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protocols::rosetta_scripts Namespace Reference

Classes

class  ParsedProtocol
 
class  ParsedProtocolCreator
 
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 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
< SavePoseMover
SavePoseMoverOP
 
typedef
utility::pointer::owning_ptr
< SavePoseMover const > 
SavePoseMoverCOP
 

Functions

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)
 
core::pack::task::TaskFactoryOP parse_task_operations (utility::tag::TagPtr const tag, protocols::moves::DataMap const &data)
 
core::pack::task::TaskFactoryOP parse_task_operations (std::string const task_list, protocols::moves::DataMap const &data)
 
core::pack::task::TaskFactoryOP parse_task_operations (utility::tag::TagPtr const tag, protocols::moves::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::TagPtr const tag, protocols::moves::DataMap const &data)
 
core::scoring::ScoreFunctionOP parse_score_function (utility::tag::TagPtr const tag, protocols::moves::DataMap const &data, std::string const dflt_key)
 
core::pose::PoseOP saved_reference_pose (utility::tag::TagPtr const in_tag, protocols::moves::DataMap &data_map)
 convenience function to access pointers to poses that will be stored in the data map at an arbitrary point during an RS protocol More...
 
void foreach_movemap_tag (utility::tag::TagPtr 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::TagPtr const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP &mm, protocols::moves::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::TagPtr const in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP mm)
 
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::TagPtr 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...
 
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...
 
static basic::Tracer TR ("protocols.rosetta_scripts.util.hh")
 

Typedef Documentation

Function Documentation

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::foreach_movemap_tag ( utility::tag::TagPtr const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP  mm 
)
utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::rosetta_scripts::get_task_operations ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap const &  data 
)
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::TagPtr const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP mm,
protocols::moves::DataMap data,
bool const  reset_map 
)
void protocols::rosetta_scripts::parse_movemap ( utility::tag::TagPtr const  in_tag,
core::pose::Pose const &  pose,
core::kinematics::MoveMapOP  mm 
)

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

References foreach_movemap_tag(), and TR().

protocols::moves::MoverOP protocols::rosetta_scripts::parse_mover ( std::string const  mover_name,
protocols::moves::Movers_map const &  movers 
)
core::scoring::ScoreFunctionOP protocols::rosetta_scripts::parse_score_function ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap const &  data,
std::string const  dflt_key 
)

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

References protocols::moves::DataMap::get(), and protocols::moves::DataMap::has().

Referenced by protocols::jd2::DockDesignParser::generate_mover_from_pose(), protocols::simple_moves::ForceDisulfidesMover::parse_my_tag(), protocols::simple_moves::DumpPdb::parse_my_tag(), protocols::simple_moves::SwitchChainOrderMover::parse_my_tag(), protocols::simple_filters::RelativePoseFilter::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::simple_moves::TaskAwareMinMover::parse_my_tag(), protocols::design_opt::ParetoOptMutationMover::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::flexpep_docking::FlexPepDockingProtocol::parse_my_tag(), protocols::analysis::InterfaceAnalyzerMover::parse_my_tag(), protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag(), protocols::simple_moves::ConsensusDesignMover::parse_my_tag(), protocols::protein_interface_design::movers::Splice::parse_my_tag(), protocols::moves::RampingMover::parse_my_tag(), protocols::comparative_modeling::LoopRelaxMover::parse_my_tag(), protocols::hotspot_hashing::movers::PlaceProbeMover::parse_place_probe_tag(), protocols::simple_moves::RepackSidechainsMover::parse_score_function(), protocols::simple_moves::MinPackMover::parse_score_function(), and protocols::simple_moves::PackRotamersMover::parse_score_function().

core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations ( utility::tag::TagPtr const  tag,
protocols::moves::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::simple_moves::AddConstraintsToCurrentConformationMover::parse_my_tag(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::RandomMutation::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::BuildAlaPose::parse_my_tag(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::parse_my_tag(), protocols::protein_interface_design::filters::Torsion::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::simple_moves::DesignRepackMover::parse_my_tag(), protocols::protein_interface_design::filters::AverageDegreeFilter::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::protein_interface_design::filters::AtomicContactCountFilter::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::design_opt::GreedyOptMutationMover::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::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::simple_moves::ddG::parse_my_tag(), protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::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::protein_interface_design::movers::Splice::parse_my_tag(), protocols::relax::FastRelax::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,
protocols::moves::DataMap const &  data 
)
core::pack::task::TaskFactoryOP protocols::rosetta_scripts::parse_task_operations ( utility::tag::TagPtr const  tag,
protocols::moves::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 protocols::moves::DataMap::add(), core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), and TR().

numeric::xyzVector< core::Real > protocols::rosetta_scripts::parse_xyz_vector ( utility::tag::TagPtr 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 
)
static numeric::random::RandomGenerator protocols::rosetta_scripts::RG ( 48569  )
static
core::pose::PoseOP protocols::rosetta_scripts::saved_reference_pose ( utility::tag::TagPtr const  in_tag,
protocols::moves::DataMap data_map 
)
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.util.hh"  )
static
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.ParsedProtocol"  )
static
static basic::Tracer protocols::rosetta_scripts::TR_call_order ( "protocols.rosetta_scripts.ParsedProtocol_call_order"  )
static
static basic::Tracer protocols::rosetta_scripts::TR_report ( "protocols.rosetta_scripts.ParsedProtocol.REPORT"  )
static