Reduce loc

validation/test-suite.py

@@ -355,8 +355,8 @@ def _main():
                 + '"atom_site"',
             ],
         },
-        # duplicated item in _loop category
         # missing category (entity)
+        # duplicated item in _loop category
         # parent-child relationship issue (remove an atom_type.symbol)
     }
 

validation/validate-mmcif-file.py

@@ -57,14 +57,24 @@ def _parse_command_line():
         + "external files attached.",
         default=None,
     )
-    parser.add_argument(
+    dic_grp = parser.add_mutually_exclusive_group()
+    dic_grp.add_argument(
         "--dict-sdb",
         "-d",
         type=str,
         metavar="<SDB FILE>",
-        help="The dictionary in SDB format used for checking.",
+        help="The dictionary in SDB format used for checking. Can't be "
+        + "combined with --modelcif-mode/-m and --pdbx-mmcif-mode/-p.",
         default="/usr/local/share/mmcif-dict-suite/mmcif_ma.sdb",
     )
+    dic_grp.add_argument(
+        "--pdbx-mmcif-mode",
+        "-p",
+        action="store_true",
+        help="Check with the PDBX/mmCIF dictionary, for verbatim mmCIF files. "
+        + "Can't be combined with --dict-sdb/-d and --modelcif-mode/-m. "
+        + "Default is to check with the ModelCIF dictionary.",
+    )
     parser.add_argument(
         "--out-file",
         "-o",
@@ -106,6 +116,8 @@ def _parse_command_line():
     if opts.extend_validated_file is not None:
         if opts.extend_validated_file == " same ":
             opts.extend_validated_file = opts.model_cif
+    if opts.pdbx_mmcif_mode is True:
+        opts.dict_sdb = "/usr/local/share/mmcif-dict-suite/mmcif_pdbx_v50.sdb"
 
     return opts
 
@@ -135,42 +147,23 @@ def _parse_cifcheck_stderr(stderr):
     return error_lst
 
 
-def _parse_parser_file(filename):
-    """Parse the parser output file of CifCheck."""
-    parserfile = filename + "-parser.log"
-    if not os.path.exists(parserfile):
-        return []
-
-    error_lst = []
-    with open(parserfile, encoding="utf-8") as dfh:
-        for line in dfh:
-            line = line.strip()
-            error_lst.append(line)
-
-    # remove the diag file
-    os.unlink(parserfile)
-
-    return error_lst
-
-
-def _parse_diag_file(filename):
+def _get_cifcheck_out(filename, suffix, encoding):
     """Parse the diagnosis file of CifCheck."""
     # CifCheck places the diag file in the current working directory.
-    diagfile = filename + "-diag.log"
-    if not os.path.exists(diagfile):
+    cifcheck = filename + suffix
+    if not os.path.exists(cifcheck):
         return []
 
     error_lst = []
     # CifCheck outputs diag files as iso-8859
-    with open(diagfile, encoding="iso-8859-1") as dfh:
+    with open(cifcheck, encoding=encoding) as dfh:
         for line in dfh:
             line = line.strip()
             if line == "":
                 continue
             error_lst.append(line)
-
     # remove the diag file
-    os.unlink(diagfile)
+    os.unlink(cifcheck)
 
     return error_lst
 
@@ -592,12 +585,14 @@ class _CifCheck:
         error_lst = []
         # get error messages on the command line
         error_lst.extend(_parse_cifcheck_stderr(cps.stderr))
-        error_lst.extend(_parse_parser_file(filepath))
+        error_lst.extend(_get_cifcheck_out(filepath, "-parser.log", "utf-8"))
         if len(error_lst) > 0:
             raise _CifCheckFailedError(cifcheck_cmd, error_lst)
 
         # get messages from diagnosis file
-        error_lst.extend(_parse_diag_file(filepath))
+        error_lst.extend(
+            _get_cifcheck_out(filepath, "-diag.log", "iso-8859-1")
+        )
 
         return error_lst