#include <P_AA.hh>

Inheritance diagram for core::scoring::P_AA:

Public Member Functions
	P_AA ()
	ctor – Initialize the amino acid probability data structures More...

	~P_AA () override

bool	defines_p_aa_pp_energy_for_res (conformation::Residue const &res) const
	Do the tables define a non-zero energy for a given residue? More...

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

bool core::scoring::P_AA::defines_p_aa_pp_energy_for_res ( conformation::Residue const & res ) const

Do the tables define a non-zero energy for a given residue?

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

Referenced by core::energy_methods::P_AA_pp_Energy::atoms_with_dof_derivatives(), and P_AA_pp_energy().

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 defines_p_aa_pp_energy_for_res(), 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

References protocols::cluster::calibur::aa, core::conformation::Residue::aa(), core::conformation::Residue::backbone_aa(), core::id::BB, get_aa_to_use(), core::conformation::Residue::has_property(), core::chemical::ResidueType::is_alpha_aa(), 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_, core::id::TorsionID::torsion(), core::id::TorsionID::type(), and core::conformation::Residue::type().

Referenced by core::energy_methods::P_AA_pp_Energy::eval_dof_derivative(), and core::energy_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.

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::energy_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)

Probability energies from P(aa|phi,psi) This function handles L- and D- canonical amino acids, as well as noncanonical alpha amino acids templated on canonical alpha amino acids.

References protocols::cluster::calibur::aa, core::conformation::Residue::aa(), core::conformation::Residue::backbone_aa(), defines_p_aa_pp_energy_for_res(), get_aa_to_use(), core::conformation::Residue::has_property(), core::conformation::Residue::mainchain_torsion(), P_AA_, P_AA_pp_, and P_AA_pp_energy_splines_.

Referenced by core::energy_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 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().