Rosetta Protocols
2014.35

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 sasapacklike 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 nonterminal, nondisulfide, 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 residuetype 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 SASA1.4 and the average SASA1.4 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 nonterminal, nondisulfide, protein residues. The "avge" score for a residue is the difference between its perresidue score and the expected perresidue 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 SASA1.4 and the average SASA1.4 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 nonterminal, nondisulfide, protein residues. The "avge" score for a residue is the difference between its perresidue score and the expected perresidue 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 SASA1.4 and the average SASA1.4 for that residue type.
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, get_score_function_legacy(), load_avge_polynomial_coefficients(), 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 sasapacklike 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 nonterminal, nondisulfide, 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 residuetype 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 SASA1.4 and the average SASA1.4 for that residue type.
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, F, getline(), 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, F, getline(), 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  
) 