Patch to Openbabel Stable Release 2.1.1 tarball

It has an added flag to OBAtom OBFixed which means that the atom
will remaini fixed
during OBForceField operations.

This particular part of the patch isn’t something I can add in 2.1.1
– it changes the API, which is only something we do between
releases. So it can certainly go into the 2.2 code, but not 2.1.x.
I’d also prefer OB_ATOM_FIXED, since we may want to fix bonds or
other things in the future.

I’d also like to fix up a few things with the way conjugate gradients
are handled right now by the force field, and that will require the
2.2 release as well. Hopefully we can reach a point of releasing it
relatively soon.

It also includes some checks for nan values in the torsion energy
calculations as
it was causing some molecules with loops to “explode” after a
period of stability.

That is most definitely, appreciated. I found that bug recently and
it’s filed for both Avogadro and Open Babel right now.

That part of the patch I’ll apply in a few minutes. It’ll go into the
2.1.2 release.

Cheers,
-Geoff

Le jeudi 04 octobre 2007 à 20:46 -0400, Geoffrey Hutchison a écrit :

I’d also like to fix up a few things with the way conjugate gradients
are handled right now by the force field, and that will require the
2.2 release as well. Hopefully we can reach a point of releasing it
relatively soon.

Geoff, what do you mean by relatively soon? I’d like to add some
enhancements in the cdx* formats (especially related to reactions) for
that release. If it is a matter of a few days or weeks, I’ll probably
short, if it’s months, it should be ready.

Cheers,
Jean