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/).
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## 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
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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):