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
