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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  RosettaScriptsJobQueen
 
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
 
class  XmlObjects
 

Typedefs

typedef
utility::pointer::shared_ptr
< MultiplePoseMover
MultiplePoseMoverOP
 
typedef
utility::pointer::shared_ptr
< MultiplePoseMover const > 
MultiplePoseMoverCOP
 
using Real = core::Real
 
using Pose = core::pose::Pose
 
typedef
utility::pointer::shared_ptr
< ParsedProtocol
ParsedProtocolOP
 
typedef
utility::pointer::shared_ptr
< ParsedProtocol const > 
ParsedProtocolCOP
 
typedef
utility::pointer::weak_ptr
< ParsedProtocol
ParsedProtocolAP
 
typedef
utility::pointer::weak_ptr
< ParsedProtocol const > 
ParsedProtocolCAP
 
typedef
utility::pointer::shared_ptr
< PosePropertyReporter
PosePropertyReporterOP
 
typedef
utility::pointer::shared_ptr
< PosePropertyReporter const > 
PosePropertyReporterCOP
 
typedef
utility::pointer::shared_ptr
< PosePropertyReporterCreator
PosePropertyReporterCreatorOP
 
typedef
utility::pointer::shared_ptr
< PosePropertyReporterCreator
const > 
PosePropertyReporterCreatorCOP
 
typedef
utility::pointer::shared_ptr
< PosePropertyReporterFactory
PosePropertyReporterFactoryOP
 
typedef
utility::pointer::shared_ptr
< PosePropertyReporterFactory
const > 
PosePropertyReporterFactoryCOP
 
typedef
utility::pointer::shared_ptr
< PoseSelector
PoseSelectorOP
 
typedef
utility::pointer::shared_ptr
< PoseSelector const > 
PoseSelectorCOP
 
typedef
utility::pointer::shared_ptr
< PoseSelectorCreator
PoseSelectorCreatorOP
 
typedef
utility::pointer::shared_ptr
< PoseSelectorCreator const > 
PoseSelectorCreatorCOP
 
typedef
utility::pointer::shared_ptr
< PoseSelectorFactory
PoseSelectorFactoryOP
 
typedef
utility::pointer::shared_ptr
< PoseSelectorFactory const > 
PoseSelectorFactoryCOP
 
using TagCOPs = utility::vector0< TagCOP >
 
typedef
utility::pointer::shared_ptr
< RosettaScriptsParser
RosettaScriptsParserOP
 
typedef
utility::pointer::shared_ptr
< RosettaScriptsParser const > 
RosettaScriptsParserCOP
 
typedef
utility::pointer::shared_ptr
< SavePoseMover
SavePoseMoverOP
 
typedef
utility::pointer::shared_ptr
< SavePoseMover const > 
SavePoseMoverCOP
 
typedef
utility::pointer::shared_ptr
< XmlObjects
XmlObjectsOP
 
typedef
utility::pointer::shared_ptr
< XmlObjects const > 
XmlObjectsCOP
 
typedef
utility::pointer::weak_ptr
< XmlObjects
XmlObjectsAP
 
typedef
utility::pointer::weak_ptr
< XmlObjects const > 
XmlObjectsCAP
 

Enumerations

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

Functions

static basic::Tracer TR ("protocols.rosetta_scripts.AdditionalOutputWrapper")
 
static basic::Tracer TR ("protocols.rosetta_scripts.MultipleOutputWrapper")
 
static basic::Tracer TR ("protocols.rosetta_scripts.MultiplePoseMover")
 
void recursively_access_all_attributes (utility::tag::TagCOP tag)
 Recurse through the tree of Tags and for each one, read each option, so that every option is set as "read". More...
 
std::string mpm_mangler (std::string const &element_name)
 
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")
 
std::pair< moves::MoverOP,
std::string > 
parse_mover_subtag (utility::tag::TagCOP const tag_ptr, basic::datacache::DataMap &data)
 
std::string complex_type_name_for_parsed_protocol_subelement (std::string const &foo)
 
static basic::Tracer TR ("protocols.rosetta_scripts.PosePropertyReporterFactory")
 
static basic::Tracer TR ("protocols.rosetta_scripts.PoseSelectorFactory")
 
static basic::Tracer TR ("protocols.rosetta_scripts.RosettaScriptsJobQueen")
 
static basic::Tracer TR ("protocols.rosetta_scripts.RosettaScriptsParser")
 
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 attributes_for_parse_residue_selector (utility::tag::AttributeList &attributes, std::string const &description)
 Appends the attributes read by parse_residue_selector. More...
 
void attributes_for_saved_reference_pose (utility::tag::AttributeList &attributes, std::string const &attribute_name="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 attributes_for_saved_reference_pose_w_description (utility::tag::AttributeList &attributes, std::string const &description, std::string const &attribute_name="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...
 
core::pose::PoseOP saved_reference_pose (utility::tag::TagCOP const in_tag, basic::datacache::DataMap &data_map, std::string const &tag_name)
 
core::pose::PoseCOP legacy_saved_pose_or_input (utility::tag::TagCOP tag, basic::datacache::DataMap &data, std::string const &class_name, bool use_native=true, std::string const &refname="reference_name")
 Retrieve the reference pose. If not given, fall back to the native pose (if asked for), or the input pose as a last resort. Will print a warning message if the input pose is used. More...
 
void foreach_movemap_tag (utility::tag::TagCOP const in_tag, basic::datacache::DataMap &data, core::select::movemap::MoveMapFactoryOP mmf)
 utility function for parse_movemap which goes over each of the tags in a movemap section More...
 
void parse_movemap_tag (utility::tag::TagCOP const in_tag, core::select::movemap::MoveMapFactoryOP mmf)
 
core::select::movemap::MoveMapFactoryOP parse_movemap_factory_legacy (utility::tag::TagCOP in_tag, basic::datacache::DataMap &data, bool const reset_movemap=true,core::select::movemap::MoveMapFactoryOP mmf_to_modify=nullptr)
 Parse a MoveMap factory from tags using the old MoveMap specification syntax. More...
 
core::select::movemap::MoveMapFactoryOP parse_named_movemap_factory_legacy (utility::tag::TagCOP in_tag, std::string const &name, basic::datacache::DataMap &data, bool const reset_movemap=true,core::select::movemap::MoveMapFactoryOP mmf_to_modify=nullptr)
 Parse a MoveMap factory from tags using the old MoveMap specification syntax. Will look for a MoveMap entry with a particular name entry. More...
 
std::string move_map_tag_namer (std::string const &subelement_name)
 
std::string optionally_named_move_map_ct_namer (std::string const &)
 
void common_movemap_complex_type_def (utility::tag::XMLSchemaComplexTypeGenerator &ct_gen)
 
void append_subelement_for_parse_movemap_factory_legacy (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaSimpleSubelementList &subelements, std::string const &description="")
 Adds a subelement to an input subelement list describing a MoveMap subtag that will be used by the parse_movemap_legacy function. More...
 
protocols::filters::FilterOP parse_filter (std::string const &filter_name, basic::datacache::DataMap const &d)
 Return the Filter with the given name. Raise a RosettaScriptsOptionError if not present. More...
 
protocols::filters::FilterOP parse_filter_or_null (std::string const &filter_name, basic::datacache::DataMap const &d)
 Return the Filter with the given name. Return nullptr if not present. More...
 
protocols::moves::MoverOP parse_mover (std::string const &mover_name, basic::datacache::DataMap const &d)
 Return the Mover with the given name. Raise a RosettaScriptsOptionError if not present. More...
 
protocols::moves::MoverOP parse_mover_or_null (std::string const &mover_name, basic::datacache::DataMap const &d)
 Return the Mover with the given name. Return nullptr if not present. More...
 
void attributes_for_parse_xyz_vector (utility::tag::AttributeList &attlist)
 
numeric::xyzVector< core::Realparse_xyz_vector (utility::tag::TagCOP const xyz_vector_tag)
 utility function for parsing xyzVector More...
 
utility::sql_database::sessionOP parse_database_session (utility::tag::TagCOP tag, basic::datacache::DataMap const &datamap)
 This is kind of a strange place for this, but for library-level reasons it needs to be more accessible than a more logical home with ReportToDB, and cannot live in basic because it needs other functions in this file. (There is also value in not creating a new file b/c it breaks the fast-compile system XML XSD XRW is using, and it's 6pm on Friday!) More...
 
void attributes_for_parse_database_session (utility::tag::XMLSchemaDefinition &xsd, utility::tag::AttributeList &attlist)
 
void print_template_script ()
 Prints out an empty template RosettaScript to the tracer. More...
 
bool print_information (std::string const &component_name, std::stringstream &outstream)
 Prints out XSD information about the XML-accessible options for a given RosettaScipts-accessible mover, filter, task operation, residue selector, simple_metric, or packer palette. More...
 
void print_information (utility::vector1< std::string > const &component_names)
 Prints out XSD information about the XML-accessible options for a given set of RosettaScipts-accessible movers, filters, task operations, residue selectors, simple metric, or packer palette. More...
 
void save_schema (std::string const &filename)
 Saves the XSD to the given file. More...
 
std::ostream & operator<< (std::ostream &output, XmlObjects const &object_to_output)
 Insertion operator (overloaded so that XmlObjects can be "printed" in PyRosetta). More...
 

Typedef Documentation

typedef utility::pointer::shared_ptr< MultiplePoseMover const > protocols::rosetta_scripts::MultiplePoseMoverCOP
typedef utility::pointer::shared_ptr< MultiplePoseMover > protocols::rosetta_scripts::MultiplePoseMoverOP
typedef utility::pointer::weak_ptr< ParsedProtocol > protocols::rosetta_scripts::ParsedProtocolAP
typedef utility::pointer::weak_ptr< ParsedProtocol const > protocols::rosetta_scripts::ParsedProtocolCAP
typedef utility::pointer::shared_ptr< ParsedProtocol const > protocols::rosetta_scripts::ParsedProtocolCOP
typedef utility::pointer::shared_ptr< ParsedProtocol > protocols::rosetta_scripts::ParsedProtocolOP
typedef utility::pointer::shared_ptr< PosePropertyReporter const > protocols::rosetta_scripts::PosePropertyReporterCOP
typedef utility::pointer::shared_ptr< PoseSelector const > protocols::rosetta_scripts::PoseSelectorCOP
typedef utility::pointer::shared_ptr< PoseSelectorCreator const > protocols::rosetta_scripts::PoseSelectorCreatorCOP
typedef utility::pointer::shared_ptr< PoseSelectorFactory const > protocols::rosetta_scripts::PoseSelectorFactoryCOP
typedef utility::pointer::shared_ptr< PoseSelector > protocols::rosetta_scripts::PoseSelectorOP
typedef utility::pointer::shared_ptr< RosettaScriptsParser const > protocols::rosetta_scripts::RosettaScriptsParserCOP
typedef utility::pointer::shared_ptr< SavePoseMover const > protocols::rosetta_scripts::SavePoseMoverCOP
typedef utility::pointer::shared_ptr< SavePoseMover > protocols::rosetta_scripts::SavePoseMoverOP
using protocols::rosetta_scripts::TagCOPs = typedef utility::vector0<TagCOP>
typedef utility::pointer::weak_ptr< XmlObjects > protocols::rosetta_scripts::XmlObjectsAP
typedef utility::pointer::weak_ptr< XmlObjects const > protocols::rosetta_scripts::XmlObjectsCAP
typedef utility::pointer::shared_ptr< XmlObjects const > protocols::rosetta_scripts::XmlObjectsCOP
typedef utility::pointer::shared_ptr< XmlObjects > protocols::rosetta_scripts::XmlObjectsOP

Enumeration Type Documentation

Enumerator
PSF_NONE 
PSF_NEED_FULL_POSE_SET 

Function Documentation

void protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy ( utility::tag::XMLSchemaDefinition &  xsd,
utility::tag::XMLSchemaSimpleSubelementList &  subelements,
std::string const &  description 
)
void protocols::rosetta_scripts::attributes_for_parse_database_session ( utility::tag::XMLSchemaDefinition &  xsd,
utility::tag::AttributeList &  attlist 
)
void protocols::rosetta_scripts::attributes_for_parse_residue_selector ( utility::tag::AttributeList &  attributes,
std::string const &  description 
)
void protocols::rosetta_scripts::attributes_for_parse_xyz_vector ( utility::tag::AttributeList &  attlist)
void protocols::rosetta_scripts::attributes_for_saved_reference_pose ( utility::tag::AttributeList &  attributes,
std::string const &  attribute_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 attributes_for_saved_reference_pose_w_description().

Referenced by protocols::grafting::AnchoredGraftMover::complex_type_generator_for_anchored_graft_mover(), protocols::simple_filters::SidechainRmsdFilter::provide_xml_schema(), protocols::rosetta_scripts::SavePoseMover::provide_xml_schema(), protocols::simple_moves::SuperimposeMover::provide_xml_schema(), protocols::protein_interface_design::filters::LRmsdFilter::provide_xml_schema(), protocols::protein_interface_design::filters::FNatFilter::provide_xml_schema(), protocols::protein_interface_design::filters::IRmsdFilter::provide_xml_schema(), protocols::protein_interface_design::filters::SSamountFilter::provide_xml_schema(), protocols::protein_interface_design::filters::RmsdSimpleFilter::provide_xml_schema(), protocols::protein_interface_design::filters::RmsdFilter::provide_xml_schema(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::provide_xml_schema(), protocols::grafting::simple_movers::InsertPoseIntoPoseMover::provide_xml_schema(), protocols::simple_filters::DeltaFilter::provide_xml_schema(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::provide_xml_schema(), protocols::grafting::simple_movers::ReplaceRegionMover::provide_xml_schema(), protocols::features::ProteinRMSDFeatures::provide_xml_schema(), protocols::features::ProteinRMSDNoSuperpositionFeatures::provide_xml_schema(), protocols::matdes::SymUnsatHbondFilter::provide_xml_schema(), protocols::matdes::MatDesGreedyOptMutationMover::provide_xml_schema(), and protocols::antibody::AntibodyCDRGrafter::provide_xml_schema().

void protocols::rosetta_scripts::attributes_for_saved_reference_pose_w_description ( utility::tag::AttributeList &  attributes,
std::string const &  description,
std::string const &  attribute_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 core::pose::attributes_for_saved_reference_pose_w_description().

Referenced by attributes_for_saved_reference_pose(), and protocols::fold_from_loops::utils::Nub::provide_xml_definition().

void protocols::rosetta_scripts::common_movemap_complex_type_def ( utility::tag::XMLSchemaComplexTypeGenerator &  ct_gen)
std::string protocols::rosetta_scripts::complex_type_name_for_parsed_protocol_subelement ( std::string const &  foo)
core::Size protocols::rosetta_scripts::find_nearest_disulfide ( core::pose::Pose const &  pose,
core::Size const  res 
)
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 
)

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.

find source residue that is nearest to res on source. If distance is greater than 2.0A, return 0. chain=0, search all chains, chain=1,2,3 etc. search only that chain

References core::conformation::Residue::chain(), core::conformation::Residue::is_ligand(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::Splice::add_coordinate_constraints(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::Splice::add_dihedral_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::splice::SpliceOutAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceManager::adjust_stem_positions_by_template(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::alter_rotamer_set_from_pdb(), protocols::protein_interface_design::filters::RelativeSegmentFilter::apply(), protocols::simple_filters::StemFinder::apply(), protocols::legacy_sewing::LegacyAddStartnodeFragments::apply(), protocols::task_operations::DatabaseThread::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::task_operations::RestrictIdentitiesAtAlignedPositionsOperation::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::splice::Splice::copy_stretch(), protocols::splice::Splice::find_dbase_entry(), protocols::task_operations::DatabaseThread::find_length(), protocols::splice::RotLibOut::find_matching_res(), protocols::task_operations::DatabaseThread::mark_designable(), protocols::task_operations::DatabaseThread::mark_leave_as_is(), protocols::splice::nearest_to_entry_stop_on_pose(), protocols::relax::AtomCoordinateCstMover::set_constraints_on_func_groups(), protocols::splice::Splice::set_fold_tree(), protocols::splice::SpliceOutTail::set_source_from_to_res(), protocols::splice::SpliceOut::set_source_from_to_res(), and protocols::splice::SpliceOutTail::superimpose_source_on_pose().

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,
basic::datacache::DataMap &  data,
core::select::movemap::MoveMapFactoryOP  mmf 
)

utility function for parse_movemap which goes over each of the tags in a movemap section

References core::sequence::end, core::select::movemap::mm_disable, core::select::movemap::mm_enable, and core::select::residue_selector::parse_residue_selector().

Referenced by parse_movemap_factory_legacy().

core::pose::PoseCOP protocols::rosetta_scripts::legacy_saved_pose_or_input ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data,
std::string const &  class_name,
bool  use_native = true,
std::string const &  refname = "reference_name" 
)

Retrieve the reference pose. If not given, fall back to the native pose (if asked for), or the input pose as a last resort. Will print a warning message if the input pose is used.

The XSD is the same as for saved_reference_pose.

References protocols::jd2::get_current_jobs_starting_pose(), protocols::jd2::jd2_used(), core::pose::saved_native_pose(), core::pose::saved_reference_pose(), and TR().

Referenced by protocols::rbsegment_relax::MakeStarTopologyMover::parse_my_tag(), protocols::simple_filters::SidechainRmsdFilter::parse_my_tag(), protocols::seeded_abinitio::GrowPeptides::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::fold_from_loops::movers::AlignByResidueSelectorMover::parse_my_tag(), protocols::protein_interface_design::movers::InterfaceRecapitulationMover::parse_my_tag(), protocols::simple_moves::FavorSequenceProfile::parse_my_tag(), protocols::protein_interface_design::movers::PlacementMinimizationMover::parse_my_tag(), protocols::protein_interface_design::filters::LRmsdFilter::parse_my_tag(), protocols::protein_interface_design::filters::StubScoreFilter::parse_my_tag(), protocols::protein_interface_design::filters::FNatFilter::parse_my_tag(), protocols::protein_interface_design::filters::IRmsdFilter::parse_my_tag(), protocols::contact_map::ContactMap::parse_my_tag(), protocols::protein_interface_design::filters::RmsdFilter::parse_my_tag(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::parse_my_tag(), protocols::protein_interface_design::movers::PlacementAuctionMover::parse_my_tag(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::parse_my_tag(), protocols::simple_filters::MutationsFilter::parse_my_tag(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::parse_my_tag(), protocols::features::ProteinRMSDFeatures::parse_my_tag(), protocols::features::ProteinRMSDNoSuperpositionFeatures::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), and protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag().

std::string protocols::rosetta_scripts::move_map_tag_namer ( std::string const &  subelement_name)
std::string protocols::rosetta_scripts::mpm_mangler ( std::string const &  element_name)
std::ostream& protocols::rosetta_scripts::operator<< ( std::ostream &  output,
XmlObjects const &  object_to_output 
)

Insertion operator (overloaded so that XmlObjects can be "printed" in PyRosetta).

References protocols::rosetta_scripts::XmlObjects::show().

std::string protocols::rosetta_scripts::optionally_named_move_map_ct_namer ( std::string const &  )
utility::sql_database::sessionOP protocols::rosetta_scripts::parse_database_session ( utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)

This is kind of a strange place for this, but for library-level reasons it needs to be more accessible than a more logical home with ReportToDB, and cannot live in basic because it needs other functions in this file. (There is also value in not creating a new file b/c it breaks the fast-compile system XML XSD XRW is using, and it's 6pm on Friday!)

References TR().

Referenced by protocols::loops::loops_definers::LoopsDatabaseDefiner::parse_my_tag(), protocols::features::ReportToDB::parse_my_tag(), and protocols::task_operations::ReadResfileFromDB::parse_tag().

protocols::filters::FilterOP protocols::rosetta_scripts::parse_filter ( std::string const &  filter_name,
basic::datacache::DataMap const &  data 
)

Return the Filter with the given name. Raise a RosettaScriptsOptionError if not present.

Referenced by protocols::monte_carlo::ResetBaselineMover::parse_my_tag(), protocols::simple_moves::ContingentAcceptMover::parse_my_tag(), protocols::protein_interface_design::movers::SetTemperatureFactor::parse_my_tag(), protocols::calc_taskop_filters::Operator::parse_my_tag(), protocols::calc_taskop_filters::Sigmoid::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::filters::ReplicateFilter::parse_my_tag(), protocols::protein_interface_design::filters::BoltzmannFilter::parse_my_tag(), protocols::protein_interface_design::movers::LoopOver::parse_my_tag(), protocols::simple_filters::ReportFilter::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::filters::CalculatorFilter::parse_my_tag(), protocols::loophash::LoopHashMoverWrapper::parse_my_tag(), protocols::moves::IteratedConvergenceMover::parse_my_tag(), protocols::enzdes::RemoveLigandFilter::parse_my_tag(), protocols::simple_ddg::DdgFilter::parse_my_tag(), protocols::moves::FilterReportAsPoseExtraScoresMover::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::protein_interface_design::filters::FilterScanFilter::parse_my_tag(), protocols::simple_ddg::ddG::parse_my_tag(), protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(), protocols::helical_bundle::BackboneGridSampler::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::features::DdGFeatures::parse_my_tag(), protocols::splice::Splice::parse_my_tag(), protocols::loophash::LoopHashDiversifier::parse_my_tag(), protocols::simple_filters::RangeFilter::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), protocols::filters::FilterValueMetric::parse_my_tag(), protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag(), protocols::motif_grafting::movers::MotifGraftMover::parse_my_tag(), protocols::filters::IfThenFilter::parse_my_tag(), and protocols::splice::SpliceOut::parse_SpliceOut_tags().

protocols::filters::FilterOP protocols::rosetta_scripts::parse_filter_or_null ( std::string const &  filter_name,
basic::datacache::DataMap const &  data 
)
core::select::movemap::MoveMapFactoryOP protocols::rosetta_scripts::parse_movemap_factory_legacy ( utility::tag::TagCOP  in_tag,
basic::datacache::DataMap &  data,
bool const  reset_movemap = true,
core::select::movemap::MoveMapFactoryOP  mmf_to_modify = nullptr 
)

Parse a MoveMap factory from tags using the old MoveMap specification syntax.

Will return nullptr if the tag doesn't contain a MoveMap specification.

References foreach_movemap_tag(), core::select::movemap::get_movemap_factory(), core::select::movemap::movemap_factory_category(), parse_movemap_tag(), and TR().

Referenced by protocols::md::CartesianMD::parse_movemap(), protocols::minimization_packing::MinMover::parse_movemap_factory(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::simple_moves::RandomOmegaFlipMover::parse_my_tag(), protocols::simple_moves::RandomTorsionMover::parse_my_tag(), protocols::simple_moves::DisulfideInsertionMover::parse_my_tag(), protocols::normalmode::NormalModeRelaxMover::parse_my_tag(), protocols::normalmode::NormalModeMinimizer::parse_my_tag(), protocols::simple_moves::RingConformationMover::parse_my_tag(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::parse_my_tag(), protocols::carbohydrates::RingPlaneFlipMover::parse_my_tag(), protocols::minimization_packing::PertMinMover::parse_my_tag(), protocols::cryst::SetCrystWeightMover::parse_my_tag(), protocols::nonlocal::SingleFragmentMover::parse_my_tag(), protocols::relax::FastRelax::parse_my_tag(), protocols::simple_moves::BBGaussianMover::parse_my_tag(), protocols::simple_moves::BackboneMover::parse_my_tag(), protocols::flxbb::FlxbbDesign::parse_my_tag(), and parse_named_movemap_factory_legacy().

void protocols::rosetta_scripts::parse_movemap_tag ( utility::tag::TagCOP const  in_tag,
core::select::movemap::MoveMapFactoryOP  mmf 
)
protocols::moves::MoverOP protocols::rosetta_scripts::parse_mover ( std::string const &  mover_name,
basic::datacache::DataMap const &  data 
)

Return the Mover with the given name. Raise a RosettaScriptsOptionError if not present.

Referenced by protocols::simple_moves::ContingentAcceptMover::parse_my_tag(), protocols::simple_filters::DeltaFilter::parse_my_tag(), protocols::protein_interface_design::movers::LoopOver::parse_my_tag(), protocols::calc_taskop_filters::RelativePoseFilter::parse_my_tag(), protocols::protein_interface_design::filters::BindingStrainFilter::parse_my_tag(), protocols::protein_interface_design::movers::MapHotspot::parse_my_tag(), protocols::evolution::AlignmentAAFinder::parse_my_tag(), protocols::moves::IteratedConvergenceMover::parse_my_tag(), protocols::forge::constraints::RemoveRemodelCsts::parse_my_tag(), protocols::recon_design::MSDMover::parse_my_tag(), protocols::features::InterfaceDdGMover::parse_my_tag(), protocols::enzdes::RemoveLigandFilter::parse_my_tag(), protocols::simple_ddg::DdgFilter::parse_my_tag(), protocols::features::RotamerRecoveryFeatures::parse_my_tag(), protocols::generalized_kinematic_closure::GeneralizedKIC::parse_my_tag(), protocols::design_opt::GreedyOptMutationMover::parse_my_tag(), protocols::simple_ddg::ddG::parse_my_tag(), protocols::rotamer_recovery::RotamerRecoveryMover::parse_my_tag(), protocols::helical_bundle::BackboneGridSampler::parse_my_tag(), protocols::simple_ddg::DdGScan::parse_my_tag(), protocols::docking::DockSetupMover::parse_my_tag(), protocols::helical_bundle::BundleGridSampler::parse_my_tag(), protocols::pose_creation::SliceToMiniProteinMover::parse_my_tag(), protocols::monte_carlo::GenericSimulatedAnnealer::parse_my_tag(), protocols::simple_ddg::SSElementBisectddGFilter::parse_my_tag(), protocols::canonical_sampling::MetropolisHastingsMover::parse_my_tag(), protocols::backrub::BackrubProtocol::parse_my_tag(), protocols::moves::RampingMover::parse_my_tag(), and protocols::fldsgn::BluePrintBDR::parse_my_tag().

protocols::moves::MoverOP protocols::rosetta_scripts::parse_mover_or_null ( std::string const &  mover_name,
basic::datacache::DataMap const &  data 
)
std::pair< moves::MoverOP, std::string > protocols::rosetta_scripts::parse_mover_subtag ( utility::tag::TagCOP const  tag_ptr,
basic::datacache::DataMap &  data 
)
core::select::movemap::MoveMapFactoryOP protocols::rosetta_scripts::parse_named_movemap_factory_legacy ( utility::tag::TagCOP  in_tag,
std::string const &  name,
basic::datacache::DataMap &  data,
bool const  reset_movemap = true,
core::select::movemap::MoveMapFactoryOP  mmf_to_modify = nullptr 
)

Parse a MoveMap factory from tags using the old MoveMap specification syntax. Will look for a MoveMap entry with a particular name entry.

Will return nullptr if the tag doesn't contain a MoveMap specification.

References parse_movemap_factory_legacy().

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

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().

bool protocols::rosetta_scripts::print_information ( std::string const &  component_name,
std::stringstream &  outstream 
)
void protocols::rosetta_scripts::print_information ( utility::vector1< std::string > const &  component_names)

Prints out XSD information about the XML-accessible options for a given set of RosettaScipts-accessible movers, filters, task operations, residue selectors, simple metric, or packer palette.

Prints out XSD information about the XML-accessible options for a given set of RosettaScipts-accessible movers, filters, task operations, residue selectors, simple metrics, or packer palettes.

Calls the single string version.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References print_information(), and TR().

void protocols::rosetta_scripts::print_template_script ( )

Prints out an empty template RosettaScript to the tracer.

This is kind of a strange place for this, but for library-level reasons it needs to be more accessible than a more logical home with ReportToDB, and cannot live in basic because it needs other functions in this file. (There is also value in not creating a new file b/c it breaks the fast-compile system XML XSD XRW is using, and it's 6pm on Friday!)

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Prints out an empty template RosettaScript to the tracer.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References TR().

void protocols::rosetta_scripts::recursively_access_all_attributes ( utility::tag::TagCOP  tag)

Recurse through the tree of Tags and for each one, read each option, so that every option is set as "read".

As a safety check to make sure that no options are misspelled, at the conclusion of parsing, all options contained in all tags are examined to determine if they have been accessed or not. If an option has not been accessed, then an error message is written to the screen, and the program exits. However, it is not possible to parse all movers in the absence of the Pose that is going to be used, and that Pose isn't available to the MPM until execution. So we work around this issue by accessing each of the options in the input tag and all of its children

Referenced by protocols::rosetta_scripts::MultiplePoseMover::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 
)
void protocols::rosetta_scripts::save_schema ( std::string const &  filename)

Saves the XSD to the given file.

References TR(), and protocols::rosetta_scripts::RosettaScriptsParser::xsd_for_rosetta_scripts().

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 
)
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.PosePropertyReporterFactory"  )
static
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.PoseSelectorFactory"  )
static
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.AdditionalOutputWrapper"  )
static

Referenced by protocols::rosetta_scripts::MultiplePoseMover::apply(), protocols::rosetta_scripts::ParsedProtocol::apply(), protocols::rosetta_scripts::ParsedProtocol::apply_filter(), protocols::rosetta_scripts::ParsedProtocol::apply_mover(), protocols::rosetta_scripts::RosettaScriptsJobQueen::complete_larval_job_maturation(), protocols::rosetta_scripts::XmlObjects::create_from_file(), protocols::rosetta_scripts::XmlObjects::create_from_string(), protocols::rosetta_scripts::RosettaScriptsJobQueen::derived_process_deallocation_message(), protocols::rosetta_scripts::MultiplePoseMover::fill_input_cache(), protocols::rosetta_scripts::RosettaScriptsParser::finish_creating_tag(), protocols::rosetta_scripts::ParsedProtocol::finish_protocol(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover(), protocols::rosetta_scripts::RosettaScriptsParser::generate_mover_for_protocol(), protocols::rosetta_scripts::MultipleOutputWrapper::generate_pose(), protocols::rosetta_scripts::ParsedProtocol::get_additional_output(), protocols::rosetta_scripts::RosettaScriptsParser::import_tags(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_filter(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_mover(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_packer_palette(), protocols::rosetta_scripts::RosettaScriptsParser::instantiate_taskoperation(), legacy_saved_pose_or_input(), protocols::rosetta_scripts::RosettaScriptsParser::load_native(), protocols::rosetta_scripts::PosePropertyReporterFactory::newPosePropertyReporter(), protocols::rosetta_scripts::PoseSelectorFactory::newPoseSelector(), protocols::rosetta_scripts::RosettaScriptsParser::parse_apply_to_pose_tag(), parse_database_session(), parse_movemap_factory_legacy(), parse_mover_subtag(), protocols::rosetta_scripts::SavePoseMover::parse_my_tag(), protocols::rosetta_scripts::PosePropertyReporter::parse_my_tag(), protocols::rosetta_scripts::PoseSelector::parse_my_tag(), protocols::rosetta_scripts::MultiplePoseMover::parse_my_tag(), protocols::rosetta_scripts::ParsedProtocol::parse_my_tag(), protocols::rosetta_scripts::RosettaScriptsParser::parse_resources_tag(), print_information(), print_template_script(), protocols::rosetta_scripts::MultiplePoseMover::process_pose(), protocols::rosetta_scripts::MultiplePoseMover::process_poses(), protocols::rosetta_scripts::RosettaScriptsParser::read_in_and_recursively_replace_includes(), protocols::rosetta_scripts::RosettaScriptsJobQueen::RosettaScriptsJobQueen(), save_schema(), protocols::rosetta_scripts::MultiplePoseMover::select_poses(), protocols::rosetta_scripts::XmlObjects::static_get_filter(), protocols::rosetta_scripts::XmlObjects::static_get_mover(), protocols::rosetta_scripts::XmlObjects::static_get_residue_selector(), protocols::rosetta_scripts::XmlObjects::static_get_score_function(), protocols::rosetta_scripts::XmlObjects::static_get_simple_metric(), protocols::rosetta_scripts::XmlObjects::static_get_task_operation(), protocols::rosetta_scripts::RosettaScriptsParser::substitute_variables_in_stream(), protocols::rosetta_scripts::RosettaScriptsParser::validate_input_script_against_xsd(), and protocols::rosetta_scripts::RosettaScriptsParser::xsd_for_rosetta_scripts().

static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.MultiplePoseMover"  )
static
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.MultipleOutputWrapper"  )
static
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.RosettaScriptsJobQueen"  )
static
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.ParsedProtocol"  )
static
static basic::Tracer protocols::rosetta_scripts::TR ( "protocols.rosetta_scripts.RosettaScriptsParser"  )
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