Bugzilla Bug 35945

Tinker is a molecular modeling and computations package geared towards
high-speed calculations on large systems and molecules.  It comes with a
java-based interface called "Force Field Explorer", which is still under
development - i.e. it is sometimes quite cranky and unstable, depending on the
version of JRE and Java3D you have installed.  Tinker itself, however, which
runs from the command line, is rock-solid.

Reproducible: Always
Steps to Reproduce:
1.
2.
3.




This package depends upon Java3D for FFE, and FFE is totally unstable with the
1.3.1 beta of Java3D.  As a result, you should use the 1.3-FCS version with
this
package for right now.

Though FFE is problematic, the core Tinker application, as stated above, works
very well, and is very stable.

Tinker is VERY fast when it comes to large-scale computations.

Created an attachment (id=22301) [edit]
Tinker 4.1 ebuild

Ah, cool. This is one of the things I've wanted to get to but haven't had the
chance. I'll look at it soon.

Created an attachment (id=26329) [edit]
Updated Tinker 4.1 ebuild

This is a full ebuild for Tinker 4.1 which fixes the problem associated with
the missing parameter files.  Energy minimizations now work fine - all
parameter files are now properly placed into the "/usr/local/tinker/params"
directory where the belong.

Gentoo can't install to /usr/local, that's for personal use. We stick to /usr.

Created an attachment (id=26330) [edit]
DIFF patch to fix the paths for the ebuild

This patch fixes all of the destinations to the proper /usr/tinker directory.

Created an attachment (id=26333) [edit]
Diff to fix Tinker ebuild to use the Java3D now in Portage

Now depends upon dev-java/blackdown-java3d.

I think the version of Java3d in Portage works ok now.  With the path fixes and
the portage Java3D, the Force Field Explorer GUI runs pretty well, being much
less prone to random crashes.

I think all things being equal, this is about as stable as this package is
going to be short of actual updates on the part of the program itself.  I'll
make an updated ebuild for this app to use ICC/IFC during compilation, and
upload a full ebuild.  Other than that, though, I think this one is about as
good as it's gonna get. 

For the ICC/IFC stuff, make sure it doesn't use USE flags. It should just
respect the environment variables $CC and $FC.

Please turn all the spaces indenting the various parts into tabs. I'd like to
take a look at this.

WebMO 5.0, just released, added support for >=tinker-4.2. Since I'm a huge fan
of WebMO, I've suddenly become more interested in making something happen with
this.

I emailed the upstream author and requested a friendlier distribution style,
with a versioned tarball.

By the way, 4.2's distribution method really sucks, the way it looks. There's
crap all over the place, and most of it isn't even in the (unversioned)
tarball.

That's an understatement.  I did spend some time messing with it, but was
unable to figure out how to manually dig out all of the necessary files out of
the distribution - I was able to update the tinker executables themselves to
the 4.2 rev, but the ffe GUI is still a nightmare.

Since I have no experience with JBuilder or building java apps period, I'm not
sure how to proceed on this.  In theory, I would suggest we go with grabbing
the tinker source executable from:

ftp://dasher.wustl.edu/pub/tinker.tar.gz

And the FFE source from:
http://dasher.wustl.edu/ffe/ffe-source.jar

And compiling ffe from the source.

It's really a shame that the distribution method is so bad - as I'm forced to
use the Windows version now.  Sadly, the 4.2 rev, when installed, works VERY
well.  I still use it via CLI on a linux box to do long-term calculations, but
for simple stuff I use the Windows one, since that is the only thing which
plays nice for the time being.

I just got an email from Jay Ponder that basically said, (summary) "We won't
make it easier to start using because it's difficult to use properly once it
does work."

We'd probably be better off just creating a custom tarball with whatever we
need in it, in addition to the tinker.tar.gz.

I've just added tinker-4.2 to the tree, but I can't get FFE working. I'd really
appreciate if you could take a look at that.