@@ -16,7 +16,7 @@ Upon completion, if there hasn't been any error running the command, the validat
-`status` "completed"
- no messages in the `diagnosis` list
-`version` of the dictionaries the file was tested against
-`versions` of the dictionaries the file was tested against
Format violations will be listed in `diagnosis`.
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@@ -30,7 +30,27 @@ $
### Add validation dictionary to ModelCIF file
Since both dictionaries, ModelCIF and PDBx/mmCIF, represent actively developed file formats, different versions exist. While extending them, quite some thinking goes into making only non-breaking changes. The idea is that a ModelCIF file formatted following dictionary 1.3, is still valid with version 1.4. But the version number also tells you which feature to expect from a ModelCIF file, so it seems like a good idea to keep the version inside the file.
The validation tool can add the version upon positive validation, enabled by the `--extend-validated-file` (`-e`).
`-e` can take an alternative file name to write the validated ModelCIF file to, e.g. if one wants to keep the original ModelCIF file unaltered:
The last command will generate a new file `validated_model.cf` upon positive validation (`diagnosis` points to an empty list), with the `versions` added to the `_audit_conform` list inside the file.
To add the validation dictionaries to `_audit_conform` in the original ModelCIF file, just invoke `-e` without an alternative file name... well almost. By the way Python handles this kind of command line arguments, `-e` consumes everything after it, that does not start with a `-`, as a file name. So `validate-mmcif-file -e model.cif` would mean that `-e` assumes `model.cif` as its file name but then the command fails because it is missing the ModelCIF file to be validated. The solution is either putting `-e` at the beginning of the arguments list or after the ModelCIF file name at the very end, if there are no other command line arguments:
