Hi Noel,
thanks a lot...
I am still working with OB 2.2.3 and I think it is not implemented in this
version. I will try to migrate to the last version.
Thank you to everyone
David
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Thanks Geoff...
but I still have problem...I tried in svg and png and I have this message:
==
*** Open Babel Warning in PNG Format
Embedding in InChI format.
Use the -xO (uppercase O) option for a different format
==
*** Open Babel Warning
We added --highlight to provide this functionality. This is an
operation, and is used as follows:
import pybel
mol = pybel.readstring(smi, CC(=O)Cl)
highlighter = pybel._operations[highlight]
highlighter.Do(mol.OBMol, C(=O) green)
mol.write(svg, tmp.svg, opt={u:None, C:None}, overwrite=True)
Dear all,
By reading Noel O'Boyle's blog, and his post Portrait of the molecule
as a green substructure
(http://baoilleach.blogspot.fr/2012/02/portrait-of-molecule-as-green.html),
I understood that it is possible to depict a molecule in svg with obabel
and highlight some substructures in
But, is it possible with pybel?
Of course. You can set output flags when writing molecules with Pybel.
molecule.write(svg, test.svg, False, opt)
opt -- a dictionary of format-specific options
For format options with no parameters, specify the
value as None.
