Hi all,
When I use gen3d with P#P I get a molecule with two hydrogens. Should it not
be the diphosphorus molecule with chemical formula P2? Using [P]#[P]
produces the desired result but I wanted to find out why gen3d does this.
Best wishes,
Scott
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Hi,
Currently I'm working on GOLD docking results, and try to process them
through OB. Unfortunately OB doesn't understand GOLD's explicit lone pair
pseudo atoms (atom type: Lp). For mol2 - mol2 conversion it changes it to
Xx type atoms, for sdf (sdf defines them as * type) - mol2 they are
On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
However even for good geometries OB has problems with bond orders
sometimes as I pointed out the other day. Is there anything that can be
done about that? Changing smiles?
Bond order perception is never going to be bullet-proof,
On 2013-11-08 18:54, Geoffrey Hutchison wrote:
On Nov 8, 2013, at 2:50 AM, David van der Spoel wrote:
However even for good geometries OB has problems with bond orders
sometimes as I pointed out the other day. Is there anything that can be
done about that? Changing smiles?
Bond order
I don't have the exact code to hand, but it's something like the
following in Python:
myop = OBOp.FindType(gen3d)
success = myop.Do(myOBMol)
- Noel
On 7 November 2013 18:13, Wallace Chan walla...@umich.edu wrote:
Dear All,
I am having some frustration trying to generate a 3D SDF file from
Thank you, Noel.
I already copied all the files from the Open Babel GUI installation folder, the
web page can display without error, but the part calling OpenBabel functions
just return zero or empty. However it worked fine under Visual studio
environment. I also tried to change some IIS
