From 56a5a63d35045011ab94fd182156734dd6408166 Mon Sep 17 00:00:00 2001
From: Bienchen <stefan.bienert@unibas.ch>
Date: Fri, 6 May 2022 14:10:25 +0000
Subject: [PATCH] Update validation/README.md
---
validation/README.md | 19 +++++++++++++++----
1 file changed, 15 insertions(+), 4 deletions(-)
diff --git a/validation/README.md b/validation/README.md
index 5123638..2cfa38d 100644
--- a/validation/README.md
+++ b/validation/README.md
@@ -1,14 +1,16 @@
# 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_]]
## 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
@@ -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`.
+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
-- explain output
- add version of dict validated against
- remaining options
--
GitLab