Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Attributes | List of all members
core::scoring::P_AA_ss Class Reference

#include <P_AA_ss.hh>

Inheritance diagram for core::scoring::P_AA_ss:
Inheritance graph
[legend]

Public Member Functions

 P_AA_ss ()
 ctor – Initialize the amino acid probability data structures More...
 
void read_P_AA_ss ()
 Read the ss-dep amino acid probability file into P_AA_ss. More...
 
core::Real P_AA_ss_energy (chemical::AA aa, char ss) const
 Probability energies from P(aa|ss) More...
 

Private Attributes

utility::vector1< core::Realp_L_
 
utility::vector1< core::Realp_H_
 
utility::vector1< core::Realp_E_
 
core::Real p0_L_
 
core::Real p0_H_
 
core::Real p0_E_
 

Constructor & Destructor Documentation

core::scoring::P_AA_ss::P_AA_ss ( )

ctor – Initialize the amino acid probability data structures

References read_P_AA_ss().

Member Function Documentation

core::Real core::scoring::P_AA_ss::P_AA_ss_energy ( chemical::AA  aa,
char  ss 
) const

Probability energies from P(aa|ss)

Probability energies from P(aa|phi,psi): Low level calculation for non-terminus position You must pass an L amino acid 1-20 to this function! - if res have a backbone aa, apply it first and if res is D, switch to L first!

References protocols::cluster::calibur::aa, core::chemical::num_canonical_aas, p0_E_, p0_H_, p0_L_, p_E_, p_H_, p_L_, and core::scoring::TR().

Referenced by core::scoring::methods::P_AA_ss_Energy::residue_energy().

void core::scoring::P_AA_ss::read_P_AA_ss ( )

Read the ss-dep amino acid probability file into P_AA_ss.

Read the amino acid probability file into P_AA_ss.

Note
Only the keys present in the file are given entries

References protocols::cluster::calibur::aa, core::chemical::aa_from_name(), core::chemical::num_canonical_aas, p0_E_, p0_H_, p0_L_, p_E_, p_H_, and p_L_.

Referenced by P_AA_ss().

Member Data Documentation

core::Real core::scoring::P_AA_ss::p0_E_
private

Referenced by P_AA_ss_energy(), and read_P_AA_ss().

core::Real core::scoring::P_AA_ss::p0_H_
private

Referenced by P_AA_ss_energy(), and read_P_AA_ss().

core::Real core::scoring::P_AA_ss::p0_L_
private

Referenced by P_AA_ss_energy(), and read_P_AA_ss().

utility::vector1< core::Real > core::scoring::P_AA_ss::p_E_
private

Referenced by P_AA_ss_energy(), and read_P_AA_ss().

utility::vector1< core::Real > core::scoring::P_AA_ss::p_H_
private

Referenced by P_AA_ss_energy(), and read_P_AA_ss().

utility::vector1< core::Real > core::scoring::P_AA_ss::p_L_
private

Referenced by P_AA_ss_energy(), and read_P_AA_ss().


The documentation for this class was generated from the following files: