def run(self):
if not os.path.isfile(pdb_path(self._pdbid)):
whynot_path = datetime.datetime.now().strftime(
'/srv/data/scratch/whynot2/comment/%Y%m%d_pdbredo.txt')
with open(whynot_path, 'a') as f:
f.write('COMMENT: No PDB-format coordinate file available\n')
f.write('PDB_REDO, %s\n' % self._pdbid)
elif not os.path.isfile(pdb_flat_path(self._pdbid)):
PdbExtractJob(pdb_path(self._pdbid)).run()
_log.info("[pdbredo] running pdbredo for %s" % self._pdbid)
days = 3 * 24 * 60 * 60
if not log_command(_log, 'pdbredo',
"%s %s" % (redo_script, self._pdbid),
timeout=days):
_log.error("[pdbredo] pdbredo timeout for %s" % self._pdbid)
whynot_path = os.path.join(zata_dir, 'whynot.txt')
with open(whynot_path, 'a') as f:
f.write(
'COMMENT: PDB REDO script timed out\nPDB_REDO, %s'
% self._pdbid
)
tot_path = os.path.join(pdbredo_path(self._pdbid),
"%s_final_tot.pdb" % self._pdbid)
if os.path.isfile(tot_path):
link_path = os.path.join(settings["DATADIR"],
"pdb_redo/flat/%s" % self._pdbid)
if os.path.islink(link_path):
os.symlink(tot_path, link_path)
def pdbreport_obsolete(pdbid):
paths = glob(os.path.join(settings["DATADIR"], "pdbreport/??", pdbid))
if len(paths) <= 0:
return False
out_path = os.path.join(paths[0], "index.html")
in_path = pdb_path(pdbid)
return os.path.isfile(out_path) and not os.path.isfile(in_path)
def find_input(pdbid):
cif_path = mmcif_path(pdbid)
p_path = pdb_path(pdbid)
if os.path.isfile(p_path):
return p_path
else:
return cif_path
def bdb_uptodate(pdbid):
in_path = pdb_path(pdbid)
dir_path = bdb_path(pdbid)
file_path = os.path.join(dir_path, "%s.bdb" % pdbid)
whynot_path = os.path.join(dir_path, "%s.whynot" % pdbid)
for path in [file_path, whynot_path]:
if os.path.isfile(path) and (not os.path.isfile(in_path) or \
os.path.getmtime(path) >= os.path.getmtime(in_path)):
return True
return False
def scene_obsolete(src, lis_type, pdbid):
if src.lower() == 'pdb':
in_path = pdb_path(pdbid)
elif src.lower() == 'redo':
in_path = final_path(pdbid)
else:
raise Exception("no such structure type: %s" % src)
sce_path = os.path.join(scene_path(src, lis_type, pdbid),
"%s_%s.sce" % (pdbid, lis_names[lis_type]))
return os.path.isfile(sce_path) and not os.path.isfile(in_path)
def run(self):
if self._src.lower() == 'pdb':
struct_path = pdb_path(self._pdbid)
elif self._src.lower() == 'redo':
struct_path = final_path(self._pdbid)
else:
raise Exception("unknown structure type %s" % self._src)
in_path = wilist_data_path(self._src, self._lis_type, self._pdbid)
root_dir = os.path.join(settings["DATADIR"], "wi-lists/%s" % self._src)
if os.path.isfile(in_path):
os.environ["SCENES_SETTINGS"] = scene_settings
log_command(_log,
'scene',
"%s %d %s %s %s %s %s" %
(script, os.getpid(), struct_path, self._pdbid,
self._src.upper(), commands[self._lis_type], in_path),
cwd=root_dir)
def scene_uptodate(src, lis_type, pdbid):
if src.lower() == 'pdb':
in_path = pdb_path(pdbid)
elif src.lower() == 'redo':
in_path = structurefactors_path(pdbid)
else:
raise Exception("no such structure type: %s" % src)
dir_path = scene_path(src, lis_type, pdbid)
sce_path = os.path.join(dir_path,
"%s_%s.sce" % (pdbid, lis_names[lis_type]))
whynot_path = os.path.join(dir_path,
"%s_%s.whynot" % (pdbid, lis_names[lis_type]))
for path in [sce_path, whynot_path]:
if os.path.isfile(path) and (not os.path.isfile(in_path) or \
os.path.getmtime(path) >= os.path.getmtime(in_path)):
return True
return False
def bdb_obsolete(pdbid):
out_path = os.path.join(bdb_path(pdbid), '%s.bdb' % pdbid)
in_path = pdb_path(pdbid)
return os.path.isfile(out_path) and (not os.path.isfile(in_path) or \
os.path.getmtime(out_path) < os.path.getmtime(in_path))
import os
import sys
import logging
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
root_path = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
sys.path.append(root_path)
from databanks.fetch import FetchPdbJob
from databanks.pdb import PdbCleanupJob, PdbExtractJob, pdb_path
if len(sys.argv) == 1:
fetch_job = FetchPdbJob()
fetch_job.run()
PdbCleanupJob(fetch_job).run()
elif len(sys.argv) == 2:
PdbExtractJob(pdb_path(sys.argv[1])).run()
else:
print("Usage: %s pdbid" % sys.argv[0])
print("Usage: %s" % sys.argv[0])
def dssp_obsolete(pdbid):
out_path = dssp_path(pdbid)
in_path = pdb_path(pdbid)
return os.path.isfile(out_path) and not os.path.isfile(in_path)
def pdbreport_uptodate(pdbid):
in_path = pdb_path(pdbid)
out_dir = pdbreport_path(pdbid)
index_path = os.path.join(out_dir, "index.html")
return os.path.isfile(index_path) and \
os.path.getmtime(index_path) >= os.path.getmtime(in_path)
return strftime("%Y %B %d, %H:%M:%S", gmtime(os.path.getmtime(path)))
if len(sys.argv) == 2:
pdbid = sys.argv[1]
print("mmcif:")
path = mmcif_path(pdbid)
print("\tpath:", path)
if os.path.isfile(path):
print("\tmodification time:", s_mtime(path))
else:
print("\t<absent>")
print("pdb:")
for path in [pdb_path(pdbid), pdb_flat_path(pdbid)]:
print("\tpath:", path)
if os.path.isfile(path):
print("\tmodification time:", s_mtime(path))
else:
print("\t<absent>")
print("bdb:")
path = bdb_path(pdbid)
print("\tpath:", path)
if os.path.isdir(path):
print("\tmodification time:", s_mtime(path))
print("\tup to date:", yesno(bdb_uptodate(pdbid)))
print("\tobsolete:", yesno(bdb_obsolete(pdbid)))
else:
print("\t<absent>")
def run(self):
in_path = pdb_path(self._pdbid)
out_path = dssp_path(self._pdbid)
if os.path.isfile(in_path):
log_command(_log, 'dssp', "%s %s %s" % (MKDSSP, in_path, out_path))
def dssp_uptodate(pdbid):
in_path = pdb_path(pdbid)
out_path = dssp_path(pdbid)
return os.path.isfile(out_path) and \
os.path.getmtime(out_path) >= os.path.getmtime(in_path)
def hbonds_uptodate(pdbid):
in_path = pdb_path(pdbid)
dir_path = hbonds_path(pdbid)
log_path = os.path.join(dir_path, "%s.hb2.bz2" % pdbid)
return os.path.isfile(log_path) and \
os.path.getmtime(log_path) >= os.path.getmtime(in_path)
def hbonds_obsolete(pdbid):
out_path = os.path.join(hbonds_path(pdbid),
"%s.hb2.bz2" % pdbid)
in_path = pdb_path(pdbid)
return os.path.isfile(out_path) and not os.path.isfile(in_path)
def nmr_obsolete(pdbid):
out_path = nmr_path(pdbid)
in_path = pdb_path(pdbid)
return os.path.isfile(out_path) and not os.path.isfile(in_path)
