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Static Public Member Functions | Static Private Attributes | List of all members
protocols::constel::FilterBySASA Class Reference

#include <FilterBySASA.hh>

Static Public Member Functions

static void init (core::Real const smax, core::pose::Pose const &ps)
 Initializes the data structures needed to filter out constellations based on SASA. More...
 
static bool has_low_per_atom_sasa (core::pose::Pose const &ps, utility::vector1< core::Size > const &cnl)
 Tells whether a constellation has a sufficiently low per-atom SASA. More...
 

Static Private Attributes

static std::map< char,
utility::vector1< std::string > > 
aa_sasa_atoms
 A table listing, for each amino acid type, the atoms whose SASA value is relevant to filtering. More...
 
static core::id::AtomID_Map
< core::Real
atom_sasa
 A table holding the SASA values of all atoms in the pose to which constellations belong. More...
 
static core::Real MAX_ATOM_SASA
 Maximum allowed SASA value for a constellation atom. More...
 

Member Function Documentation

bool protocols::constel::FilterBySASA::has_low_per_atom_sasa ( core::pose::Pose const &  ps,
utility::vector1< core::Size > const &  cnl 
)
static

Tells whether a constellation has a sufficiently low per-atom SASA.

Parameters
[in]pspose to which all residues in the constellation belong.
[in]cnlindexes in the pose of the residues forming the constellation.
Returns
true if the constellation has a sufficiently low per-atom SASA; false otherwise.

In the current implementation, the function returns true if each atom whose SASA is relevant to filtering has a SASA lower than or equal to a given cutoff, specified in MAX_ATOM_SASA; the function returns false otherwise.

Remarks
It is assumed that:
  1. The residues forming the constellation have non-zero occupancy only for the atoms that belong to the constellation. This is guaranteed if the residues forming the constellation had their indexes previously passed as arguments to function "SingResCnlCrea::zero_occ_for_deleted_atoms()".
  2. Pose ps has the same per-atom solvent accessibility as the pose passed to function init().

References core::pose::Pose::aa(), aa_sasa_atoms, atom_sasa, MAX_ATOM_SASA, core::chemical::oneletter_code_from_aa(), core::pose::Pose::pdb_info(), and core::pose::Pose::residue().

void protocols::constel::FilterBySASA::init ( core::Real const  smax,
core::pose::Pose const &  ps 
)
static

Initializes the data structures needed to filter out constellations based on SASA.

Parameters
[in]smaxmaximum allowed SASA value for an atom.
[in]pspose to which constellations belong.

References aa_sasa_atoms, atom_sasa, core::scoring::calc_per_atom_sasa(), MAX_ATOM_SASA, and core::pose::Pose::size().

Member Data Documentation

std::map< char, utility::vector1< std::string > > protocols::constel::FilterBySASA::aa_sasa_atoms
staticprivate

A table listing, for each amino acid type, the atoms whose SASA value is relevant to filtering.

Referenced by has_low_per_atom_sasa(), and init().

core::id::AtomID_Map< Real > protocols::constel::FilterBySASA::atom_sasa
staticprivate

A table holding the SASA values of all atoms in the pose to which constellations belong.

A table holding the sasa values of all atoms in the pose to which constellations belong.

Referenced by has_low_per_atom_sasa(), and init().

double protocols::constel::FilterBySASA::MAX_ATOM_SASA
staticprivate

Maximum allowed SASA value for a constellation atom.

Maximum allowed sasa value for a constellation atom.

Referenced by has_low_per_atom_sasa(), and init().


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