util.hh File Reference

#include <core/pose/Pose.fwd.hh>
#include <protocols/filters/Filter.fwd.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <core/types.hh>
#include <basic/datacache/DataMap.hh>
#include <core/pack/task/TaskFactory.fwd.hh>
#include <core/pack/task/operation/TaskOperation.fwd.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <utility/tag/Tag.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <string>
#include <set>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>

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

Functions
utility::vector1 < core::pack::task::operation::TaskOperationOP >	protocols::rosetta_scripts::get_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
core::pack::task::TaskFactoryOP	protocols::rosetta_scripts::parse_task_operations (utility::tag::TagCOP tag, 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) More...
core::pack::task::TaskFactoryOP	protocols::rosetta_scripts::parse_task_operations (std::string const &task_list, basic::datacache::DataMap const &data)
core::select::residue_selector::ResidueSelectorCOP	protocols::rosetta_scripts::parse_residue_selector (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
	returns a residue selector given a tag and datamap More...
core::select::residue_selector::ResidueSelectorCOP	protocols::rosetta_scripts::get_residue_selector (std::string const &selector_name, basic::datacache::DataMap const &data)
	returns a residue selector given a selector's name and datamap More...
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="talaris2013")
	Look up the score function defined in the <SCOREFXNS> through the given option. Default to 'talaris2013' by default. More...
core::scoring::ScoreFunctionOP	protocols::rosetta_scripts::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	protocols::rosetta_scripts::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	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. More...
core::pose::PoseOP	protocols::rosetta_scripts::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	protocols::rosetta_scripts::parse_movemap (utility::tag::TagCOP in_tag, core::pose::Pose const &pose, core::kinematics::MoveMapOP &mm, basic::datacache::DataMap &, bool const reset_movemap=true)
	variant of parse_movemap that takes in a datamap and searches it for already existing movemaps Still resets movemap if MoveMap branch not found! More...
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)
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=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	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. More...
protocols::filters::FilterOP	protocols::rosetta_scripts::parse_filter (std::string const &filter_name, protocols::filters::Filters_map const &filters)
protocols::moves::MoverOP	protocols::rosetta_scripts::parse_mover (std::string const &mover_name, protocols::moves::Movers_map const &movers)
numeric::xyzVector< core::Real >	protocols::rosetta_scripts::parse_xyz_vector (utility::tag::TagCOP const xyz_vector_tag)
	utility function for parsing xyzVector More...
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::Size >	protocols::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::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...