protocols::sasa_scores Namespace Reference

Classes
class	Poly
class	PPoly

Typedefs
typedef utility::vector1< Real >	Reals

Functions
std::istream &	operator>> (std::istream &is, Poly &p)
std::istream &	operator>> (std::istream &is, PPoly &pp)
void	load_sasapack_polynomial_coefficients (vector1< PPoly > &polys, Reals &avg_sasa14s)
void	load_avge_polynomial_coefficients (vector1< PPoly > &polys, Reals &avg_sasa14s)
void	compute_residue_sasas_for_sasa_scores (Real const probe_radius, Pose const &pose, Reals &rsd_sasa)
	NOTE: this does not include the probe radius in the sasa value, hence somewhat specialized for sasapack. More...
void	compute_avge_scores (Pose const &pose_in, Reals &residue_avge, Reals &residue_normsasa, Real &average_avge, Real &average_normsasa)
void	compute_sasapack_scores (Pose const &pose, Reals &residue_sasapack, Reals &residue_normsasa, Real &average_sasapack, Real &average_normsasa)
void	compute_residue_sasas_for_sasa_scores (core::Real const probe_radius, core::pose::Pose const &pose, utility::vector1< core::Real > &rsd_sasa)
	Compute residue sasa values for use in deriving and assigning sasapack-like scores. More...
void	compute_sasapack_scores (core::pose::Pose const &pose, utility::vector1< core::Real > &residue_sasapack, utility::vector1< core::Real > &residue_normsasa, core::Real &average_sasapack, core::Real &average_normsasa)
	Compute sasapack scores for the given pose. Currently only scores non-terminal, non-disulfide, protein residues. The sasapack score for a residue is the difference between its SASA with a 0.5A probe and the average SASA value for that residue-type in a large set of pdb structures, conditioned on the SASA with a 1.4A probe. The normsasa is just the difference between a residues SASA-1.4 and the average SASA-1.4 for that residue type. More...
void	compute_avge_scores (core::pose::Pose const &pose, utility::vector1< core::Real > &residue_avge, utility::vector1< core::Real > &residue_normsasa, core::Real &average_avge, core::Real &average_normsasa)
	Compute normalize scores for the given pose based on average energies (hence "avgE") for pdb structures. Currently only scores non-terminal, non-disulfide, protein residues. The "avge" score for a residue is the difference between its per-residue score and the expected per-residue score for that residue type, conditioned on the residue SASA with a 1.4A probe. Right now, the following scores are excluded from the avge sum since they are often very large in native structures: fa_rep, fa_dun, pro_close, omega as well as paa_pp for glycine, since it's just weird. Could consider refitting these The normsasa is just the difference between a residues SASA-1.4 and the average SASA-1.4 for that residue type. More...

Typedef Documentation

typedef utility::vector1< Real > protocols::sasa_scores::Reals

Function Documentation

void protocols::sasa_scores::compute_avge_scores	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	residue_avge,
		utility::vector1< core::Real > &	residue_normsasa,
		core::Real &	average_avge,
		core::Real &	average_normsasa
	)

Compute normalize scores for the given pose based on average energies (hence "avgE") for pdb structures. Currently only scores non-terminal, non-disulfide, protein residues. The "avge" score for a residue is the difference between its per-residue score and the expected per-residue score for that residue type, conditioned on the residue SASA with a 1.4A probe. Right now, the following scores are excluded from the avge sum since they are often very large in native structures: fa_rep, fa_dun, pro_close, omega as well as paa_pp for glycine, since it's just weird. Could consider refitting these The normsasa is just the difference between a residues SASA-1.4 and the average SASA-1.4 for that residue type.

Note

Refitting app and python code will be checked in shortly.

void protocols::sasa_scores::compute_avge_scores	(	Pose const &	pose_in,
		Reals &	residue_avge,
		Reals &	residue_normsasa,
		Real &	average_avge,
		Real &	average_normsasa
	)

NOTE: for this to make any sense it's critical that the same scorefxn be used in scoring decoys and natives

References aa_cys, compute_residue_sasas_for_sasa_scores(), core::pose::Pose::energies(), fa_dun, fa_rep, getScoreFunctionLegacy(), load_avge_polynomial_coefficients(), protocols::stepwise::sampling::protein::omega(), p_aa_pp, core::scoring::PRE_TALARIS_2013_STANDARD_WTS, pro_close, probe_radius, core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), runtime_assert, and core::pose::Pose::total_residue().

void protocols::sasa_scores::compute_residue_sasas_for_sasa_scores	(	core::Real const	probe_radius,
		core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	rsd_sasa
	)

Compute residue sasa values for use in deriving and assigning sasapack-like scores.

void protocols::sasa_scores::compute_residue_sasas_for_sasa_scores	(	Real const	probe_radius,
		Pose const &	pose,
		Reals &	rsd_sasa
	)

NOTE: this does not include the probe radius in the sasa value, hence somewhat specialized for sasapack.

References calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), include_probe_radius_in_atom_radii, and core::pose::initialize_atomid_map().

Referenced by compute_avge_scores(), and compute_sasapack_scores().

void protocols::sasa_scores::compute_sasapack_scores	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	residue_sasapack,
		utility::vector1< core::Real > &	residue_normsasa,
		core::Real &	average_sasapack,
		core::Real &	average_normsasa
	)

Compute sasapack scores for the given pose. Currently only scores non-terminal, non-disulfide, protein residues. The sasapack score for a residue is the difference between its SASA with a 0.5A probe and the average SASA value for that residue-type in a large set of pdb structures, conditioned on the SASA with a 1.4A probe. The normsasa is just the difference between a residues SASA-1.4 and the average SASA-1.4 for that residue type.

Note

Refitting app and python code will be checked in shortly.

void protocols::sasa_scores::compute_sasapack_scores	(	Pose const &	pose,
		Reals &	residue_sasapack,
		Reals &	residue_normsasa,
		Real &	average_sasapack,
		Real &	average_normsasa
	)

References aa_cys, compute_residue_sasas_for_sasa_scores(), load_sasapack_polynomial_coefficients(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

void protocols::sasa_scores::load_avge_polynomial_coefficients	(	vector1< PPoly > &	polys,
		Reals &	avg_sasa14s
	)

References aa_ala, aa_from_oneletter_code(), utility::io::izstream::close(), cout, getline(), protocols::abinitio::abscript::I, protocols::sasa_scores::PPoly::max_degree(), mean, num_canonical_aas, basic::database::open(), runtime_assert, and protocols::TR.

Referenced by compute_avge_scores().

void protocols::sasa_scores::load_sasapack_polynomial_coefficients	(	vector1< PPoly > &	polys,
		Reals &	avg_sasa14s
	)

References aa_ala, aa_from_oneletter_code(), utility::io::izstream::close(), cout, getline(), protocols::abinitio::abscript::I, protocols::sasa_scores::PPoly::max_degree(), mean, num_canonical_aas, basic::database::open(), runtime_assert, and protocols::TR.

Referenced by compute_sasapack_scores().

std::istream& protocols::sasa_scores::operator>>	(	std::istream &	is,
		Poly &	p
	)

References protocols::sasa_scores::Poly::coeffs_.

std::istream& protocols::sasa_scores::operator>>	(	std::istream &	is,
		PPoly &	pp
	)

References protocols::sasa_scores::PPoly::polys_, protocols::sasa_scores::PPoly::xmaxs_, and protocols::sasa_scores::PPoly::xmins_.