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core::scoring::P_AA Class Reference

#include <P_AA.hh>

Inheritance diagram for core::scoring::P_AA:
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Public Member Functions

 P_AA ()
 ctor – Initialize the amino acid probability data structures More...
 
 ~P_AA () override
 
Energy P_AA_pp_energy (conformation::Residue const &) const
 Probability energies from P(aa|phi,psi) More...
 
Energy P_AA_pp_energy (chemical::AA aa, Angle const phi, Angle const psi) const
 Low-level probability energies from P(aa|phi,psi) More...
 
EnergyDerivative get_Paa_pp_deriv (conformation::Residue const &res, id::TorsionID const &tor_id) const
 
Energy P_AA_energy (conformation::Residue const &) const
 Probability energies for P(aa) More...
 

Private Types

typedef utility::vector1
< Probability
Probability_AA
 Amino acid probability array: P(aa) More...
 
typedef utility::vector1
< utility::vector1
< Probability > > 
Probability_AA_n
 Amino acid conditional probability wrt number of neighbors array: P(aa|neighbors) More...
 
typedef utility::vector1
< FArray2D_Probability
Probability_AA_pp
 Amino acid conditional probability wrt (phi,psi) array: P(aa|phi,psi) More...
 

Private Member Functions

core::chemical::AA get_aa_to_use (core::chemical::AA const aa, core::chemical::AA const backbone_aa) const
 Given a residue's AA and BACKBONE_AA types, return the AA enum type to use. More...
 
void P_AA_initialize ()
 Initialize the amino acid probability data structures. More...
 
void read_P_AA ()
 Read the amino acid probability file into P_AA. More...
 
void read_P_AA_n ()
 Read the amino acid conditional probability wrt (neighbors) file into P_AA_n. More...
 
void read_P_AA_pp ()
 Read the amino acid conditional probability wrt (phi,psi) file into P_AA_pp. More...
 
void symmetrize_gly_table ()
 Symmetrize the glyceine P_AA_pp table, if the user has used the -symmetric_gly_tables option. More...
 

Private Attributes

Probability_AA P_AA_
 
Probability_AA_n P_AA_n_
 
Probability_AA_pp P_AA_pp_
 
utility::vector1
< numeric::interpolation::spline::BicubicSpline > 
P_AA_pp_energy_splines_
 

Member Typedef Documentation

typedef utility::vector1< Probability > core::scoring::P_AA::Probability_AA
private

Amino acid probability array: P(aa)

typedef utility::vector1< utility::vector1< Probability > > core::scoring::P_AA::Probability_AA_n
private

Amino acid conditional probability wrt number of neighbors array: P(aa|neighbors)

typedef utility::vector1< FArray2D_Probability > core::scoring::P_AA::Probability_AA_pp
private

Amino acid conditional probability wrt (phi,psi) array: P(aa|phi,psi)

Constructor & Destructor Documentation

core::scoring::P_AA::P_AA ( )

ctor – Initialize the amino acid probability data structures

References read_P_AA(), read_P_AA_n(), and read_P_AA_pp().

core::scoring::P_AA::~P_AA ( )
overridedefault

Member Function Documentation

core::chemical::AA core::scoring::P_AA::get_aa_to_use ( core::chemical::AA const  aa,
core::chemical::AA const  backbone_aa 
) const
private

Given a residue's AA and BACKBONE_AA types, return the AA enum type to use.

Uses backbone_aa over aa; flips types to the l-equivalent.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

References protocols::cluster::calibur::aa, core::chemical::aa_unk, core::chemical::get_L_equivalent(), and core::chemical::is_canonical_D_aa().

Referenced by get_Paa_pp_deriv(), P_AA_energy(), and P_AA_pp_energy().

EnergyDerivative core::scoring::P_AA::get_Paa_pp_deriv ( conformation::Residue const &  res,
id::TorsionID const &  tor_id 
) const
Energy core::scoring::P_AA::P_AA_energy ( conformation::Residue const &  res) const

Probability energies for P(aa)

Remarks
No derivative function since there are no degrees of freedom to vary for a P_AA energy like for P_AA_pp.

References protocols::cluster::calibur::aa, core::conformation::Residue::aa(), core::conformation::Residue::backbone_aa(), get_aa_to_use(), core::chemical::num_canonical_aas, and P_AA_.

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

void core::scoring::P_AA::P_AA_initialize ( )
private

Initialize the amino acid probability data structures.

Energy core::scoring::P_AA::P_AA_pp_energy ( conformation::Residue const &  res) const
Energy core::scoring::P_AA::P_AA_pp_energy ( chemical::AA  aa,
Angle const  phi,
Angle const  psi 
) const

Low-level probability energies from P(aa|phi,psi)

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!

Probability energies from P(aa|phi,psi): Low level calculation for non-terminus position

References protocols::cluster::calibur::aa, core::chemical::num_canonical_aas, P_AA_, P_AA_pp_, and P_AA_pp_energy_splines_.

void core::scoring::P_AA::read_P_AA ( )
private

Read the amino acid probability file into P_AA.

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, P_AA_, and protocols::simple_moves::bb_sampler::probability.

Referenced by P_AA().

void core::scoring::P_AA::read_P_AA_n ( )
private

Read the amino acid conditional probability wrt (neighbors) file into P_AA_n.

Note
Only the keys present in the file are given entries
The file entries can be in any order

References protocols::cluster::calibur::aa, core::chemical::aa_from_name(), core::chemical::num_canonical_aas, P_AA_n_, and protocols::simple_moves::bb_sampler::probability.

Referenced by P_AA().

void core::scoring::P_AA::read_P_AA_pp ( )
private

Read the amino acid conditional probability wrt (phi,psi) file into P_AA_pp.

Read the amino acid conditional probability wrt (phi,psi) file into P_AA_pp_.

Note
Only the keys present in the file are given entries
The file entries can be in any order
Missing entries for a present key are assigned zero

References protocols::cluster::calibur::aa, core::chemical::aa_from_name(), core::chemical::num_canonical_aas, P_AA_, core::scoring::p_aa_pp, P_AA_pp_, P_AA_pp_energy_splines_, protocols::simple_moves::bb_sampler::probability, protocols::hybridization::score, symmetrize_gly_table(), and core::scoring::TR().

Referenced by P_AA().

void core::scoring::P_AA::symmetrize_gly_table ( )
private

Symmetrize the glyceine P_AA_pp table, if the user has used the -symmetric_gly_tables option.

The gly table must already be loaded before this is called. Also, this should be called before the bicubic splines are set up for the energy table.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::chemical::aa_gly, P_AA_pp_, and core::scoring::TR().

Referenced by read_P_AA_pp().

Member Data Documentation

Probability_AA core::scoring::P_AA::P_AA_
private
Probability_AA_n core::scoring::P_AA::P_AA_n_
private

Referenced by read_P_AA_n().

Probability_AA_pp core::scoring::P_AA::P_AA_pp_
private
utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::P_AA::P_AA_pp_energy_splines_
private

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