Rosetta Protocols  2014.35
Namespaces | Functions | Variables
util.cc File Reference

Utility functions useful in RosettaScripts. More...

#include <protocols/rosetta_scripts/util.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/types.hh>
#include <core/init/score_function_corrections.hh>
#include <protocols/filters/Filter.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/pose/PDBInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <boost/foreach.hpp>
#include <core/pack/task/operation/TaskOperation.hh>
#include <core/pack/task/TaskFactory.hh>
#include <basic/datacache/DataMap.hh>
#include <protocols/moves/Mover.hh>
#include <core/id/types.hh>
#include <core/chemical/VariantType.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/inout.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <utility/tag/Tag.hh>
#include <utility/sql_database/types.hh>
#include <utility/vector0.hh>
#include <utility/excn/Exceptions.hh>

Namespaces

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

Functions

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 (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) More...
 
utility::vector1
< core::pack::task::operation::TaskOperationOP
protocols::rosetta_scripts::get_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
 
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::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 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)
 variant of parse_movemap that takes in a datamap and searches it for already existing movemaps 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::Realprotocols::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...
 
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...
 
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...
 
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...
 

Variables

static basic::Tracer TR ("protocols.RosettaScripts.util")
 

Detailed Description

Utility functions useful in RosettaScripts.

Authors
Sarel Fleishman (sarel.nosp@m.f@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), Jacob Corn (jecor.nosp@m.n@u..nosp@m.washi.nosp@m.ngto.nosp@m.n.edu), Rocco Moretti (rmore.nosp@m.tti@.nosp@m.u.was.nosp@m.hing.nosp@m.ton.e.nosp@m.du), Eva-Maria Strauch (evas0.nosp@m.1@uw.nosp@m..edu)

Variable Documentation

basic::Tracer TR("protocols.RosettaScripts.util")
static