def __init__(self, pdbid, pdb_extract_job=None):
deps = []
if pdb_extract_job is not None:
deps.append(pdb_extract_job)
Job.__init__(self, "pdbreport_%s" % pdbid, deps)
self._pdbid = pdbid
self._out_dir = os.path.join(settings["DATADIR"], "pdbreport",
self._pdbid[1:3], self._pdbid)
def __init__(self, gz_path):
self._pdbid = os.path.basename(gz_path)[3:7]
Job.__init__(self, "pdb_extract_%s" % self._pdbid)
self._gz_path = gz_path
self._out_path = os.path.join(settings['DATADIR'],
'pdb/flat/pdb%s.ent' % self._pdbid)
def __init__(self, pdbid, dssp_job=None, hssp_job=None):
dependent_jobs = []
if dssp_job is not None:
dependent_jobs.append(dssp_job)
if hssp_job is not None:
dependent_jobs.append(hssp_job)
Job.__init__(self, "pdbfinder_%s" % pdbid, dependent_jobs)
self._pdbid = pdbid
def __init__(self, src, lis_type, pdbid, wilist_job=None):
if wilist_job is None:
Job.__init__(self, "scene_%s_%s_%s" % (src, lis_type, pdbid), [])
else:
Job.__init__(self, "scene_%s_%s_%s" % (src, lis_type, pdbid),
[wilist_job])
self._src = src
self._lis_type = lis_type
self._pdbid = pdbid
def __init__(self, queue):
Job.__init__(self, "hssp_schedule", [])
self._queue = queue
def __init__(self, queue):
Job.__init__(self, "test_job")
self.test_done = False
self._queue = queue
def __init__(self, dat_jobs=[]):
Job.__init__(self, "pdbfinder2_join", dat_jobs)
def __init__(self, pdb_fetch_job=None):
dependent_jobs = []
if pdb_fetch_job is not None:
dependent_jobs.append(pdb_fetch_job)
Job.__init__(self, "bdb_clean", dependent_jobs)
def __init__(self, databank, path, data_jobs):
Job.__init__(self, "whynot_%s" % databank, data_jobs)
self._databank = databank
self._path = path
def __init__(self, queue, mmcif_fetch_job, pdb_fetch_job,
uniprot_fetch_job):
Job.__init__(self, "schedule_mmcif", [mmcif_fetch_job, pdb_fetch_job])
self._queue = queue
self._uniprot_fetch_job = uniprot_fetch_job
self._mmcif_fetch_job = mmcif_fetch_job
def __init__(self):
Job.__init__(self, "fetch_refseq")
def __init__(self):
Job.__init__(self, "fetch_pdbredo")
def __init__(self):
Job.__init__(self, "fetch_rebase")
def __init__(self):
Job.__init__(self, "fetch_prosite")
def __init__(self):
Job.__init__(self, "fetch_prints")
def __init__(self, queue, pdb_fetch_job, redo_fetch_job):
Job.__init__(self, "schedule_scenes", [pdb_fetch_job, redo_fetch_job])
self._queue = queue
self._pdb_fetch_job = pdb_fetch_job
self._redo_fetch_job = redo_fetch_job
def __init__(self, queue, pdbredo_fetch_job):
Job.__init__(self, "schedule_pdbredo", [pdbredo_fetch_job])
self._queue = queue
self._pdbredo_fetch_job = pdbredo_fetch_job
def __init__(self):
Job.__init__(self, "fetch_taxonomy")
def __init__(self, structurefactors_fetch_job, mmcif_fetch_job):
Job.__init__(self, "sf_clean",
[structurefactors_fetch_job, mmcif_fetch_job])
def __init__(self):
Job.__init__(self, "fetch_unigene")
def __init__(self, pdbid, pdb_extract_job=None):
deps = []
if pdb_extract_job is not None:
deps.append(pdb_extract_job)
Job.__init__(self, "bdb_%s" % pdbid, deps)
self._pdbid = pdbid
def __init__(self):
Job.__init__(self, "fetch_enzyme")
def __init__(self, pdbid, pdbfinder_job=None):
if pdbfinder_job is None:
Job.__init__(self, "pdbfinder2_%s" % pdbid)
else:
Job.__init__(self, "pdbfinder2_%s" % pdbid, [pdbfinder_job])
self._pdbid = pdbid
def __init__(self):
Job.__init__(self, "fetch_mmcif")
def __init__(self, mmcif_fetch_job):
Job.__init__(self, "pdbfinder2_clean", [mmcif_fetch_job])
def __init__(self):
Job.__init__(self, "fetch_nmr")
def __init__(self):
Job.__init__(self, "test")
self.test_done = False
def __init__(self):
Job.__init__(self, "fetch_sf")
def __init__(self, pdbid, pdb_extract_job=None):
if pdb_extract_job is None:
Job.__init__(self, "hbonds_%s" % pdbid)
else:
Job.__init__(self, "hbonds_%s" % pdbid, [pdb_extract_job])
self._pdbid = pdbid
def __init__(self):
Job.__init__(self, "fetch_genbank")