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util.hh File Reference

Utilities for JD2, which are somewhat safe to use outside of the JD2 system itself. More...

#include <core/pose/Pose.fwd.hh>
#include <core/io/silent/SilentStruct.fwd.hh>
#include <core/types.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <utility/vector1.hh>
#include <utility/file/FileName.hh>
#include <utility/options/OptionCollection.fwd.hh>
#include <utility/options/keys/OptionKeyList.fwd.hh>
#include <string>
#include <map>
#include <list>


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


bool protocols::jd2::jd2_used ()
 is this application running with JD2? Useful for code that might not be running under JD2. More...
std::string protocols::jd2::current_input_tag ()
 What is the tag of the current input structure? More...
core::Size protocols::jd2::current_nstruct_index ()
 What 'nstruct' value are we currently processing? More...
core::Size protocols::jd2::max_nstruct_index ()
 What's the maximum nstruct we're processing? More...
std::string protocols::jd2::current_output_name ()
 gets used output name of pose ask jd for current-job —> ask jobOutputter for name of this job More...
std::string protocols::jd2::current_output_filename ()
 call the 'filename' accessor of the current job-distributor with the current job More...
std::string protocols::jd2::current_batch ()
core::Size protocols::jd2::current_batch_id ()
core::Size protocols::jd2::current_replica ()
 returns 0 if no replicas (i.e., multiple processes per job ) otherwise it returns the sub-rank of the process within the job starting at 1 More...
core::pose::PoseCOP protocols::jd2::get_current_jobs_starting_pose ()
 Get the starting structure for the current run. Will return a null pointer if that is not possible. More...
void protocols::jd2::output_intermediate_pose (core::pose::Pose const &pose, std::string const &stage_tag, int copy_count, bool score_only)
 end parser interface, start Job Distributor interface///////////// More...
void protocols::jd2::add_string_to_current_job (std::string const &string_in)
 add output string More...
void protocols::jd2::add_strings_to_current_job (std::list< std::string > const &strings)
 add output strings More...
void protocols::jd2::add_string_string_pair_to_current_job (std::string const &string1, std::string const &string2)
 add a string/string pair More...
void protocols::jd2::add_string_real_pair_to_current_job (std::string const &string_in, core::Real const real_in)
 add a string/real pair More...
std::list< std::string > protocols::jd2::get_strings_from_current_job ()
std::map< std::string,
std::string > 
protocols::jd2::get_string_string_pairs_from_current_job ()
std::map< std::string, core::Realprotocols::jd2::get_string_real_pairs_from_current_job ()
void protocols::jd2::add_current_job_data_to_ss (core::io::silent::SilentStructOP ss)
void protocols::jd2::write_score_tracer (core::pose::Pose const &pose_in, std::string tracer_point)
< utility::file::FileName > 
protocols::jd2::input_pdb_files_from_command_line ()
 Read the -s and -l flags to get a list of PDB files that should be read in and operated upon. More...
void protocols::jd2::set_native_in_mover (protocols::moves::Mover &mover)
 Set the "native" for the Mover by reading from the global option collection. More...
void protocols::jd2::set_native_in_mover (protocols::moves::Mover &mover, utility::options::OptionCollection const &options)
 Set the "native" for the Mover by reading from a possibly-local option collection. More...
void protocols::jd2::options_for_set_native_in_mover (utility::options::OptionKeyList &opts)
 Companion function for set_native_in_mover that reports on the options that are read out of the (possibly-local) option collection. More...

Detailed Description

Utilities for JD2, which are somewhat safe to use outside of the JD2 system itself.

For utilities internal to the jd2 system, see internal_util.hh

Andrew Leaver-Fay
Steven Lewis