> What I can't figure is how such a glaring error has never been noticed.
> Surely I'm not the first guy to use OpenBabel on an atom with a B=O bond?
It's not an extremely common bond order in valence, and boron is not extremely
common in "default organic chemistry." (And this is speaking from
> But better still, all in favor of replacing this impval business, say "aye".
"Aye." I think Chris brought this up a few weeks ago and I can't recall if I
pushed the issue then. I'd be happy to see "what's new in 2.4" include
"replaced old default valence model." I think this would mesh very we
On Tue, Mar 26, 2013 at 3:02 PM, Noel O'Boyle wrote:
> It might be a good idea to sit down while you read this. You seem to
> have forgotten that Implicit Valence is not implicit valence, but
> rather the number of bonds to an atom.
I'm finally getting this through my head, and based on your ad
It might be a good idea to sit down while you read this. You seem to
have forgotten that Implicit Valence is not implicit valence, but
rather the number of bonds to an atom. atomtyp.txt says 3 bonds to a
boron. The =O and the OH is two bonds, so there's one missing. That's
the reason for the two th
Anyone know what's going on with boron? The atomtyp.txt file looks right
to me. A double bond to oxygen seems to mess it up. I'm no chemist, but
everything I can find says this is just wrong.
$ echo "O=BO" | obabel -i smi -o smi
O=[BH]O
Note the extra H on the boron atom. Here's the same thi
To get things to work in Python, I have to set some dlopen flags as follows:
sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
The following discussion hints at something similar for R:
http://www.mail-archive.com/r-help@r-project.org/msg143108.html.
- Noel
On 25 March 2013 20:30, Kevin
Thanks, but swig did not help.
After some more experimentation, I have discovered I can get it to work
in the following way, but I think it is a bit impractical. If I compile
the shared library as:
g++ -shared -o libobtest2.so obtest2.o -fpic
/usr/lib/openbabel/2.2.3/mdlformat.so -lopenba
On Thu, Mar 14, 2013 at 07:57:23AM -0500, Geoffrey Hutchison wrote:
> > I have previously asked some questions here about bond-order/atom type
> > detection and we are now going through a dataset of ~2000 molecules
> > manually to see whether double bonds generated by OB are in the right
> > pla
