HELP-23803 generate script for parsing OBS CCD IDs

[shaochenghua]

No description provided.

[Copilot]

Pull request overview

Adds a standalone Python utility script under the chemical-components example use cases to download the wwPDB CCD components CIF, parse for obsolete chemical component IDs, and write them to obsolete_ccd_id.list.

Changes:

• Introduces parse_obsolete_ccd_ids.py to download components.cif.gz and unzip it locally.
• Parses chem_comp.pdbx_release_status == "OBS" records and collects their chem_comp.id values.
• Writes the obsolete CCD IDs to a newline-delimited output file.

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[Copilot]

Pull request overview

Copilot reviewed 1 out of 1 changed files in this pull request and generated 2 comments.

Comments suppressed due to low confidence (1)

example-use-cases/chemical-components/parse_obsolete_ccd_ids.py:71

• Printing once per CCD data block will produce tens of thousands of lines for components.cif and can slow the script substantially. Consider removing this line or making it conditional (e.g., a --verbose flag or periodic progress updates).

    for data_container in l_data_container:
        print("check CCD %s" % data_container.getName())
        if data_container.getObj("chem_comp").getValue("pdbx_release_status", 0) == "OBS":

[valasatava]

It's great! Thank you!

[piehld]

Thanks @shaochenghua! Sorry for the delay in review. Please see my comments below.

[piehld]

Note that the mmcif package is only built for Linux and Mac, so if the user has a Windows, they will need to run this in a Unix environment (or via a Jupyter notebook).

[piehld]

This URL is going to change in the Beta Archive: https://files-beta.wwpdb.org/pub/wwpdb/refdata/chem_comp/components.cif.gz

You may want to introduce a try/except for when the transition happens, so that this script doesn't break.

E.g., first try https://files.wwpdb.org/pub/pdb/data/monomers/components.cif.gz, else try https://files.wwpdb.org/pub/wwpdb/refdata/chem_comp/components.cif.gz

[piehld]

Suggested change

	This script requires the following package, which can be installed with:
	pip install mmcif
	This script requires the `mmcif` package, which can be installed with:
	pip install mmcif
	To run this script:
	python3 parse_obsolete_ccd_ids.py

[piehld]

This produces a huge output to stdout. I would either remove this, or replace all print statements to be logging statements, and make this one a DEBUG statement.