Yes, but I don't see how that helps work out how to call it from Python.
I was trying something like this:
obConversion.AddOption("p", obConversion.GENOPTIONS, "3.0")
That seems vaguely consistent with how to set the option from Python
given how the CLI option works, but unfortunately it doesn't seem to work.
Tim
On 15/04/2019 13:03, Noel O'Boyle wrote:
Hi Tim,
Many of these options are just wrappers around API functions, so it's
worthwhile taking a look at the API documentation. In this case,
here's the link to the relevant docs:
http://openbabel.org/api/2.3/classOpenBabel_1_1OBPhModel.shtml
Regards,
- Noel
On Thu, 11 Apr 2019 at 16:11, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Another Python options question.
I can use the protonation option on the CLI:
> echo "C1=C(NC=N1)C[C@@H](C(=O)O)N" | obabel -i smi -o mol -p 3
But I can't figure it out with the Python API:
> import openbabel
>
> obConversion = openbabel.OBConversion()
> obConversion.SetInAndOutFormats("smi", "mol")
> mol = openbabel.OBMol()
> obConversion.AddOption("p", obConversion.GENOPTIONS, "3.0")
> obConversion.ReadString(mol, "C1=C(NC=N1)C[C@@H](C(=O)O)N")
> output = obConversion.WriteString(mol)
> print output
Output is generated but it's not protonated. Same if using OUTOPTIONS
instead of GENOPTIONS.
Is the use of the options in Python documented anywhere?
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