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Classes | Typedefs | Functions
core::io::external Namespace Reference

Classes

struct  PsiPredResult
 
class  PsiPredInterface
 

Typedefs

typedef utility::pointer::shared_ptr< PsiPredInterfacePsiPredInterfaceOP
 
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::Realgenerate_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::Sizenonmatching_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

◆ PsiPredInterfaceCOP

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

◆ PsiPredInterfaceOP

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

◆ PsiPredResultMap

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

Function Documentation

◆ generate_prob()

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().

◆ nonmatching_residues()

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

◆ runpsipred_name_mangle_check()

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 protocols::abinitio::filename(), and core::io::TR().

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