def is_aa(residue, standard=0): """ Return 1 if residue object/string is an amino acid. @param residue: a L{Residue} object OR a three letter amino acid code @type residue: L{Residue} or string @param standard: flag to check for the 20 AA (default false) @type standard: boolean """ if not type(residue) == StringType: residue = residue.get_resname() residue = residue.upper() if standard: return d3_to_index.has_key(residue) else: return to_one_letter_code.has_key(residue)
def is_aa(residue, standard=0): """ Return 1 if residue object/string is an amino acid. @param residue: a L{Residue} object OR a three letter amino acid code @type residue: L{Residue} or string @param standard: flag to check for the 20 AA (default false) @type standard: boolean """ if not type(residue)==StringType: residue=residue.get_resname() residue=residue.upper() if standard: return d3_to_index.has_key(residue) else: return to_one_letter_code.has_key(residue)
def get_sequence(self): """ Return the AA sequence. @return: polypeptide sequence @rtype: L{Seq} """ s = "" for res in self: resname = res.get_resname() if to_one_letter_code.has_key(resname): resname = to_one_letter_code[resname] else: resname = 'X' s = s + resname seq = Seq(s, ProteinAlphabet) return seq
def get_sequence(self): """ Return the AA sequence. @return: polypeptide sequence @rtype: L{Seq} """ s="" for res in self: resname=res.get_resname() if to_one_letter_code.has_key(resname): resname=to_one_letter_code[resname] else: resname='X' s=s+resname seq=Seq(s, ProteinAlphabet) return seq