I definitely agree. Perhaps a modification of the -m option, e.g. "-m
50" would be chunks of 50 molecules, and "-m 50p" would be 50 parts.
In this way, "-m" on its own would be equivalent to "-m 1". The only
problem would be if someone wrote "-m 2" by accident, instead of "-m
2p".
- Noel
On 4 Jun
Very helpful - thanks.
I think incorporating this functionality in future OpenBabel releases
would be very useful...
Found a number of posts online of people (e.g.
http://blueobelisk.shapado.com/questions/how-to-split-large-sdf-files-into-series-of-smaller-files)
of people wanting to do this...
Hi Geoff,
Thanks for the reply. Looks like I'm using a slightly older version
(obtained via the Ubuntu 10.10 repositories).
babel -v
No output file or format spec!
Open Babel 2.2.3 -- Mar 7 2010 -- 03:47:42
Usage: babel [-i] [-o]
Try -H option for more information.
I downloaded the 2.3.0 ve
Get the neighbouring atom (obatom_b) of obatom_a, and then use the
information on the two atoms to get the associated OBBond with:
my_obbond = my_obmol.GetBond(obatom_a, obatom_b).
See the API for OBMol at
http://openbabel.org/api/2.3/classOpenBabel_1_1OBMol.shtml.
- Noel
On 4 June 2011 09:34
Hi,
I would like to be able to associate an atom with its bond type to
a neighbouring atom using Pybel. I've found out how to identify the
neighbouring atoms (breadth-first) and can see how to get bond info too. What
I cannot see is a strategy for is matching the right neighbour atom with the
