helical_bundle_predict.cc File Reference

An application that attempts to predict helical bundle structures, without using PDB fragments. More...

#include <devel/init.hh>
#include <protocols/helical_bundle_predict/HelicalBundlePredictApplication.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/options/OptionCollection.hh>
#include <utility/pointer/memory.hh>
#include <basic/Tracer.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/helical_bundle_predict.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/citation_manager/CitationManager.hh>
#include <basic/citation_manager/UnpublishedModuleInfo.hh>

Functions
void	register_options ()
	Indicate what options are relevant for this application. More...
void	get_options_from_options_collection (protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions &options, utility::options::OptionCollection const &option_collection)
	Set relevant options. More...
void	set_file_output (protocols::helical_bundle_predict::HelicalBundlePredictApplication &application)
	In the non-MPI build, set the file output options. More...
int	main (int argc, char *argv[])
	Entry point for program execution. More...

Variables
static basic::Tracer	TR ("apps.public.helical_bundle.helical_bundle_predict")

Detailed Description

An application that attempts to predict helical bundle structures, without using PDB fragments.

Author

Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Function Documentation

get_options_from_options_collection()

void get_options_from_options_collection	(	protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions &	options,
		utility::options::OptionCollection const &	option_collection
	)

Set relevant options.

Triggers reads from disk!

References errmsg(), basic::options::OptionKeys::in::file::fasta, basic::options::OptionKeys::helical_bundle_predict::helix_assignment_file, basic::options::OptionKeys::helical_bundle_predict::psipred_file, runtime_assert, runtime_assert_string_msg, basic::options::OptionKeys::helical_bundle_predict::sequence_file, subloop_histogram::size, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and basic::Tracer::Warning.

Referenced by main().

main()

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

Entry point for program execution.

References basic::citation_manager::Application, argv, basic::options::OptionKeys::cyclic_peptide::compute_rmsd_to_lowest, utility::io::oc::cout, test.T009_Exceptions::e, basic::Tracer::flush(), utility::SingletonBase< CitationManager >::get_instance(), get_options_from_options_collection(), basic::options::OptionKeys::helical_bundle_predict::helical_bundle_predict, basic::init(), basic::options::option, options, output_filename, register_options(), set_file_output(), basic::options::OptionKeys::cyclic_peptide::threads_per_worker, basic::options::TR, and basic::Tracer::visible().

register_options()

void register_options

(

)

Indicate what options are relevant for this application.

Referenced by main().

set_file_output()

void set_file_output

(

protocols::helical_bundle_predict::HelicalBundlePredictApplication &

application

)

In the non-MPI build, set the file output options.

References basic::options::OptionKeys::out::mmCIF, basic::options::OptionKeys::out::mmtf, basic::options::option, basic::options::OptionKeys::out::prefix, basic::options::OptionKeys::out::file::silent, basic::options::OptionKeys::out::suffix, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and value.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("apps.public.helical_bundle.helical_bundle_predict") ( "apps.public.helical_bundle.helical_bundle_predict"  )

static