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protocols::constel::PresenceCommon Class Reference

A class to hold data structures and functions shared by filters that check whether the amino acids and atoms they require in the constellation are indeed present. More...

#include <Primitives.hh>

Static Public Member Functions

static bool are_aa_pres (core::pose::Pose const &ps, utility::vector1< core::Size > const &cnl, utility::vector1< core::chemical::AA > const &aa_typs, utility::vector1< core::Size > &aa_idxs)
 Records the presence of given amino acid types in a given constellation. More...
 
static bool are_atoms_pres (core::conformation::Residue const &res, utility::vector1< std::string > const &anams, utility::vector1< core::Size > &aidxs)
 Records the presence of given atoms in a given residue. More...
 

Detailed Description

A class to hold data structures and functions shared by filters that check whether the amino acids and atoms they require in the constellation are indeed present.

Member Function Documentation

bool protocols::constel::PresenceCommon::are_aa_pres ( core::pose::Pose const &  ps,
utility::vector1< core::Size > const &  cnl,
utility::vector1< core::chemical::AA > const &  aa_typs,
utility::vector1< core::Size > &  aa_idxs 
)
static

Records the presence of given amino acid types in a given constellation.

Parameters
[in]psa pose containing a target constellation.
[in]cnlindexes in 'ps' of the residues contributing to the constellation.
[in]aa_typsdesired amino acid types for the residues contributing to the constellation.
[out]aa_idxsvector that will map the desired amino acid types to the residue indexes in 'cnl'.
Returns
false if at least one amino acid type in 'aa_typs' is absent from the constellation. Returns true otherwise; in this case, the ith value of 'aa_idxs' is the least index in 'cnl' of a residue having the ith amino acid type in 'aa_typs' (i=1,...,aa_typs.size()).
Remarks
It is assumed that:
  1. 'cnl', 'aa_typs', and 'aa_idxs' have the same size.
    1. different elements in 'aa_typs' have different values.

References core::pose::Pose::aa(), and core::chemical::element::N.

Referenced by protocols::constel::FilterByIndoleCOO::is_satisfied(), protocols::constel::FilterByTryptamine::is_satisfied(), protocols::constel::FilterByAmphetamine::is_satisfied(), and protocols::constel::FilterByHistamine::is_satisfied().

bool protocols::constel::PresenceCommon::are_atoms_pres ( core::conformation::Residue const &  res,
utility::vector1< std::string > const &  anams,
utility::vector1< core::Size > &  aidxs 
)
static

Records the presence of given atoms in a given residue.

Parameters
[in]resa residue.
[in]anamsvector of atom names to be found in the residue.
[out]aidxsvector that will map the desired atom names to their indexes in the residue.
Returns
false if at least one atom with a desired name is absent from the residue. Returns true otherwise; in this case, the ith element of 'aidxs' will hold the index in 'res' of the atom having the ith name in 'anams' (i=1,...,anams.size()).

References core::conformation::Residue::atom_index(), core::conformation::Residue::has(), and core::chemical::element::N.

Referenced by protocols::constel::FilterByIndoleCOO::is_satisfied(), protocols::constel::FilterByTryptamine::is_satisfied(), and protocols::constel::FilterByAmphetamine::is_satisfied().


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