>AFAIK OB checks all
>fingerprints in a list one by one so there is much room for
>improvement.
That is a killer for OpenCL on the GPU, because there is a considerable penalty
for moving memory between Host and Device (GPU). Generally, you want to move
large blocks of memory and do as much as po
That's great, many thanks for the help. One other thing, I mentioned pybel
because I haven't got the OBMol conversion from input smiles string to
output file with 3D coordinates. Would you mind giving a quick example of
this (or directing me to online documentation, I couldn't find much here)?
Wha
Hello,
You should use:
ff.GetCoordinates(mol)
Where ff is your OBForceField class and mol is OBMol.
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2012/7/13 scott_m
> That's great, many thanks for the help. One other thing, I mentioned pybel
> because I haven't g
I have what may be a simple question. I'm taking the 2D molfile for Naproxen:
[cid:image001.png@01CD5F96.2CB3DAD0]
When I convert this to a 3D molfile with "add explicit H" checked in the
OpenBabel GUI or I try the same in code the OH seems to become O- (O with a
negative charge).
Even
Thanks for the reply but that doesn't seem to be working for me (code below).
If I just want to get a rough set of coordinates, what should I do? I see
that gen3d (see link below) does a weighted rotor search as part of the
process of making 3d coords but I wanted to just get the 3d coords and
spec
On 13/07/2012 14:46, scott_m wrote:
> Thanks for the reply but that doesn't seem to be working for me (code below).
> If I just want to get a rough set of coordinates, what should I do? I see
> that gen3d (see link below) does a weighted rotor search as part of the
> process of making 3d coords but
Thanks Chris, do you have a link for that?
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On 11/07/2012 18:51, James Jack wrote:
>
> When I convert this to a 3D molfile with "add explicit H" checked in the
> OpenBabel GUI or I try the same in code the OH seems to become O- (O
> with a negative charge).
>
In the GUI you need to check "Add hydrogens (make explicit)" but have
the editbox
