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)
print("\tmodification time:", s_mtime(path))
print("\tup to date:", yesno(hssp_uptodate(pdbid)))
print("\tobsolete:", yesno(hssp_obsolete(pdbid)))
else:
print("\t<absent>")
print("structure factors:")
path = structurefactors_path(pdbid)
print("\tpath:", path)
if os.path.isfile(path):
print("\tmodification time:", s_mtime(path))
else:
print("\t<absent>")
print("pdbredo:")
path = final_path(pdbid)
print("\tpath:", path)
if os.path.isfile(path):
print("\tmodification time:", s_mtime(final_path(pdbid)))
print("\tup to date:", yesno(pdbredo_uptodate(pdbid)))
print("\tobsolete:", yesno(pdbredo_obsolete(pdbid)))
else:
print("\t<absent>")
print("pdbreport:")
path = pdbreport_path(pdbid)
print("\tpath:", path)
if os.path.isfile(path):
print("\tmodification time:", s_mtime(pdbreport_path(pdbid)))
print("\tup to date:", yesno(pdbreport_uptodate(pdbid)))
print("\tobsolete:", yesno(pdbreport_obsolete(pdbid)))
def dsspredo_uptodate(pdbid):
in_path = final_path(pdbid)
out_path = dsspredo_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))
def dsspredo_obsolete(pdbid):
out_path = dsspredo_path(pdbid)
in_path = final_path(pdbid)
return os.path.isfile(out_path) and not os.path.isfile(in_path)
def run(self):
in_path = final_path(self._pdbid)
out_path = dsspredo_path(self._pdbid)
if os.path.isfile(in_path):
log_command(_log, 'dssp', "%s %s %s" % (MKDSSP, in_path, out_path))