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# Copyright 2002 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from Bio.config.DBRegistry import CGIDB, DBGroup
from _support import *
from Martel import *
not_header_expr = AssertNot(Str("HEADER"))
pdb_rcsb_cgi = CGIDB(
name="pdb-rcsb-cgi",
cgi="http://www.rcsb.org/pdb/cgi/export.cgi",
url="XXX PLEASE FILL THIS IN XXX",
delay=5.0,
params=[("format", "PDB"),
("compression", "None")
],
key="pdbId",
# failure cases for file not found are making retrieval freeze up
# while Martel checks for them, for some reason I can't figure
# so we go with checking to make sure results look like PDB
# failure_cases=[(has_str("File not found"), "ID does not exist")],
failure_cases=[(not_header_expr, "results do not look like PDB format")]
)
pdb_ebi_cgi = CGIDB(
name="pdb-ebi-cgi",
cgi="http://www.ebi.ac.uk/cgi-bin/dbfetch",
url="http://www.ebi.ac.uk/cgi-bin/dbfetch",
delay=5.0,
params=[("db", "PDB"),
("format", "default"), # also Fasta, bsml, agave available
("style", "raw"),
],
key="id",
failure_cases=[(not_header_expr, "results do not look like PDB format")]
)
pdb = DBGroup(
name="pdb",
behavior="serial"
)
pdb.add(pdb_rcsb_cgi)
pdb.add(pdb_ebi_cgi)
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