remodel.cc File Reference

#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.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/ufv.OptionKeys.gen.hh>
#include <basic/options/keys/remodel.OptionKeys.gen.hh>
#include <basic/Tracer.hh>
#include <utility/file/FileName.hh>
#include <utility/io/izstream.hh>
#include <utility/options/keys/OptionKey.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.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/jd2/JobDistributor.hh>
#include <protocols/jd2/JobOutputter.hh>
#include <protocols/simple_filters/PoseMetricEvaluator.hh>
#include <protocols/viewer/viewers.hh>
#include <protocols/moves/PyMolMover.hh>
#include <devel/init.hh>
#include <boost/lexical_cast.hpp>
#include <boost/tokenizer.hpp>
#include <boost/algorithm/string.hpp>
#include <string>
#include <vector>
#include <utility/excn/Exceptions.hh>

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

Functions
static THREAD_LOCAL basic::Tracer	TR ("apps.public.remodel")
void	init_usage_prompt (std::string exe)
	the usage prompt that gets printed when the user doesn't enter any arguments or uses the -h flag since the application specific help Rosetta bring up with the -help flag is, in fact, not helpful. More...
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
std::string	usage_string

Detailed Description

Author

Yih-En Andrew Ban (yab@u.nosp@m..was.nosp@m.hingt.nosp@m.on.e.nosp@m.du)

Possu Huang

Typedef Documentation

typedef std::vector< OptionKey const * > KeyVec

typedef std::string String

Function Documentation

bool check_option_conflicts

(

)

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

bool check_required_options

(

KeyVec &

keys

)

References basic::options::option.

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::out::file::silent, basic::options::OptionKeys::in::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().

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.

void* graphics_main

(

void *

)

References utility::options::OptionKeys::options::exit, and basic::options::option.

Referenced by main().

void init_usage_prompt

(

std::string

exe

)

the usage prompt that gets printed when the user doesn't enter any arguments or uses the -h flag since the application specific help Rosetta bring up with the -help flag is, in fact, not helpful.

References usage_string.

Referenced by main().

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::io::izstream::close(), clean_pdb_keep_ligand::count, basic::Tracer::Error, utility::options::OptionKeys::options::exit, ObjexxFCL::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, basic::options::OptionKeys::mh::match::ss, and basic::options::TR().

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

References utility::io::oc::cout, utility::options::OptionKeys::options::exit, fill_optional_options(), graphics_main(), devel::init(), init_usage_prompt(), utility::excn::EXCN_Base::msg(), register_options(), and usage_string.

void register_options

(

KeyVec &

keys

)

References utility::options::OptionCollection::add_relevant(), and basic::options::option.

Referenced by main().

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, basic::options::option, basic::options::OptionKeys::ufv::right, basic::options::OptionKeys::ufv::ss, and basic::options::OptionKeys::inout::dbms::user.

static THREAD_LOCAL basic::Tracer TR ( "apps.public.remodel"  )

static

Variable Documentation

std::string usage_string

Referenced by init_usage_prompt(), and main().