sasapack.hh File Reference

sasapack and other scores that are normalized by residue sasa More...

#include <core/types.hh>
#include <core/pose/Pose.fwd.hh>
#include <utility/vector1.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::sasa_scores

Functions
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. More...
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. More...
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. More...

Detailed Description

sasapack and other scores that are normalized by residue sasa

Author

Phil Bradley