def __call__(self):
from iotbx.pdb import download
return download.openurl(
url = "%s/%s" % ( self.job_folder, self.OUTPUTFILE ),
storage = download.no_storage,
)
def get_request(url, identifier): lcase = identifier.lower() stream = openurl( url = ( url + lcase ).encode() ) result_for = json.load( stream ) assert lcase in result_for return result_for[ lcase ]
def multiple(self, identifiers):
for ident in identifiers:
try:
stream = openurl(
url = ( self.url + self.namer( identifier = ident ) ).encode(),
)
except NotFound:
yield None
else:
yield stream
def post_request(url, identifiers):
if len( identifiers ) == 0:
return ( i for i in () )
try:
stream = openurl( url = url, data = ( ",".join( identifiers ) ).encode() )
except NotFound:
return ( None for i in identifiers )
result_for = json.load( stream )
return ( result_for.get( ident.lower() ) for ident in identifiers )
def __init__(self):
stream = openurl(
url="ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat", )
chain_redirection_for = parse_pdb_redirections(lineiter=stream)
self.redirection_for = {}
for key in chain_redirection_for:
self.redirection_for[key] = end_of_chain(
identifier=key,
replacement_for=chain_redirection_for,
)
def __init__(self):
stream = openurl(
url = "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat",
)
chain_redirection_for = parse_pdb_redirections( lineiter = stream )
self.redirection_for = {}
for key in chain_redirection_for:
self.redirection_for[ key ] = end_of_chain(
identifier = key,
replacement_for = chain_redirection_for,
)
def __init__(self, pdbstr, name):
from iotbx.pdb import download
import urllib
data_for = {
"pdb": pdbstr,
"bfactorPDB": "Yes",
"name": name,
"nomail": "Yes",
"do": "Submit",
}
stream = download.openurl(
url=self.SERVERURL,
data=urllib.urlencode(data_for.items()),
)
self.job_folder = parse_submission_page(stream=stream)
stream.close()
def __init__(self, pdbstr, name):
from iotbx.pdb import download
import urllib
data_for = {
"pdb": pdbstr,
"bfactorPDB": "Yes",
"name": name,
"nomail": "Yes",
"do": "Submit",
}
stream = download.openurl(
url = self.SERVERURL,
data = urllib.urlencode( data_for.items() ),
)
self.job_folder = parse_submission_page( stream = stream )
stream.close()
def __init__(self, pdbstr, name):
from iotbx.pdb import download
import urllib
data_for = {
"pdb": pdbstr,
"bfactorPDB": "Yes",
"name": name,
"email": "*****@*****.**",
"do": "Submit",
}
stream = download.openurl(
url = self.SERVERURL,
data = urllib.urlencode( data_for.items() ),
encodings = [],
storage = download.no_storage,
)
self.job_folder = parse_submission_page( stream = stream )
def __call__(self):
from iotbx.pdb import download
return download.openurl(url="%s/%s" %
(self.job_folder, self.OUTPUTFILE), )
def single(self, identifier):
stream = openurl(
url = ( self.url + self.namer( identifier = identifier ) ).encode(),
)
return stream