[BUG] Custom CCD is not properly read #109
Description
Describe the bug
When running inference with a custom CCD file, it is not properly respected by the query builder. This means that inference workflows with custom compounds will not work properly, whereas AlphaFold3 supports this workflow.
To Reproduce
Set ccd_file_path to a custom CCD that contains different chemical component IDs, then run an inference query.
Expected behavior
The inference pipeline should featurize the custom compounds as detailed in their CCD information.
Additional context
This function uses get_residue_cached, which obtains its information from biotite.structure.info. Biotite uses its internal CCD for these operations, not the user-supplied one.