Beispiel #1
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 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)
Beispiel #2
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    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)
Beispiel #3
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 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
Beispiel #4
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 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
Beispiel #5
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 def __init__(self, queue):
     Job.__init__(self, "hssp_schedule", [])
     self._queue = queue
Beispiel #6
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 def __init__(self, queue):
     Job.__init__(self, "test_job")
     self.test_done = False
     self._queue = queue
Beispiel #7
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 def __init__(self, dat_jobs=[]):
     Job.__init__(self, "pdbfinder2_join", dat_jobs)
Beispiel #8
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 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)
Beispiel #9
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 def __init__(self, databank, path, data_jobs):
     Job.__init__(self, "whynot_%s" % databank, data_jobs)
     self._databank = databank
     self._path = path
Beispiel #10
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 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
Beispiel #11
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 def __init__(self):
     Job.__init__(self, "fetch_refseq")
Beispiel #12
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 def __init__(self):
     Job.__init__(self, "fetch_pdbredo")
Beispiel #13
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 def __init__(self):
     Job.__init__(self, "fetch_rebase")
Beispiel #14
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 def __init__(self):
     Job.__init__(self, "fetch_prosite")
Beispiel #15
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 def __init__(self):
     Job.__init__(self, "fetch_prints")
Beispiel #16
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    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
Beispiel #17
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 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
Beispiel #18
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 def __init__(self):
     Job.__init__(self, "fetch_taxonomy")
Beispiel #19
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 def __init__(self, structurefactors_fetch_job, mmcif_fetch_job):
     Job.__init__(self, "sf_clean",
                  [structurefactors_fetch_job, mmcif_fetch_job])
Beispiel #20
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 def __init__(self):
     Job.__init__(self, "fetch_unigene")
Beispiel #21
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 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
Beispiel #22
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 def __init__(self):
     Job.__init__(self, "fetch_enzyme")
Beispiel #23
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 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
Beispiel #24
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 def __init__(self):
     Job.__init__(self, "fetch_mmcif")
Beispiel #25
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 def __init__(self, mmcif_fetch_job):
     Job.__init__(self, "pdbfinder2_clean", [mmcif_fetch_job])
Beispiel #26
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 def __init__(self):
     Job.__init__(self, "fetch_nmr")
Beispiel #27
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 def __init__(self):
     Job.__init__(self, "test")
     self.test_done = False
Beispiel #28
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 def __init__(self):
     Job.__init__(self, "fetch_sf")
Beispiel #29
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 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
Beispiel #30
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 def __init__(self):
     Job.__init__(self, "fetch_genbank")