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
Thanks Chris, do you have a link for that?
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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 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
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
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
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
>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
