I wish I could use Avogadro from the terminal, either Windows or Linux. I don’t
need GUI and actually need to use Avogadro as a file translator for 100K files
(approximately), avogadro reads my file properly and is able to save it as
smiles (as the test has shown), but I need somewhat like:
for file in folder…
I can write Python scripts as well, but I just don’t get it from the
instructions: a) how to start python console in Avogadro b) How to open file
and save it?
If it is a Python script I would do somewhat like:
import os
folderInp = “blablabla1”
folderOutp = “blablabla2”
for fileMol2 in os.listdir(folderInp):
file = Avogadro.open(folderInp + fileMol2)
newPath = folderOutp + fileMol2.split(‘.mol2’)[0] + ‘.smi'
fileSave = Avogadro.save(“.smi”, file, newPath)
But I don’t know how to do that in Avogadro/with Avogadro?
Here is what I have ion settings:
And here’s what I have in the toolbox:
So there’s no Python Console. O_O
Thank you,
Regards,
Ana------------------------------------------------------------------------------
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