ufv.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 <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/io/pdb/pdb_writer.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/evaluation/PoseMetricEvaluator.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <protocols/jd2/JobOutputter.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <protocols/viewer/viewers.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/options/keys/OptionKey.hh>
#include <utility/excn/Exceptions.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>
#include <protocols/evaluation/PoseEvaluator.hh>
#include <protocols/jumping/StrandPairing.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	setup_segment_insert (protocols::forge::components::BDR &bdr)
void *	graphics_main (void *)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("apps.pilot.yab.ufv")

Typedef Documentation

KeyVec

typedef std::vector< OptionKey const * > KeyVec

String

typedef std::string String

Function Documentation

check_option_conflicts()

bool check_option_conflicts

(

)

References aa, basic::options::OptionKeys::ufv::aa_during_build, basic::options::OptionKeys::ufv::aa_during_design_refine, basic::Tracer::Fatal, basic::options::OptionKeys::ufv::left, basic::options::OptionKeys::run::max_retry_job, basic::options::option, basic::options::OptionKeys::ufv::right, basic::options::OptionKeys::ufv::ss, basic::options::TR, basic::options::OptionKeys::ufv::ufv_loops, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

check_required_options()

bool check_required_options

(

KeyVec &

keys

)

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

Referenced by main().

fill_optional_options()

void fill_optional_options

(

KeyVec &

keys

)

References basic::options::OptionKeys::ufv::aa_during_build, basic::options::OptionKeys::ufv::aa_during_design_refine, basic::options::OptionKeys::ufv::insert::attached_pdb, basic::options::OptionKeys::ufv::centroid_loop_mover, basic::options::OptionKeys::ufv::centroid_sfx, basic::options::OptionKeys::ufv::centroid_sfx_patch, basic::options::OptionKeys::ufv::insert::connection_scheme, basic::options::OptionKeys::ufv::dr_cycles, basic::options::OptionKeys::ufv::fullatom_sfx, basic::options::OptionKeys::ufv::fullatom_sfx_patch, basic::options::OptionKeys::ufv::insert::insert_pdb, basic::options::OptionKeys::ufv::keep_junction_torsions, basic::options::OptionKeys::ufv::left, basic::options::OptionKeys::ufv::no_neighborhood_design, basic::options::OptionKeys::out::file::o, basic::options::OptionKeys::out::pdb, basic::options::OptionKeys::out::pdb_gz, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::ufv::right, 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, basic::options::OptionKeys::ufv::ss, basic::options::OptionKeys::ufv::ufv_loops, basic::options::OptionKeys::ufv::use_fullmer, 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.

Referenced by main().

graphics_main()

void* graphics_main

(

void *

)

References basic::options::OptionKeys::ufv::aa_during_build, basic::options::OptionKeys::ufv::aa_during_design_refine, basic::options::OptionKeys::ufv::centroid_loop_mover, basic::options::OptionKeys::ufv::centroid_sfx, basic::options::OptionKeys::ufv::centroid_sfx_patch, pyrosetta::create_score_function, basic::options::OptionKeys::ufv::dr_cycles, basic::options::OptionKeys::ufv::fullatom_sfx, basic::options::OptionKeys::ufv::fullatom_sfx_patch, basic::options::OptionKeys::ufv::insert::insert_pdb, basic::options::OptionKeys::ufv::keep_junction_torsions, basic::options::OptionKeys::ufv::left, load_loops_from_file(), basic::options::OptionKeys::ufv::no_neighborhood_design, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::packing::resfile, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::ufv::right, basic::options::OptionKeys::in::file::s, setup_segment_insert(), basic::options::OptionKeys::ufv::ss, basic::options::OptionKeys::ufv::ufv_loops, basic::options::OptionKeys::ufv::use_fullmer, basic::options::OptionKeys::inout::dbms::user, and value.

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.

Referenced by graphics_main().

main()

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

References argv, check_option_conflicts(), check_required_options(), test.T009_Exceptions::e, fill_optional_options(), fill_required_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().

setup_segment_insert()

void setup_segment_insert

(

protocols::forge::components::BDR &

bdr

)

References basic::options::OptionKeys::ufv::aa_during_build, basic::options::OptionKeys::ufv::aa_during_design_refine, basic::options::OptionKeys::ufv::insert::attached_pdb, C, basic::options::OptionKeys::ufv::insert::connection_scheme, basic::options::OptionKeys::ufv::insert::insert, basic::options::OptionKeys::ufv::insert::insert_pdb, basic::options::OptionKeys::ufv::left, N, basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::ufv::right, basic::options::OptionKeys::ufv::ss, and basic::options::OptionKeys::inout::dbms::user.

Referenced by graphics_main().

Variable Documentation

TR

basic::Tracer TR("apps.pilot.yab.ufv") ( "apps.pilot.yab.ufv"  )

static