helical_param.cc File Reference

#include <devel/init.hh>
#include <core/chemical/ChemicalManager.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <basic/options/keys/pose_metrics.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/ufv.OptionKeys.gen.hh>
#include <basic/options/keys/remodel.OptionKeys.gen.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/io/pdb/pose_io.hh>
#include <basic/Tracer.hh>
#include <protocols/forge/build/ConnectRight.hh>
#include <protocols/forge/build/RelativeConnectRight.hh>
#include <protocols/forge/build/RelativeSequencePosition.hh>
#include <protocols/forge/build/SegmentInsert.hh>
#include <protocols/forge/build/SegmentRebuild.hh>
#include <protocols/forge/components/BDR.hh>
#include <protocols/forge/remodel/RemodelMover.hh>
#include <protocols/forge/remodel/RemodelGlobalFrame.hh>
#include <protocols/forge/remodel/RemodelGlobalFrame.fwd.hh>
#include <protocols/simple_filters/PoseMetricEvaluator.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/JobOutputter.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/PyMOLMover.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/options/keys/OptionKey.hh>
#include <boost/lexical_cast.hpp>
#include <boost/tokenizer.hpp>
#include <boost/algorithm/string.hpp>
#include <string>
#include <vector>
#include <core/import_pose/import_pose.hh>
#include <core/pose/annotated_sequence.hh>

Typedefs
typedef std::string	String
typedef std::vector< OptionKey const * >	KeyVec

Functions
void	fill_required_options (KeyVec &keys)
void	fill_optional_options (KeyVec &keys)
void	register_options (KeyVec &keys)
bool	check_required_options (KeyVec &keys)
bool	check_option_conflicts ()
core::Size	load_loops_from_file (protocols::forge::components::BDR &bdr, utility::file::FileName const &filename)
	load ufv loops from file More...
void *	graphics_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.possu.helical_param")

Typedef Documentation

KeyVec

typedef std::vector< OptionKey const * > KeyVec

String

typedef std::string String

Function Documentation

check_option_conflicts()

bool check_option_conflicts

(

)

References basic::Tracer::Fatal, basic::options::OptionKeys::run::max_retry_job, basic::options::option, and basic::options::TR.

check_required_options()

bool check_required_options

(

KeyVec &

keys

)

References create_a3b_hbs::i, basic::options::option, and option.

fill_optional_options()

void fill_optional_options

(

KeyVec &

keys

)

References basic::options::OptionKeys::remodel::blueprint, basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::out::pdb, basic::options::OptionKeys::out::pdb_gz, basic::options::OptionKeys::in::file::s, basic::options::OptionKeys::in::file::silent, basic::options::OptionKeys::out::file::silent, basic::options::OptionKeys::out::silent_gz, basic::options::OptionKeys::out::file::silent_struct_type, and basic::options::OptionKeys::in::file::vall.

Referenced by main().

fill_required_options()

void fill_required_options

(

KeyVec &

keys

)

References basic::options::OptionKeys::in::path::database, basic::options::OptionKeys::run::max_retry_job, basic::options::OptionKeys::pose_metrics::neighbor_by_distance_cutoff, and basic::options::OptionKeys::out::nstruct.

graphics_main()

void* graphics_main

(

void *

)

References basic::options::OptionKeys::ufv::aa_during_build, basic::options::OptionKeys::ufv::aa_during_design_refine, utility::io::oc::cout, basic::options::option, pyrosetta.io::pose_from_pdb(), kic_runner::remodel, basic::options::OptionKeys::remodel::repeat_structure, basic::options::OptionKeys::in::file::s, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

load_loops_from_file()

core::Size load_loops_from_file	(	protocols::forge::components::BDR &	bdr,
		utility::file::FileName const &	filename
	)

load ufv loops from file

Returns

number of loops read

References basic::options::OptionKeys::ufv::aa_during_build, basic::options::OptionKeys::ufv::aa_during_design_refine, utility::vectorL< L, T, A >::at(), count, basic::Tracer::Error, utility::options::OptionKeys::options::exit, lactamize::filename, getline(), basic::options::OptionKeys::in::in, basic::options::OptionKeys::ufv::keep_junction_torsions, basic::options::OptionKeys::ufv::left, line, basic::options::option, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::ufv::right, challenge::ss, and basic::options::TR.

main()

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

References argv, fill_optional_options(), graphics_main(), basic::init(), basic::options::option, register_options(), and viewer_main().

register_options()

void register_options

(

KeyVec &

keys

)

References create_a3b_hbs::i, basic::options::option, and option.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.possu.helical_param") ( "apps.pilot.possu.helical_param"  )

static