core::io::external Namespace Reference

Classes
class	PsiPredInterface
struct	PsiPredResult

Typedefs
typedef utility::pointer::shared_ptr < PsiPredInterface >	PsiPredInterfaceOP
typedef utility::pointer::shared_ptr < PsiPredInterface const >	PsiPredInterfaceCOP
typedef std::map< std::string const, PsiPredResult const >	PsiPredResultMap

Functions
void	runpsipred_name_mangle_check (std::string &filename, std::string const &ref_filename, std::string const &extension)
utility::vector1< core::Real >	generate_prob (PsiPredResult const &psipred_result, std::string desired_ss)
	generates scores for each residue based on psipred confidence and the desired secondary structure More...
utility::vector1< core::Size >	nonmatching_residues (std::string const &blueprint_ss, std::string const &pred_ss)
	finds which positions in the blueprint and predicted secondary structure string don't match returns a vector of the residue numbers More...

Typedef Documentation

typedef utility::pointer::shared_ptr< PsiPredInterface const > core::io::external::PsiPredInterfaceCOP

typedef utility::pointer::shared_ptr< PsiPredInterface > core::io::external::PsiPredInterfaceOP

typedef std::map< std::string const, PsiPredResult const > core::io::external::PsiPredResultMap

Function Documentation

utility::vector1< core::Real > core::io::external::generate_prob	(	PsiPredResult const &	psipred_result,
		std::string	desired_ss
	)

generates scores for each residue based on psipred confidence and the desired secondary structure

References core::io::external::PsiPredResult::pred_ss, and core::io::external::PsiPredResult::psipred2_confidence.

Referenced by protocols::denovo_design::filters::SSPredictionFilter::compute().

utility::vector1< core::Size > core::io::external::nonmatching_residues	(	std::string const &	blueprint_ss,
		std::string const &	pred_ss
	)

finds which positions in the blueprint and predicted secondary structure string don't match returns a vector of the residue numbers

void core::io::external::runpsipred_name_mangle_check	(	std::string &	filename,
		std::string const &	ref_filename,
		std::string const &	extension
	)

Local-only utility function

References core::io::TR().

Referenced by core::io::external::PsiPredInterface::run_psipred().