core::scoring::Rama2BOffset Class Reference

#include <Rama2BOffset.hh>

Public Types
typedef pose::Pose	Pose
typedef chemical::AA	AA

Public Member Functions
	Rama2BOffset ()
	~Rama2BOffset ()
void	eval_r2bo_rama_score (AA const res_aa1, AA const res_aa2, Real const psi, Real const omega, Real const phi, Real &score_rama, Real &denergy_dpsi1, Real &denergy_domega2, Real &denergy_dphi2) const
void	eval_r2bo_omega_score (AA const res_aa1, AA const res_aa2, Real const psi, Real const omega, Real const phi, Real &score_rama, Real &denergy_dpsi1, Real &denergy_domega2, Real &denergy_dphi2) const
void	eval_p_aa_pp_score (AA const res_aa1, AA const res_aa2, Real const psi, Real const phi, Real &score_paapp, Real &denergy_dpsi1, Real &denergy_dphi2) const
	Probability energies from P(aa|phi,psi): Low level calculation for non-terminus position. More...

Protected Member Functions
Size	aapair_to_table_index (chemical::AA const res_aa1, chemical::AA const res_aa2, bool cis) const
void	read_r2bo_tables ()
	load tables More...
void	read_paapp_tables ()
void	read_table_from_stream (utility::io::izstream &, ObjexxFCL::FArray2D< Real > &, ObjexxFCL::FArray2D< Real > &, ObjexxFCL::FArray2D< Real > &)
void	read_paapp_table_from_stream (utility::io::izstream &, utility::vector1< ObjexxFCL::FArray2D< Real > > &)
void	setup_interpolation (ObjexxFCL::FArray2D< Real > &, numeric::interpolation::spline::BicubicSpline &)

Protected Attributes
utility::vector1 < numeric::interpolation::spline::BicubicSpline >	rama_
utility::vector1 < numeric::interpolation::spline::BicubicSpline >	omega_mu_
utility::vector1 < numeric::interpolation::spline::BicubicSpline >	omega_sig_
utility::vector1 < numeric::interpolation::spline::BicubicSpline >	paapp1_
utility::vector1 < numeric::interpolation::spline::BicubicSpline >	paapp2_

Member Typedef Documentation

typedef chemical::AA core::scoring::Rama2BOffset::AA

typedef pose::Pose core::scoring::Rama2BOffset::Pose

Constructor & Destructor Documentation

core::scoring::Rama2BOffset::Rama2BOffset

(

)

References read_paapp_tables(), and read_r2bo_tables().

core::scoring::Rama2BOffset::~Rama2BOffset ( )

inline

Member Function Documentation

Size core::scoring::Rama2BOffset::aapair_to_table_index ( chemical::AA const  res_aa1, chemical::AA const  res_aa2, bool  cis  ) const

protected

References core::chemical::aa_gly, core::chemical::aa_ile, core::chemical::aa_pro, core::chemical::aa_val, core::scoring::CIS_XP, core::scoring::CIS_XX, core::scoring::TRANS_GG, core::scoring::TRANS_GP, core::scoring::TRANS_GV, core::scoring::TRANS_GX, core::scoring::TRANS_PG, core::scoring::TRANS_PP, core::scoring::TRANS_PV, core::scoring::TRANS_PX, core::scoring::TRANS_VG, core::scoring::TRANS_VP, core::scoring::TRANS_VV, core::scoring::TRANS_VX, core::scoring::TRANS_XG, core::scoring::TRANS_XP, core::scoring::TRANS_XV, and core::scoring::TRANS_XX.

Referenced by eval_r2bo_omega_score(), and eval_r2bo_rama_score().

void core::scoring::Rama2BOffset::eval_p_aa_pp_score	(	AA const	res_aa1,
		AA const	res_aa2,
		Real const	psi,
		Real const	phi,
		Real &	score_paapp,
		Real &	denergy_dpsi1,
		Real &	denergy_dphi2
	)		const

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

References paapp1_, and paapp2_.

Referenced by core::scoring::methods::Rama2BOffsetEnergy::eval_residue_pair_derivatives(), and core::scoring::methods::Rama2BOffsetEnergy::residue_pair_energy().

void core::scoring::Rama2BOffset::eval_r2bo_omega_score	(	AA const	res_aa1,
		AA const	res_aa2,
		Real const	psi,
		Real const	omega,
		Real const	phi,
		Real &	score_rama,
		Real &	denergy_dpsi1,
		Real &	denergy_domega2,
		Real &	denergy_dphi2
	)		const

References aapair_to_table_index(), log(), omega_mu_, omega_sig_, numeric::constants::d::pi, subtract_degree_angles(), basic::subtract_degree_angles(), and table.

Referenced by core::scoring::methods::Rama2BOffsetEnergy::eval_residue_pair_derivatives(), and core::scoring::methods::Rama2BOffsetEnergy::residue_pair_energy().

void core::scoring::Rama2BOffset::eval_r2bo_rama_score	(	AA const	res_aa1,
		AA const	res_aa2,
		Real const	psi,
		Real const	omega,
		Real const	phi,
		Real &	score_rama,
		Real &	denergy_dpsi1,
		Real &	denergy_domega2,
		Real &	denergy_dphi2
	)		const

References aapair_to_table_index(), rama_, basic::subtract_degree_angles(), and table.

Referenced by core::scoring::methods::Rama2BOffsetEnergy::eval_residue_pair_derivatives(), and core::scoring::methods::Rama2BOffsetEnergy::residue_pair_energy().

void core::scoring::Rama2BOffset::read_paapp_table_from_stream ( utility::io::izstream &  stream, utility::vector1< ObjexxFCL::FArray2D< Real > > &  paas  )

protected

References getline(), j, l, and core::chemical::num_canonical_aas.

Referenced by read_paapp_tables().

void core::scoring::Rama2BOffset::read_paapp_tables ( )

protected

References core::chemical::num_canonical_aas, basic::database::open(), paapp1_, paapp2_, read_paapp_table_from_stream(), and setup_interpolation().

Referenced by Rama2BOffset().

void core::scoring::Rama2BOffset::read_r2bo_tables ( )

protected

load tables

References core::scoring::CIS_XP, core::scoring::CIS_XX, core::scoring::NRAMATABLES, omega_mu_, omega_sig_, basic::database::open(), rama_, read_table_from_stream(), setup_interpolation(), core::scoring::TRANS_GG, core::scoring::TRANS_GP, core::scoring::TRANS_GV, core::scoring::TRANS_GX, core::scoring::TRANS_PG, core::scoring::TRANS_PP, core::scoring::TRANS_PV, core::scoring::TRANS_PX, core::scoring::TRANS_VG, core::scoring::TRANS_VP, core::scoring::TRANS_VV, core::scoring::TRANS_VX, core::scoring::TRANS_XG, core::scoring::TRANS_XP, core::scoring::TRANS_XV, and core::scoring::TRANS_XX.

Referenced by Rama2BOffset().

void core::scoring::Rama2BOffset::read_table_from_stream ( utility::io::izstream &  stream, ObjexxFCL::FArray2D< Real > &  ramas, ObjexxFCL::FArray2D< Real > &  om_mus, ObjexxFCL::FArray2D< Real > &  om_sigmas  )

protected

References getline(), j, l, and core::scoring::rama.

Referenced by read_r2bo_tables().

void core::scoring::Rama2BOffset::setup_interpolation ( ObjexxFCL::FArray2D< Real > &  x, numeric::interpolation::spline::BicubicSpline &  sx  )

protected

References e_Periodic, and numeric::interpolation::spline::BicubicSpline::train().

Referenced by read_paapp_tables(), and read_r2bo_tables().

Member Data Documentation

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::Rama2BOffset::omega_mu_

protected

Referenced by eval_r2bo_omega_score(), and read_r2bo_tables().

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::Rama2BOffset::omega_sig_

protected

Referenced by eval_r2bo_omega_score(), and read_r2bo_tables().

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::Rama2BOffset::paapp1_

protected

Referenced by eval_p_aa_pp_score(), and read_paapp_tables().

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::Rama2BOffset::paapp2_

protected

Referenced by eval_p_aa_pp_score(), and read_paapp_tables().

utility::vector1< numeric::interpolation::spline::BicubicSpline > core::scoring::Rama2BOffset::rama_

protected

Referenced by eval_r2bo_rama_score(), and read_r2bo_tables().

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

• symlinks/rosetta/src/core/scoring/Rama2BOffset.hh
• symlinks/rosetta/src/core/scoring/Rama2BOffset.cc