dgdp.cc File Reference

#include <basic/options/keys/edensity.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/testing.OptionKeys.gen.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/option_macros.hh>
#include <basic/Tracer.hh>
#include <core/fragment/util.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/electron_density/ElectronDensity.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <core/util/SwitchResidueTypeSet.hh>
#include <devel/init.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyzVector.io.hh>
#include <protocols/electron_density/DockPDBIntoDensityMover.hh>
#include <protocols/electron_density/SetupForDensityScoringMover.hh>
#include <protocols/electron_density/util.hh>
#include <protocols/moves/Mover.fwd.hh>
#include <protocols/simple_moves/SwitchResidueTypeSetMover.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <utility/excn/Exceptions.hh>
#include <algorithm>
#include <chrono>
#include <iostream>
#include <string>

Functions
void	check_inputs_for_errors ()
void	set_basic_dock_options (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	get_pts (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	do_search (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	combine_search (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	results_to_pdb (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	do_refinement (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	manual_refine (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	combine_refinement (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	cluster_silent (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
void	run_aio (protocols::electron_density::DockPDBIntoDensityMoverOP const &dock)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.dgdp")

Function Documentation

check_inputs_for_errors()

void check_inputs_for_errors

(

)

References CREATE_EXCEPTION, kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, SmotifHasher::mode, basic::options::OptionKeys::in::file::native, basic::options::option, basic::options::OptionKeys::in::file::s, utility::string_split(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by set_basic_dock_options().

cluster_silent()

void cluster_silent

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::options::option, basic::options::OptionKeys::in::file::silent, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and basic::Tracer::Warning.

Referenced by main().

combine_refinement()

void combine_refinement

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::options::option, basic::options::OptionKeys::in::file::silent, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

combine_search()

void combine_search

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::options::option, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::in::file::s.

Referenced by main().

do_refinement()

void do_refinement

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::options::option, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::in::file::s.

Referenced by main().

do_search()

void do_search

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::options::option, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::in::file::s.

Referenced by main().

get_pts()

void get_pts

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, create_a3b_hbs::i, basic::options::option, pyrosetta.distributed.io::pose_from_file, add_xyz_to_pose::pts, basic::options::OptionKeys::in::file::s, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

main()

int main	(	int	argc,
		char *	argv[]
	)

References argv, cluster_silent(), combine_refinement(), combine_search(), utility::io::oc::cout, CREATE_EXCEPTION, do_refinement(), do_search(), basic::options::OptionKeys::matdes::dock::dock, test.T009_Exceptions::e, end, get_pts(), basic::init(), basic::options::OptionKeys::testing::INTEGRATION_TEST, manual_refine(), min(), SmotifHasher::mode, NEW_OPT, basic::options::OptionKeys::out::nooutput, basic::options::option, results_to_pdb(), run_aio(), set_basic_dock_options(), basic::options::OptionKeys::cutoutdomain::start, basic::options::TR, and value.

manual_refine()

void manual_refine

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::options::option, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::in::file::s.

Referenced by main().

results_to_pdb()

void results_to_pdb

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::options::option, pyrosetta.distributed.io::pose_from_file, and basic::options::OptionKeys::in::file::s.

Referenced by main().

run_aio()

void run_aio

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::out::file::silent, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and basic::Tracer::Warning.

Referenced by main().

set_basic_dock_options()

void set_basic_dock_options

(

protocols::electron_density::DockPDBIntoDensityMoverOP const &

dock

)

References aa, check_inputs_for_errors(), CREATE_EXCEPTION, basic::options::OptionKeys::matdes::dock::dock, basic::Tracer::Fatal, lactamize::filename, create_a3b_hbs::i, create_a3b_hbs::j, min(), SmotifHasher::mode, basic::options::option, basic::options::OptionKeys::out::overwrite, pyrosetta.distributed.io::pose_from_file, residue, loops_kic::rms, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::out::file::silent, subloop_histogram::size, utility::string_split(), basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and basic::Tracer::Warning.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.dgdp") ( "apps.dgdp"  )

static