NAME¶

mmCQL - SQL-like tool to manipulate mmCIF files

SYNOPSIS¶

mmCQL [OPTION] input [output]

DESCRIPTION¶

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.

AUTHOR¶

Written by Maarten L. Hekkelman <maarten@hekkelman.com>

REPORTING BUGS¶

Report bugs at https://github.com/PDB-REDO/cif-tools/issues

SEE ALSO¶

cif-diff, cif-drop, cif-grep, cif-merge, cif2pdb, mmCQL, pdb2cif.