To conclude:
this small workaround works - but great care must be taken into
checking the structures:
--
import pybel, openbabel
mol=pybel.readfile("cdx", "benzene_acs.cdx").next()
factor=1.39/1.89 # this is the error of the bond length: real
valu
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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>
>
> 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
>> the feeling that is related to the document properties in chemoffice);
>> benzene bond lenght --> 70Angstrom
&g
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
