Oops, meant to reply to the list.
That indeed was the problem. Building a list of atoms to remove and
then removing then in a separate loop worked like a charm.
Thanks,
Greg
On Wed, May 16, 2012 at 7:16 AM, Noel O'Boyle wrote:
>
>> Any thoughts on why pybel.formula is not updating when I use
> Any thoughts on why pybel.formula is not updating when I use the
> underlying OBMol.DeleteAtom?
>
This is a FAQ. Don't delete atoms from whether a loop using an Open Babel
iterator as it invalidates the iterator. Instead, just create a list of
OBAtoms, and in a separate loop delete each OBAtom i
Comments inline below.
On Mon, May 14, 2012 at 11:46 PM, My Th wrote:
> You could try to align the molecules and then get the coordinates which
> are close enough. Or if the bond perception works correctly and there
> are only those Cl bonded to Rh which have to go away, then you could
> iterate
Noel,
Thanks for the input. Regarding the floating point problems, that's
what I assumed, but I didn't know what to use for a safe delta. Is
this a decent approach otherwise?
The alternate method sounds great. I'll do a little research and see
if that will work for us. Thanks for the pointer.
The coordinates should not change on copying the molecule (I just tested
this).
However, I'm guessing that you are comparing two floating point numbers
using "if x==y". If you search around the web, you will see that you should
this doesn't work for a variety of reasons. Instead, you should compar
Sv, 2012-05-13 20:49 -0700, inviso rakstīja:
> As a disclaimer, I'm an amazingly poor excuse for a chemist. In this
> case, I'm simply a programming resource in a research project so
> please forgive any amateur mistakes or abuses of terminology. The
> project is being done in Python using pybel.
As a disclaimer, I'm an amazingly poor excuse for a chemist. In this
case, I'm simply a programming resource in a research project so
please forgive any amateur mistakes or abuses of terminology. The
project is being done in Python using pybel.
As part of our process, we will be doing a scf calc
