[Biojava-dev] DownloadChemCompProvider exception

[Steve Darnell]

Andreas,

Excellent.  Works as advertised.

~Steve

-----Original Message-----
From: andreas.prlic at gmail.com [mailto:andreas.prlic at gmail.com] On Behalf Of Andreas Prlic
Sent: Tuesday, January 25, 2011 10:58 AM
To: Steve Darnell
Cc: biojava-dev at lists.open-bio.org
Subject: Re: [Biojava-dev] DownloadChemCompProvider exception

Hi Steve,


> 1. Rename the files _CON.cif.gz: Chrome and 7-Zip automatically append an underscore to the beginning of reserved filenames.  Firefox and Internet Explorer only prompt the error.  I have not found a style guideline for this condition; however, I would follow the existing "precedence" (even as limited as it is).

ok changed in SVN.

> 2. Add 'AUX' and 'NUL' to the list of protected IDs to avoid potential namespace clashes in the future


Got added


> I have one additional comment based on this snippet of code:

I am trying to simplify this... You can now do the following to get a
local install of all chemical components:

		DownloadChemCompProvider.setPath("/path/to/local/PDB_DIR/");
		DownloadChemCompProvider c = new DownloadChemCompProvider();
		c.setDownloadAll(true);
		c.checkDoFirstInstall();

The path is stored as a System property "PDB_DIR", which is used by
all classes that need to access local PDB or chem comp files.. (chem
comp files are always expected to be in PDB_DIR/chemcomp )

Andreas