#include <P_AA.hh>

Inheritance diagram for core::scoring::P_AA:

Collaboration diagram for core::scoring::P_AA:

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
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_

Detailed Description

Definition at line 40 of file P_AA.hh.

Member Typedef Documentation

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

private

Amino acid probability array: P(aa)

Definition at line 48 of file P_AA.hh.

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)

Definition at line 54 of file P_AA.hh.

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)

Definition at line 60 of file P_AA.hh.

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

Definition at line 66 of file P_AA.cc.

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

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

virtual

Definition at line 73 of file P_AA.cc.

Member Function Documentation

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

Definition at line 329 of file P_AA.cc.

References core::conformation::Residue::aa(), core::id::BB, core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::mainchain_torsion(), core::chemical::num_canonical_aas, P_AA_pp_, P_AA_pp_energy_splines_, protocols::swa::phi(), protocols::swa::psi(), core::id::TorsionID::torsion(), and core::id::TorsionID::type().

Referenced by core::scoring::methods::P_AA_pp_Energy::eval_dof_derivative(), and core::scoring::methods::P_AA_pp_Energy::eval_residue_dof_derivative().

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.

Definition at line 397 of file P_AA.cc.

References core::conformation::Residue::aa(), 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

Probability energies from P(aa|phi,psi)

Definition at line 275 of file P_AA.cc.

References core::conformation::Residue::aa(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::mainchain_torsion(), core::chemical::num_canonical_aas, P_AA_, P_AA_pp_, P_AA_pp_energy_splines_, protocols::swa::phi(), and protocols::swa::psi().

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

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

Definition at line 306 of file P_AA.cc.

References core::chemical::num_canonical_aas, P_AA_, P_AA_pp_, P_AA_pp_energy_splines_, protocols::swa::phi(), and protocols::swa::psi().

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

Definition at line 80 of file P_AA.cc.

References core::chemical::aa_from_name(), core::chemical::num_canonical_aas, and P_AA_.

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

Definition at line 115 of file P_AA.cc.

References core::chemical::aa_from_name(), core::chemical::num_canonical_aas, and P_AA_n_.

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

Definition at line 162 of file P_AA.cc.

References 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::swa::phi(), and protocols::swa::psi().

Referenced by P_AA().