Hi there Ana,
If you just need a file translator, you might want to consider using Open
Babel directly: http://openbabel.org/wiki/Main_Page
Avogadro uses Open Babel for a lot of its file translations. After you
compile/install open Babel and get the executables, you just need to run
something like:
obabel -icml -osmi -OoutputFilename
Whatever after -i is the input file type. After -o is output file type, and
I believe after -O is output file name.
https://openbabel.org/docs/dev/Command-line_tools/babel.html
You would be able to write a python script and use subprocess to run this
command multiple times.
Patrick
On Tuesday, June 28, 2016, Anastasya Karchevskaya <alsal...@me.com> wrote:
>
> 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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