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.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 <utility/options/OptionCollection.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

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, test.G202_Module_PythonPDB::filename, load_as_fullatom(), basic::options::OptionKeys::dna::specificity::mode, name, basic::options::option, options, basic::options::OptionKeys::mh::filter::restype, basic::options::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

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

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

Referenced by output_residue_types().

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, erraser_single_res_analysis::data, basic::options::OptionKeys::in::file::extra_res_mmCIF, basic::options::OptionKeys::in::file::extra_res_mol, test.G202_Module_PythonPDB::filename, basic::options::OptionKeys::in::file::fullatom, basic::options::option, options, and basic::options::OptionKeys::mh::filter::restype.

Referenced by collect_residue_types().

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

References collect_residue_types(), utility::excn::Exception::display(), test.T009_Exceptions::e, devel::init(), NEW_OPT, options, output_residue_types(), register_options(), basic::options::TR, and basic::Tracer::Warning.

void output_residue_types

(

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

restypes

)

References basic::options::OptionKeys::chemical::chemical, determine_output_name(), name, basic::options::option, options, out::pdb(), demo.D010_Pose_structure::pose, res, basic::options::OptionKeys::mh::filter::restype, basic::options::TR, and basic::Tracer::Warning.

Referenced by main().

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, basic::options::option, options, basic::options::OptionKeys::out::pdb, basic::options::OptionKeys::out::prefix, and basic::options::OptionKeys::out::suffix.

Referenced by main().

Variable Documentation

basic::Tracer TR("restype_converter")

static