Skip to content
Snippets Groups Projects
Commit 56a5a63d authored by Bienchen's avatar Bienchen
Browse files

Update validation/README.md

parent fb0a0417
No related branches found
No related tags found
No related merge requests found
# ModelCIF validation tool # ModelCIF validation tool
This is a tool to check that the formatting of ModelCIF files complies with the ModelCIF format declaration (aka "dictionary"). Upon successful validation, a ModelCIF file can be extended with the dictionary version the file was compared to (option `--extend-validated-file` ToDo: add anchor for option). For more basic mmCIF validation, the dictionary of the underlying PDBx/mmCIF format is also available. This is a tool to check that the formatting of ModelCIF files complies with the ModelCIF format declaration (aka "dictionary"). Upon successful validation, a ModelCIF file can be extended with the dictionary version the file was compared to (option [`--extend-validated-file`](#add-validation-dictionary-to-ModelCIF-file)). For more basic mmCIF validation, the dictionary of the underlying PDBx/mmCIF format is also available.
The easiest way to run validation is from Docker container. Running it out of Docker requires an installation of [OpenStructure](https://openstructure.org). The easiest way to run validation is from Docker container.
The tool itself is a wrapper around the [`CifCheck`](https://github.com/rcsb/cpp-dict-pack) tool by [RCSB](https://www.rcsb.org/).
[[_TOC_]] [[_TOC_]]
## How to run the validation tool ## How to run the validation tool
This is just a description of the validation tool itself. When running it from inside a container, the command needs to be prefixed with the instructions to start the container. Find information for running the validation container in "[How to run the container](how-to-run-the-container)". This is just a description of the validation tool itself. When running it from inside a container, the command needs to be prefixed with the instructions to start the container. Find information for running the validation container in "[How to run the container](#how-to-run-the-container)".
Upon completion, if there hasn't been any error running the command, the validation tool returns a concise report in JSON format. That output is meant to be input to a website or any kind of nicely formatted report. Output can also be stored as a file. If the tested ModelCIF file is fully compliant with the ModelCIF format, the JSON output has Upon completion, if there hasn't been any error running the command, the validation tool returns a concise report in JSON format. That output is meant to be input to a website or any kind of nicely formatted report. Output can also be stored as a file. If the tested ModelCIF file is fully compliant with the ModelCIF format, the JSON output has
...@@ -18,10 +20,19 @@ Upon completion, if there hasn't been any error running the command, the validat ...@@ -18,10 +20,19 @@ Upon completion, if there hasn't been any error running the command, the validat
Format violations will be listed in `diagnosis`. Format violations will be listed in `diagnosis`.
The most basic way to invoke the validation tool is just with a Modelcif file (example shows the command plus possible output):
```bash
$ validate-mmcif-file model.cif
{"status":"completed","diagnosis":[],"versions":[{"title":"mmcif_pdbx_v50.dic","version":"5.358","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/base/mmcif_pdbx_v50.dic"},{"title":"mmcif_ma.dic","version":"1.4.0","location":"https://raw.githubusercontent.com/ihmwg/ModelCIF/a24fcfa8d6c3ceb4b6f0676bcc341ac0cd24ff1f/dist/mmcif_ma.dic"}]}
$
```
### Add validation dictionary to ModelCIF file
- basic usage - basic usage
- explain output
- add version of dict validated against - add version of dict validated against
- remaining options - remaining options
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment