restype_converter.cc File Reference

#include <devel/init.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueTypeFinder.hh>
#include <core/chemical/residue_io.hh>
#include <core/chemical/residue_support.hh>
#include <core/chemical/sdf/MolFileIOReader.hh>
#include <core/chemical/sdf/mol_writer.hh>
#include <core/chemical/mmCIF/mmCIFParser.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/Pose.hh>
#include <utility/excn/Exceptions.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/corrections.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option_macros.hh>

Functions
void	register_options ()
utility::vector1< core::chemical::ResidueTypeCOP >	load_as_fullatom ()
	Some filetypes need to be loaded as full atom, and then converted appropriately. More...
utility::vector1< core::chemical::ResidueTypeCOP >	collect_residue_types ()
std::string	determine_output_name (std::string const &resname, std::string const &extension)
void	output_residue_types (utility::vector1< core::chemical::ResidueTypeCOP > const &restypes)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("restype_converter")

Function Documentation

collect_residue_types()

utility::vector1< core::chemical::ResidueTypeCOP > collect_residue_types

(

)

References corrections::score::cenrot(), in::file::centroid(), basic::options::OptionKeys::chemical::chemical, basic::Tracer::Error, basic::options::OptionKeys::in::file::extra_res_cen, basic::options::OptionKeys::in::file::extra_res_fa, lactamize::filename, load_as_fullatom(), SmotifHasher::mode, beta_sc_scan::name3, basic::options::option, build_restypes::restype, hbscan::restypes, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

determine_output_name()

std::string determine_output_name	(	std::string const &	resname,
		std::string const &	extension
	)

References out::path::all(), basic::options::OptionKeys::extension, basic::options::option, closure_error::path, out::path::pdb(), out::prefix(), out::suffix(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by output_residue_types().

load_as_fullatom()

utility::vector1< core::chemical::ResidueTypeCOP > load_as_fullatom

(

)

Some filetypes need to be loaded as full atom, and then converted appropriately.

References basic::options::OptionKeys::chemical::chemical, data, basic::options::OptionKeys::in::file::extra_res_mmCIF, basic::options::OptionKeys::in::file::extra_res_mol, lactamize::filename, basic::options::OptionKeys::in::file::fullatom, basic::options::option, build_restypes::restype, and hbscan::restypes.

Referenced by collect_residue_types().

main()

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

References argv, collect_residue_types(), test.T009_Exceptions::e, basic::init(), beta_sc_scan::name3, NEW_OPT, output_residue_types(), register_options(), hbscan::restypes, basic::options::TR, and basic::Tracer::Warning.

output_residue_types()

void output_residue_types

(

utility::vector1< core::chemical::ResidueTypeCOP > const &

restypes

)

References basic::options::OptionKeys::chemical::chemical, determine_output_name(), basic::options::option, out::pdb(), beta_nonlocal::pose, res, build_restypes::restype, hbscan::restypes, basic::options::TR, and basic::Tracer::Warning.

Referenced by main().

register_options()

void register_options

(

)

References utility::options::OptionCollection::add_relevant(), basic::options::OptionKeys::out::path::all, basic::options::OptionKeys::in::file::centroid, basic::options::OptionKeys::in::file::extra_res_cen, basic::options::OptionKeys::in::file::extra_res_fa, basic::options::OptionKeys::in::file::extra_res_mmCIF, basic::options::OptionKeys::in::file::extra_res_mol, beta_sc_scan::name3, basic::options::option, basic::options::OptionKeys::out::pdb, basic::options::OptionKeys::out::prefix, and basic::options::OptionKeys::out::suffix.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("restype_converter") ( "restype_converter"  )

static