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

are_aa_pres()

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]	ps	a pose containing a target constellation.
[in]	cnl	indexes in 'ps' of the residues contributing to the constellation.
[in]	aa_typs	desired amino acid types for the residues contributing to the constellation.
[out]	aa_idxs	vector 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().

are_atoms_pres()

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]	res	a residue.
[in]	anams	vector of atom names to be found in the residue.
[out]	aidxs	vector 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().

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

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