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protocols::sasa_scores Namespace Reference

Classes

class  Poly
 
class  PPoly
 

Typedefs

using Reals = utility::vector1< Real >
 

Functions

std::istream & operator>> (std::istream &is, Poly &p)
 
std::istream & operator>> (std::istream &is, PPoly &pp)
 
void help_load_data (utility::vector1< PPoly > &polys, Reals &avg_sasa14s, std::string const &datafile, std::string const &tag1, std::string const &tag2, std::string const &function_name)
 helper function to open a file and respond to appropriate flags More...
 
void load_sasapack_polynomial_coefficients (vector1< PPoly > &polys, Reals &avg_sasa14s)
 
void load_avge_polynomial_coefficients (vector1< PPoly > &polys, Reals &avg_sasa14s)
 
void help_load_data (vector1< PPoly > &polys, Reals &avg_sasa14s, string const &datafile, string const &tag1, string const &tag2, string const &function_name)
 helper function to open a file and respond to appropriate flags More...
 
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

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

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 
)
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 core::scoring::calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), 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 
)
void protocols::sasa_scores::help_load_data ( utility::vector1< PPoly > &  polys,
Reals &  avg_sasa14s,
std::string const &  datafile,
std::string const &  tag1,
std::string const &  tag2,
std::string const &  function_name 
)
void protocols::sasa_scores::help_load_data ( vector1< PPoly > &  polys,
Reals &  avg_sasa14s,
string const &  datafile,
string const &  tag1,
string const &  tag2,
string const &  function_name 
)
void protocols::sasa_scores::load_avge_polynomial_coefficients ( vector1< PPoly > &  polys,
Reals &  avg_sasa14s 
)

References help_load_data().

Referenced by compute_avge_scores().

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

References help_load_data().

Referenced by compute_sasapack_scores().

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