#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

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 ( )

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

References core::conformation::Residue::aa(), core::chemical::aa_unk, core::conformation::Residue::backbone_aa(), core::id::BB, numeric::interpolation::periodic_range::half::bilinearly_interpolated(), numeric::interpolation::periodic_range::full::bilinearly_interpolated(), bilinearly_interpolated(), numeric::conversions::degrees(), get_l_equivalent(), core::chemical::ResidueType::is_alpha_aa(), is_canonical_d_aminoacid(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::mainchain_torsion(), core::chemical::num_canonical_aas, basic::options::option, P_AA_pp_, P_AA_pp_energy_splines_, basic::options::OptionKeys::corrections::score::p_aa_pp_nogridshift, core::id::TorsionID::torsion(), core::id::TorsionID::type(), core::conformation::Residue::type(), and basic::options::OptionKeys::corrections::score::use_bicubic_interpolation.

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

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

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 core::conformation::Residue::aa(), core::chemical::aa_unk, core::conformation::Residue::backbone_aa(), bilinearly_interpolated(), numeric::interpolation::periodic_range::half::bilinearly_interpolated(), numeric::interpolation::periodic_range::full::bilinearly_interpolated(), numeric::conversions::degrees(), get_l_equivalent(), is_canonical_d_aminoacid(), core::conformation::Residue::is_terminus(), core::conformation::Residue::is_virtual_residue(), core::conformation::Residue::mainchain_torsion(), core::chemical::num_canonical_aas, basic::options::option, P_AA_, P_AA_pp_, P_AA_pp_energy_splines_, basic::options::OptionKeys::corrections::score::p_aa_pp_nogridshift, and basic::options::OptionKeys::corrections::score::use_bicubic_interpolation.

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

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.