def test_pdb_code(self):
self.assertTrue(gemmi.is_pdb_code('9ALA'))
self.assertFalse(gemmi.is_pdb_code('BAD1'))
pdb_dir = os.getenv('PDB_DIR')
if not pdb_dir:
return
cif_4xyz = pdb_dir + '/structures/divided/mmCIF/xy/4xyz.cif.gz'
self.assertEqual(gemmi.expand_pdb_code_to_path('4XYZ', 'M'), cif_4xyz)
self.assertEqual(gemmi.expand_if_pdb_code('4XYZ'), cif_4xyz)
self.assertEqual(gemmi.expand_if_pdb_code('4XYZ', filetype='P'),
pdb_dir + '/structures/divided/pdb/xy/pdb4xyz.ent.gz')
def get_file_paths_from_args():
for arg in sys.argv[1:]:
if os.path.isdir(arg):
for path in CifWalk(arg):
yield path
else:
yield expand_if_pdb_code(arg)
def get_file_paths_from_args():
"""\
Process arguments as filenames or directories with .cif(.gz) files,
and yield the file paths.
Normally we first test our scripts on a few files:
./myscript 1mru.cif another.cif
and then do pdb-wide analysis:
./myscript $PDB_DIR/structures/divided/mmCIF
If $PDB_DIR is set you can check the specifies PDB entries:
./myscript 1ABC 2def
If you have a list of PDB codes to analyze (one code per line, the code
must be the first word, but may be followed by others), do:
./myscript --only=my-list.txt $PDB_DIR/structures/divided/mmCIF
"""
parser = argparse.ArgumentParser(usage='%(prog)s [options] path [...]')
parser.add_argument('path', nargs='+', help=argparse.SUPPRESS)
parser.add_argument('--only',
metavar='LIST',
help='Use only files that match names in this file')
args = parser.parse_args()
only = None
if args.only:
with open(args.only) as list_file:
only = set(line.split()[0].lower() for line in list_file
if line.strip())
for arg in args.path:
if os.path.isdir(arg):
for root, dirs, files in os.walk(arg):
dirs.sort()
for name in sorted(files):
for ext in ['.cif', '.cif.gz']:
if name.endswith(ext):
if not only or name[:-len(ext)].lower() in only:
yield os.path.join(root, name)
break
else:
yield expand_if_pdb_code(arg)
def main():
if len(sys.argv) < 2:
sys.exit('Specify files, directories or PDB codes.')
for arg in sys.argv[1:]:
for path in gemmi.CoorFileWalk(gemmi.expand_if_pdb_code(arg)):
check_mtrix_rot(path)