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]	ps	pose to which all residues in the constellation belong.
[in]	cnl	indexes 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]	smax	maximum allowed SASA value for an atom.
[in]	ps	pose 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().

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

• src/protocols/constel/FilterBySASA.hh
• src/protocols/constel/FilterBySASA.cc