standard_mains.cc File Reference

#include <utility/io/izstream.hh>
#include <protocols/jobdist/JobDistributors.hh>
#include <protocols/jobdist/standard_mains.hh>
#include <core/types.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/ScoreFileSilentStruct.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/SilentStruct.hh>
#include <core/io/silent/SilentStructFactory.hh>
#include <basic/options/option.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/datacache/CacheableString.hh>
#include <basic/datacache/DiagnosticData.hh>
#include <basic/Tracer.hh>
#include <protocols/jobdist/Jobs.hh>
#include <protocols/moves/Mover.hh>
#include <protocols/idealize/IdealizeMover.hh>
#include <numeric/random/random_permutation.hh>
#include <utility/exit.hh>
#include <utility/file/FileName.hh>
#include <utility/pointer/owning_ptr.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/MembraneTopology.hh>
#include <core/chemical/ChemicalManager.hh>
#include <algorithm>
#include <map>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>
#include <core/import_pose/atom_tree_diffs/atom_tree_diff.hh>
#include <core/io/silent/ProteinSilentStruct.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <protocols/evaluation/PoseEvaluator.hh>
#include <protocols/evaluation/EvaluatorFactory.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>
#include <utility/file/file_sys_util.hh>

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

Functions
static thread_local basic::Tracer	protocols::jobdist::TR ("protocols.jobdist.main")
utility::vector1< BasicJobOP >	protocols::jobdist::load_s_and_l ()
	Reads inputs from -s/-l/-nstruct and writes atomtree_diff silent files. Supplied Mover is used to transform input structure into output structure. undefined - commenting out to make pyrosetta compile... More...
std::string	protocols::jobdist::get_output_tag (core::pose::Pose const &pose)
	Helper function to safely get current output tag that's cached in Pose. More...
std::map< std::string, core::Real >	protocols::jobdist::get_score_map (core::pose::Pose const &pose)
	Helper function to safely get score_map that's cached in Pose. More...
void	protocols::jobdist::register_options_universal_main ()
	Handles loading and writing of silent files and or PDB files - superseeds the bottom two functions. More...
int	protocols::jobdist::universal_main (protocols::moves::Mover &mover, float thinout_factor)
int	protocols::jobdist::main_plain_mover (protocols::moves::Mover &mover, bool random_permutation=true)
	Reads inputs from -s/-l/-nstruct and writes (possibly gzipped) PDB files. Supplied Mover is used to transform input structure into output structure. More...
int	protocols::jobdist::main_plain_pdb_mover (protocols::moves::Mover &mover, core::scoring::ScoreFunctionOP scorefxn)
	Reads inputs from -s/-l/-nstruct and writes (possibly gzipped) PDB files. Supplied Mover is used to transform input structure into output structure. More...
int	protocols::jobdist::main_atom_tree_diff_mover (protocols::moves::Mover &mover, core::scoring::ScoreFunctionOP scorefxn)

Detailed Description

Author

Ian W. Davis