This allows one to use SavePoseMovers within a protocol with the correct residue from pdb_num. This function is to prevent unused variable crash.

Referenced by protocols::grafting::simple_movers::InsertPoseIntoPoseMover::parse_my_tag(), protocols::grafting::simple_movers::ReplaceRegionMover::parse_my_tag(), protocols::grafting::simple_movers::DeleteRegionMover::parse_my_tag(), protocols::grafting::simple_movers::KeepRegionMover::parse_my_tag(), and protocols::grafting::AnchoredGraftMover::parse_my_tag().

protocols::filters::FilterOP protocols::rosetta_scripts::parse_filter ( std::string const  filter_name,
protocols::filters::Filters_map const &  filters 
)
void protocols::rosetta_scripts::parse_movemap ( utility::tag::TagCOP const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP mm,
basic::datacache::DataMap data,
bool const  reset_map 
)
void protocols::rosetta_scripts::parse_movemap ( utility::tag::TagCOP const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP  mm,
bool const  reset_movemap 
)

modifies an existing movemap according to tag the movemap defaults to move all bb, chi, and jumps.

modifies an existing movemap according to tag the movemap defaults to move all bb, chi, and jumps. Still resets movemap if MoveMap branch not found!

References foreach_movemap_tag(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), and TR.

protocols::moves::MoverOP protocols::rosetta_scripts::parse_mover ( std::string const  mover_name,
protocols::moves::Movers_map const &  movers 
)
std::pair< moves::MoverOP, std::string > protocols::rosetta_scripts::parse_mover_subtag ( utility::tag::TagCOP const  tag_ptr,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
core::scoring::ScoreFunctionOP protocols::rosetta_scripts::parse_score_function ( utility::tag::TagCOP  tag,
std::string const &  option_name,
basic::datacache::DataMap const &  data,
std::string const  dflt_key 
)

Look up the score function defined in the <SCOREFXNS> through the given option. Default to 'talaris2013' by default.

Utility function to find a scorefunction from parser-provided data. This is essentially a shameless copy of Justin's PackRotamersMover::parse_score_function.

References core::init::check_score_function_sanity(), basic::datacache::DataMap::get(), and basic::datacache::DataMap::has().

Referenced by protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), protocols::jd2::parser::MonteCarloLoader::load_data(), protocols::simple_moves::AddChainMover::parse_my_tag(), protocols::simple_moves::ForceDisulfidesMover::parse_my_tag(), protocols::cryst::SetCrystWeightMover::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::RandomMutation::parse_my_tag(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::simple_moves::DumpPdb::parse_my_tag(), protocols::simple_moves::SwitchChainOrderMover::parse_my_tag(), protocols::seeded_abinitio::SegmentHybridizer::parse_my_tag(), protocols::protein_interface_design::movers::HotspotHasherMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceOnLoop::parse_my_tag(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::simple_filters::EnergyPerResidueFilter::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::simple_filters::ResidueIEFilter::parse_my_tag(), protocols::simple_filters::ScoreTypeFilter::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::simple_moves::symmetry::TaskAwareSymMinMover::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::simple_filters::ResidueSetChainEnergyFilter::parse_my_tag(), protocols::simple_moves::TaskAwareMinMover::parse_my_tag(), protocols::enzdes::PackRotamersMoverPartGreedy::parse_my_tag(), protocols::simple_filters::DdgFilter::parse_my_tag(), protocols::enzdes::BackboneSampler::parse_my_tag(), protocols::design_opt::ParetoOptMutationMover::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::simple_filters::AlaScan::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::abinitio::abscript::AbscriptLoopCloserCM::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::parse_my_tag(), protocols::protein_interface_design::movers::DisulfideMover::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::movers::TryRotamers::parse_my_tag(), protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), protocols::simple_filters::TaskAwareAlaScan::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag(), protocols::simple_moves::ConsensusDesignMover::parse_my_tag(), protocols::simple_moves::RotamerTrialsMover::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), protocols::symmetric_docking::SymDockProtocol::parse_my_tag(), protocols::enzdes::LigInterfaceEnergyFilter::parse_my_tag(), protocols::moves::RampingMover::parse_my_tag(), protocols::enzdes::EnzScoreFilter::parse_my_tag(), protocols::comparative_modeling::LoopRelaxMover::parse_my_tag(), protocols::flxbb::FlxbbDesign::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), protocols::enzdes::RepackWithoutLigandFilter::parse_my_tag(), protocols::simple_moves::MinMover::parse_opts(), protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag(), protocols::simple_moves::RepackSidechainsMover::parse_score_function(), protocols::simple_moves::MinPackMover::parse_score_function(), protocols::simple_moves::PackRotamersMover::parse_score_function(), parse_score_function(), and protocols::toolbox::task_operations::SelectByDeltaScoreOperation::parse_tag().

core::scoring::ScoreFunctionOP protocols::rosetta_scripts::parse_score_function ( utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  data,
std::string const  dflt_key 
)

Look up the score function defined in the <SCOREFXNS> through the option 'scorefxn='. Default to 'talaris2013' by default.

Utility function to find a scorefunction from parser-provided data for the option 'scorefxn'.

References parse_score_function().

core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations ( utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  data 
)

This is essentially a shameless copy of Justin's PackRotamersMover::parse_task_operations. In truth DesignRepackMover should disappear into Justin's better organized class, but this will wait... (SJF)

References TR.

Referenced by protocols::protein_interface_design::movers::TaskAwareCsts::parse_my_tag(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::RandomMutation::parse_my_tag(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::parse_my_tag(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::toolbox::task_operations::StoreTaskMover::parse_my_tag(), protocols::simple_filters::TotalSasaFilter::parse_my_tag(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::parse_my_tag(), protocols::protein_interface_design::filters::Torsion::parse_my_tag(), protocols::relax::AtomCoordinateCstMover::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::filters::AverageDegreeFilter::parse_my_tag(), protocols::simple_filters::TaskAwareScoreTypeFilter::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), protocols::protein_interface_design::filters::DesignableResiduesFilter::parse_my_tag(), protocols::simple_filters::RotamerBoltzmannWeight::parse_my_tag(), protocols::simple_moves::symmetry::TaskAwareSymMinMover::parse_my_tag(), protocols::protein_interface_design::filters::AtomicContactCountFilter::parse_my_tag(), protocols::simple_filters::NetChargeFilter::parse_my_tag(), protocols::protein_interface_design::movers::BackrubDDMover::parse_my_tag(), protocols::simple_moves::ModifyVariantTypeMover::parse_my_tag(), protocols::enzdes::PackRotamersMoverPartGreedy::parse_my_tag(), protocols::design_opt::ParetoOptMutationMover::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::enzdes::EnzRepackMinimize::parse_my_tag(), protocols::hotspot_hashing::movers::PlaceSurfaceProbe::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::simple_filters::MutationsFilter::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::simple_filters::ResidueCountFilter::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::hybridization::BackboneTorsionSampler::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::hybridization::BackboneTorsionPerturbation::parse_my_tag(), protocols::simple_filters::TaskAwareAlaScan::parse_my_tag(), protocols::simple_moves::ReportEffectivePKA::parse_my_tag(), protocols::hybridization::CartesianHybridize::parse_my_tag(), protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag(), protocols::simple_moves::ConsensusDesignMover::parse_my_tag(), protocols::simple_moves::RotamerTrialsMover::parse_my_tag(), protocols::hybridization::HybridizeProtocol::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::matdes::ClashCheckFilter::parse_my_tag(), protocols::simple_filters::TaskAwareSASAFilter::parse_my_tag(), protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag(), protocols::simple_filters::SaveResfileToDiskFilter::parse_my_tag(), protocols::symmetric_docking::SymDockProtocol::parse_my_tag(), protocols::hybridization::FoldTreeHybridize::parse_my_tag(), protocols::features::ReportToDB::parse_my_tag(), protocols::enzdes::PredesignPerturbMover::parse_my_tag(), protocols::docking::DockingProtocol::parse_my_tag(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::parse_task_operations(), protocols::simple_moves::TaskAwareMinMover::parse_task_operations(), protocols::simple_moves::MinPackMover::parse_task_operations(), protocols::simple_moves::PackRotamersMover::parse_task_operations(), and protocols::simple_moves::GenericMonteCarloMover::parse_task_operations().

core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations ( std::string const  task_list,
basic::datacache::DataMap const &  data 
)
core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
core::pack::task::TaskFactoryOP task_factory 
)

option to add or refer to a Taskfactory through the datamap, similar to how to add/refer to movemap OPs (EMS)

allows the transfer of whole taskfactories on the datamap. This way a "base" taskfactory can be created, transferred on the datamap, and individual mover's specific taskoperations can be added on top

References basic::datacache::DataMap::add(), end, basic::datacache::DataMap::get(), basic::datacache::DataMap::has(), core::pack::task::TaskFactory::push_back(), utility::string_split(), and TR.

numeric::xyzVector< core::Real > protocols::rosetta_scripts::parse_xyz_vector ( utility::tag::TagCOP const  xyz_vector_tag)

utility function for parsing xyzVector

Referenced by protocols::rigid::RollMover::parse_my_tag().

utility::vector1< core::Size > protocols::rosetta_scripts::residue_packer_states ( core::pose::Pose const &  pose,
core::pack::task::TaskFactoryCOP  tf,
bool const  designable,
bool const  packable 
)
core::pose::PoseOP protocols::rosetta_scripts::saved_reference_pose ( utility::tag::TagCOP const  in_tag,
basic::datacache::DataMap data_map,
std::string const  tag_name 
)

convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol Will look for tag in in_tag variable

References basic::datacache::DataMap::add(), basic::datacache::DataMap::get(), and basic::datacache::DataMap::has().

Referenced by protocols::simple_filters::SidechainRmsdFilter::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::simple_moves::SuperimposeMover::parse_my_tag(), protocols::protein_interface_design::filters::LRmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::SSamountFilter::parse_my_tag(), protocols::protein_interface_design::filters::RmsdSimpleFilter::parse_my_tag(), protocols::grafting::simple_movers::InsertPoseIntoPoseMover::parse_my_tag(), protocols::grafting::simple_movers::ReplaceRegionMover::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::features::ProteinRMSDFeatures::parse_my_tag(), protocols::features::ProteinRMSDNoSuperpositionFeatures::parse_my_tag(), protocols::matdes::SymUnsatHbondFilter::parse_my_tag(), protocols::grafting::AnchoredGraftMover::parse_my_tag(), and protocols::toolbox::task_operations::SelectByDeltaScoreOperation::parse_tag().

Variable Documentation

numeric::random::RandomGenerator protocols::rosetta_scripts::RG(48569)
static
basic::Tracer protocols::rosetta_scripts::TR("protocols.rosetta_scripts.PosePropertyReporterFactory")
static
basic::Tracer protocols::rosetta_scripts::TR("protocols.rosetta_scripts.PoseSelectorFactory")
static
basic::Tracer protocols::rosetta_scripts::TR("protocols.rosetta_scripts.MultipleOutputWrapper")
static
basic::Tracer protocols::rosetta_scripts::TR("protocols.rosetta_scripts.MultiplePoseMover")
static
basic::Tracer protocols::rosetta_scripts::TR("protocols.rosetta_scripts.AdditionalOutputWrapper")
static
basic::Tracer protocols::rosetta_scripts::TR("protocols.rosetta_scripts.ParsedProtocol")
static
basic::Tracer protocols::rosetta_scripts::TR("protocols.rosetta_scripts.RosettaScriptsParser")
static
basic::Tracer protocols::rosetta_scripts::TR_call_order("protocols.rosetta_scripts.ParsedProtocol_call_order")
static
basic::Tracer protocols::rosetta_scripts::TR_report("protocols.rosetta_scripts.ParsedProtocol.REPORT")
static