seems that files converted from the cdx or cdxml have wrong bond lenght (I've
the feeling that is related to the document properties in chemoffice);
benzene bond lenght --> 70Angstrom
anyone has already find a solution? I'm thinking to something like a
"feed2babel" style, or something similar.
tha
Yes, this is a serious problem in Chemdraw. I found that using
OpenBabel to convert to 3D then back to 2D adjusted the bonds to the
correct dimensions.
Quoting cadeddu on Tue, 6 Mar 2012 03:06:02 -0800 (PST):
> seems that files converted from the cdx or cdxml have wrong bond lenght (I've
>
can you specify which 3D format? I've tested this series
babel -h -i cdxml benzeneACS.cdxml -o c3d1 benzeneACSvi.c3d
babel -h -i c3d1 benzeneACSvi.c3d -o pdb benzeneACSviac3d.pdb
and I still have 14.9 angstrom for a benzene double bond.
Did someone has already produced a stylefile (.chm?), and w
Hi,
I used the --gen3D option, so something like
babel -isdf chemdraw.sdf -osdf chemdraw3d.sdf --gen3D
babel -isdf chemdraw3D.sdf -osdf chemdraw.sdf --gen2D
cheers,
Doug
Quoting cadeddu on Tue, 06 Mar 2012 13:39:28 +0100:
> can you specify which 3D format? I've tested this series
>
> babel
Hello,
this sounds great. But i NEED Open Babel. This is not my decision.
Any other ideas why this not work?
With best
Jochen Schreiber
On Mar 5, 2012, at 3:22 AM, Jochen Schreiber wrote:
> i have download the chembl_sdf archive and unpack it.
>
> The resulting sd file from that archive has
Hi Jochen,
On Mar 6, 2012, at 10:45 AM, Jochen Schreiber wrote:
> this sounds great. But i NEED Open Babel. This is not my decision.
What does it mean to "NEED Open Babel"?
Chemfp's 'ob2fps' command-line tool uses the Open Babel Python API
for the fingerprint generation.
Hi all,
after getting "OpenBabel" running for the first time (generation of exact
masses from smiles and sdf) I wonder if there is any chance to convert
smiles to a picture. Why this? I want to add the smiles into a SQLExpress
database and it would be fine to get the structure as a picture when
I can confirm that Doug's solution works.
the series:
babel -icdxml benzene.cdxml -osdf benzene3d.sdf --gen3D
babel -isdf benzene3d.sdf -opdb benzeneViaSdfgen.pdb --gen2D
works fine.
thank you!
ps: maybe we should add this /escamotage/ to the wiki?
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