mmCQL1

Usage

Overview

The mmCIF format is a structured format and with a proper dictionary it even looks a lot like a database with relations between categories that act as tables.

In pipelines processing mmCIF files it is often required to simply change the content of a single field, or add some data, delete it, etc. For this the mmCQL tool offers a SQL like language.

This tool is not a complete and finished piece of software, it lack perhaps a lot of functionality. However, it is already very useful to simply lookup some value or change items based on some criteria.

Options

--force

Write output file even if the name of the output file is the same as the input file, which will of course overwrite the input file.

--script=<file>, -f <file>

Read commands from the file <file.

--verbose,-v

Be more verbose, useful to diagnose validation errors.

Examples

You can do simple updates, like so:

UPDATE struct_asym SET id = 'X' WHERE id = 'BBB';

This will rename the asym with ID 'BBB' to 'X'. All children of this asym will be renamed as well if the proper dictionary was loaded.