Rosetta Core  2014.35
Public Member Functions | Private Types | Private Member Functions | Private Attributes | List of all members
core::scoring::P_AA Class Reference

#include <P_AA.hh>

Public Member Functions

 P_AA ()
 Amino acid probability array: P(aa) More...
 
virtual ~P_AA ()
 
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

bool is_canonical_d_aminoacid (core::chemical::AA const res_aa) const
 Gets whether this amino acid enum type is a canonical D-amino acid. More...
 
core::chemical::AA get_l_equivalent (core::chemical::AA const d_aa) const
 When passed a d-amino acid, returns the l-equivalent. Returns aa_unk otherwise. 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...
 

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

Amino acid probability array: P(aa)

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

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

Constructor & Destructor Documentation

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

Amino acid probability array: P(aa)

Amino acid conditional probability wrt number of neighbors array: P(aa|neighbors) Amino acid conditional probability wrt (phi,psi) array: P(aa|phi,psi) 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 ( )
virtual

Member Function Documentation

core::chemical::AA core::scoring::P_AA::get_l_equivalent ( core::chemical::AA const  d_aa) const
private

When passed a d-amino acid, returns the l-equivalent. Returns aa_unk otherwise.

References core::chemical::get_L_equivalent().

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
bool core::scoring::P_AA::is_canonical_d_aminoacid ( core::chemical::AA const  res_aa) const
private

Gets whether this amino acid enum type is a canonical D-amino acid.

Returns true if passed a core::chemical::AA corresponding to a D-amino acid, and false otherwise.

References core::chemical::is_canonical_D_aa().

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

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 core::conformation::Residue::aa(), core::chemical::aa_unk, core::conformation::Residue::backbone_aa(), get_l_equivalent(), is_canonical_d_aminoacid(), 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.

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

References aa2, numeric::interpolation::periodic_range::half::bilinearly_interpolated(), numeric::interpolation::periodic_range::full::bilinearly_interpolated(), get_l_equivalent(), is_canonical_d_aminoacid(), core::chemical::num_canonical_aas, basic::options::option, P_AA_, P_AA_pp_, P_AA_pp_energy_splines_, and basic::options::OptionKeys::corrections::score::p_aa_pp_nogridshift.

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 core::chemical::aa_from_name(), numeric::eq_tol(), core::chemical::num_canonical_aas, basic::database::open(), P_AA_, and skip.

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 core::chemical::aa_from_name(), numeric::eq_tol(), core::chemical::num_canonical_aas, basic::database::open(), P_AA_n_, and skip.

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 core::chemical::aa_from_name(), e_Periodic, numeric::mod(), numeric::nint(), core::chemical::num_canonical_aas, basic::database::open(), utility::io::izstream::open(), option, basic::options::option, P_AA_, core::scoring::p_aa_pp, P_AA_pp_, P_AA_pp_energy_splines_, p_aa_pp_nogridshift, basic::options::OptionKeys::corrections::score::p_aa_pp_nogridshift, skip, numeric::interpolation::spline::BicubicSpline::train(), basic::options::OptionKeys::corrections::score::use_bicubic_interpolation, and utility_exit_with_message.

Referenced by P_AA().

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: