def hssp_uptodate(pdbid):
in_path = mmcif_path(pdbid)
out_path = hssp1_path(pdbid)
return os.path.isfile(out_path) and \
os.path.getmtime(out_path) >= os.path.getmtime(in_path) and \
not is_empty_file(out_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 run(self):
in_path = mmcif_path(self._pdbid)
out_path = dssp_mmcif_path(self._pdbid)
if os.path.isfile(in_path):
log_command(_log, 'dssp-from-mmcif',
"%s %s %s" % (MKDSSP, in_path, out_path))
def pdbfinder2_obsolete(pdbid):
in_path = mmcif_path(pdbid)
out_path = dat_path(pdbid)
return os.path.isfile(out_path) and not os.path.isfile(in_path)
def pdbfinder2_uptodate(pdbid):
in_path = mmcif_path(pdbid)
out_path = dat_path(pdbid)
return os.path.isfile(out_path) and \
os.path.getmtime(out_path) >= os.path.getmtime(in_path) and \
os.path.getmtime(out_path) >= os.path.getmtime(PDBFINDER2_SCRIPT)
def structurefactors_obsolete(pdbid):
out_path = structurefactors_path(pdbid)
in_path = mmcif_path(pdbid)
return os.path.isfile(out_path) and not os.path.isfile(in_path)
def pdb_obsolete(pdbid):
return os.path.isfile(pdb_path(pdbid)) and not os.path.isfile(mmcif_path(pdbid))
def hssp_obsolete(pdbid):
out_path = hssp1_path(pdbid)
in_path = mmcif_path(pdbid)
return os.path.isfile(out_path) and not os.path.isfile(in_path)
def yesno(boolean):
if boolean:
return "yes"
else:
return "no"
def s_mtime(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:")
def dssp_mmcif_uptodate(pdbid):
in_path = mmcif_path(pdbid)
out_path = dssp_mmcif_path(pdbid)
return os.path.isfile(out_path) and \
os.path.getmtime(out_path) >= os.path.getmtime(in_path)
