[ghemical-devel] Frozen Atoms

[Donald Ephraim Curtis]

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Hello List,

So, I'm looking at adding freezing of atoms (position specifically) and
I've added some beta support (got a few things i want to update before
posting the patch).

but here are some issues / questions:

It's not a huge deal, but frozen atoms only matter per engine, so if the
engine doesn't have support for frozen atoms, then the UI elements will
still be there.  EG: menus don't get regenerated when a user changes an
engine.  (Version 3 is a UI re-write yes?)

How many calculations really would have to be concerned with frozen
atoms?  It appears as most engines would use this strictly for changing
their "change in geometry" (d1?) which is the whole point.  so that when
you geometrically optimize your frozen atoms don't move.  So far i just
test  for the frozen property before the d1 array gets updated in
ComputeBT1, ComputeBT2, ComputeBT3 and ComputeNBT1.  (These are the same
changes I made in Ghemical-GMS before)  As of now I'm only playing with
tripos engine and it works pretty good, the changes shouldn't be too
hard for the rest of the MM engines.

To be honest, i don't have enough Chemistry knowledge to really figure
out what calculation is where, and all my resources for chemistry
knowledge don't have the CS background to decypher the C.

Here is a "coding standards" question.  If i'm coding in a boolean field
would you prefer that it be type 'bool' or 'int'?  I chose 'int' on the
basis it's C and more compatible with the GTK stuff *shrug*.

Thanks,
- -Donald

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