VMD-L Mailing List

From: FX (fxcoudert_at_gmail.com)
Date: Mon Nov 24 2008 - 17:05:26 CST

> Thanks for sending the patch. Have you done significant testing
> with this patch and current revs of openbabel?

I have tested it on quite a few different formats with 2.2.0, it works
fine so far (except for ShelX, but it's due to OpenBabel not correctly
reading the files I have, so it's not a bug in the plugin).

> I'm just trying to
> gauge how much testing will be required before I can safely apply this
> patch to the CVS tree

Of course I'm not to be trusted because I'm the patch author :)
Nevertheless, I'd say I'm pretty confident it's quite safe for OB >=
2.2.0, aside from the VMDBABELBIN issue which I mentionned (and which
I believe is an issue in my own build). Older versions of OB don't
recognize the "-L formats read" option, so they reliably won't work.
For now, this has to be selected at compile time. Another option,
which can be worked out, is to use "babel -V" (available since 2.0.0)
to determine the version and then use either a fixed format list or
autodetection.

I can work on such an amended patch if asked to, but it might be some
time before I get to it. On the other hand, it's not very hard to
write...

Best regards,
FX

PS: currently, unit cell information is not output by OpenBabel when
exporting to PDB format; I have submitted a patch to OpenBabel to
change that behaviour (http://sourceforge.net/tracker/?func=detail&atid=428742&aid=2023510&group_id=40728
), which has now been imported into the development version. The
plugin does correctly use this information if the devel OpenBabel
version is used.