[Biojava-l] AtomCache: auto-fetch and chemcompinfo

[Andreas Prlic]

Hi Daniel,

> Hello again...I have a question about the AtomCache; currently with
> AutoFetch and LoadChemCompInfo both set false the AtomCache downloads ligand
> CIF files from rcsb.org/pdb/files/ligand

That should only happen if you request the chemical components from
your end, in which case the API needs to access the file to read the
content. The first time it fetches the file from the server, from then
on it will use the files from the local directory.

> and produces a lot of errors like
> "Trying to set field pdbx_synonyms in
> org.biojava.bio.structure.io.mmcif.model.ChemComp, but not found!
> (value:GLYCERIN; PROPANE-1,2,3-TRIOL')"

It is not really an error, just a warning. I think the ' character
might be causing a hickup. I will take a look.

> Is this expected behavior given with those settings?

yes, please ignore it for now until I have cleaned the warning up.

> Also, while not
> related to BioJava, I wonder if anyone knows why the wwpdb.org FTP archive
> doesn't contain the ligand files?

you can get all of them in a single file from here:
http://www.wwpdb.org/ccd.html

Andreas