class

Chem::Residue

Inherits Comparable < Reference < Object

Constants

MODIFIED_AMINO_ACIDS = {"ALY" => 'K', "CAS" => 'C', "CME" => 'C', "CSD" => 'C', "CSO" => 'C', "CSS" => 'C', "CSX" => 'C', "HYP" => 'P', "KCX" => 'K', "LLP" => 'K', "M3L" => 'K', "MLY" => 'K', "MLZ" => 'K', "MSE" => 'M', "NEP" => 'H', "OCS" => 'C', "PCA" => 'E', "PTR" => 'Y', "SAC" => 'S', "SEP" => 'S', "TPO" => 'T', "TYS" => 'Y'}

One-letter codes of the parent amino acids of modified residues common in the PDB.

Instance methods

amino_acid?

Returns true if the residue is a standard amino acid or a modified one listed in MODIFIED_AMINO_ACIDS, else false. Caps and other protein residues without a one-letter code are not amino acids.

Source
code(default : Char = 'X') : Char

Returns the single-letter code of the residue's template, or that of the parent amino acid of a modified residue (see MODIFIED_AMINO_ACIDS). Returns default if neither is known.

Source
complete?

Returns true if every heavy atom of the residue template is present, else false. Residues without a template are considered complete.

Source
id
Source
renumber(number : Int32, insertion_code : Char | Nil = nil) : Nil

Sets the number and insertion code at once. Setting them one at a time may briefly give the residue the id of another one, and drop that one from the chain's residue lookup.

Source