Rosetta  2020.50
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Namespaces | Functions
util.hh File Reference
#include <core/types.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/pack/task/xml_util.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pack/task/operation/TaskOperation.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/xml_util.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/select/movemap/MoveMapFactory.fwd.hh>
#include <core/select/residue_selector/util.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <utility/sql_database/DatabaseSessionManager.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <utility/tag/XMLSchemaGeneration.fwd.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <basic/datacache/DataMap.hh>
#include <string>
#include <set>

Namespaces

 protocols
 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
 
 protocols::rosetta_scripts
 

Functions

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. More...
 
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 &dist, core::Size const chain=0)
 find nearest residue and also return the distance More...
 
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 More...
 
utility::vector1< core::Sizeprotocols::rosetta_scripts::residue_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...
 
void protocols::rosetta_scripts::attributes_for_parse_residue_selector (utility::tag::AttributeList &attributes, std::string const &description)
 Appends the attributes read by parse_residue_selector. More...
 
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. More...
 
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. More...
 
void protocols::rosetta_scripts::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...
 
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)
 
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. More...
 
void protocols::rosetta_scripts::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 protocols::rosetta_scripts::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...
 
protocols::filters::FilterOP protocols::rosetta_scripts::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 protocols::rosetta_scripts::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 protocols::rosetta_scripts::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 protocols::rosetta_scripts::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...
 
numeric::xyzVector< core::Realprotocols::rosetta_scripts::parse_xyz_vector (utility::tag::TagCOP const xyz_vector_tag)
 utility function for parsing xyzVector More...
 
void protocols::rosetta_scripts::attributes_for_parse_xyz_vector (utility::tag::AttributeList &attlist)
 
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!) More...
 
void protocols::rosetta_scripts::attributes_for_parse_database_session (utility::tag::XMLSchemaDefinition &xsd, utility::tag::AttributeList &attlist)
 
void protocols::rosetta_scripts::print_template_script ()
 Prints out an empty template RosettaScript to the tracer. More...
 
bool protocols::rosetta_scripts::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 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. More...
 
void protocols::rosetta_scripts::save_schema (std::string const &filename)
 Saves the XSD to the given file. More...