[Biojava-dev] DownloadChemCompProvider exception

[Steve Darnell]

Greetings,

I get the following exception when using the DownloadChemCompProvider on
Windows (XP/Vista/7):

Installing individual chem comp files ...
java.io.FileNotFoundException: C:\Users\darnells\Desktop\Chemical
Component Dictionary\chemcomp\CON.cif.gz (The handle is invalid)
	at java.io.FileOutputStream.open(Native Method)
	at java.io.FileOutputStream.<init>(Unknown Source)
	at java.io.FileOutputStream.<init>(Unknown Source)
	at
org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider.writeID(Down
loadChemCompProvider.java:159)
	at
org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider.split(Downlo
adChemCompProvider.java:130)
	at
org.biojava.bio.structure.io.mmcif.DownloadChemCompProvider.checkDoFirst
Install(DownloadChemCompProvider.java:99)
	at
steve.sandbox.playground.ChemCompDistribution.main(ChemCompDistribution.
java:14)
created 3990 chemical component files.


The problem is that CON.cif.gz and PRN.cif.gz use the reserved Windows
filenames 'CON' and 'PRN'
(http://en.wikipedia.org/wiki/Filename#Reserved_characters_and_words).
These names are reserved regardless of the file extension.  I have
spoken with RCSB in the past.  They are unable to change the code for
these records (and the five affected PDB files: 2I7S, 1TUM, 1U1N, 1U1L,
and 1CL8).

At minimum, DownloadChemCompProvider should catch the exception and
proceed with the remaining records.  This seems reasonable given the low
number of affected PDB files.

Regards,
Steve