7ca79b945accfbf1c5e435eac1e9e25c0d808272,prody/proteins/blastpdb.py,,blastPDB,#Any#Any#,13

Before Change

                    "SDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMN"
                    "DAYDIVKMKKSNISPNFNFMGQLLDFERTL")
    else:
        try:
            sequence = "".join(sequence.split())
            _ = sequence.isalpha()
        except AttributeError:
            raise TypeError("sequence must be a string")
        else:
            if not _:
                raise ValueError("not a valid protein sequence")
    headers = {"User-agent": "ProDy"}

    query = [("DATABASE", "pdb"), ("ENTREZ_QUERY", "(none)"),
             ("PROGRAM", "blastp"),]

After Change

        sequence = ("ASFPVEILPFLYLGCAKDSTNLDVLEEFGIKYILNVTPNLPNLFENAGEFKYKQIPI"
                    "SDHWSQNLSQFFPEAISFIDEARGKNCGVLVHSLAGISRSVTVTVAYLMQKLNLSMN"
                    "DAYDIVKMKKSNISPNFNFMGQLLDFERTL")
    elif isinstance(sequence, Atomic):
        sequence = sequence.select("calpha and chain %s" % chain).getSequence()
    elif isinstance(sequence, Sequence):
        sequence = str(sequence)
    elif isinstance(sequence, str):
        if len(sequence) == 4 or len(sequence) == 5:
            ag = parsePDB(sequence)
            sequence = ag.select("calpha and chain %s" % chain).getSequence()
    else:
        raise TypeError("seq must be an atomic class, sequence class, or str not {0}"
                        .format(type(sequence)))

    headers = {"User-agent": "ProDy"}
    query = [("DATABASE", "pdb"), ("ENTREZ_QUERY", "(none)"),

Instances