> Q: The weighted rotor conformer gives only one conformer (lowest energy)?
> What happens when you specify the num of conformers to say 50 ?
At the moment, the weighted search runs a stochastic search for the lowest
energy across some number of test conformers. So specifying 50 conformers mean
> Furthermore, why do I get no co-ordinates?
I started from a 3D molecule. So you'll want to add a --gen3d to your
command-line. (I'd feel a bit better if it was in 2 steps: generate
coordinates, then conformer search, but it looks OK on one command-line.)
Hope that helps,
-Geoff
Furthermore, why do I get no co-ordinates?
obabel ligand.babel.smi -O ligand.babel.sdf --conformer --nconf 20
--weighted
Using OpenBabel 2.3.1
==
*** Open Babel Warning in WriteMolecule
No 2D or 3D coordinates exist. Any stereochemical information will be
lost. To
Or more succintly, with obabel 2.3.1 I have:
C:\Users\Noel>obabel -:[Al]C#N -oinchi -xK -xX Recmet
==
*** Open Babel Warning in InChI code
#1 :Metal was disconnected
♥
1 molecule converted
...which is rather sweet, but probably not the desired outcome. :-)
Do you h
Folks
I'm trying to use Openbabel to generate a non-standard InChIKey for a few of my
metal cyanides and isocyanides (because configurations produce the same
Standard InChIKey).
Below is my code. Execution of the code leaving the comments intact yields the
Standard InChI and Standard InChIKey
yes Geoff, this does help *a lot* - especially considering the call from
the command line.
One more question and a suggestion please.
Q: The weighted rotor conformer gives only one conformer (lowest energy)?
What happens when you specify the num of conformers to say 50 ?
S: Also a suggestion oba
On Dec 9, 2011, at 12:12 PM, Geoffrey Hutchison wrote:
> As of yet, no. That could be done new scoring function (e.g., minenergy)
> which determines the energy after some minimization. It's a good idea.
OK, that seemed like an easy task, so SVN trunk now has "min" as a score option
with 250 st
Thank you Geoff,
but the problem is still there.
provide copies of the commands, list of generated files, and an output
file below.
What I unfortunately see -- the output contains one molecule.
The connectivity is established as needed, but fragments are not
separated in different records.
I want
> Specifically, I was wondering if there is an example of how to use
> OBConformerSearch from Python (and is there a way how to use this directly
> from the command line?).
Sorry the documentation isn't online -- we should definitely fix that. It's
easy to use from the command-line:
obabel -L
Hi there
I would like to generate a fixed number of conformers for particular
molecules.
I have read through http://openbabel.org/dev-api/group__conformer.shtml -
is there more documentation about this?
(There is nothing in the excellent bible -
http://openbabel.org/docs/current/)
Specifically,
Very cool! :-) I'd be for having this in Open Babel. In fact, I think
you should also consider it as an output format. In Cinfony, I use the
CIR to return 1 or multiple names for a compound (could be controlled
by an output option), or the IUPAC name.
Regarding the specifics, I'm just wondering wh
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