Awesome, thanks. I'll give It a shot
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________________________________
From: Noel O'Boyle <baoille...@gmail.com>
Sent: Wednesday, June 6, 2018 11:38:45 PM
To: John Michael Bruning
Cc: Geoffrey Hutchison; openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] obfit question
Just to add, if you wish to align two depictions it's possible via the obabel
executable:
$ obabel tmp.smi -s "[#6]Cl blue" -O tmp.svg --align "[#6]Cl"
Unfortunately, the align operation does not appear to work if not outputting to
an image:
$ obabel tmp.smi -O tmp.sdf --align "[#6]Cl"
==============================
*** Open Babel Error in OpenBabel::OBAlign::Align
Cannot align the reference and target as they are of different size
1 molecule converted
...so you would have to do this programmatically via the API.
- Noel
On 7 June 2018 at 01:57, John Michael Bruning
<brun...@stanford.edu<mailto:brun...@stanford.edu>> wrote:
Ahhh, that makes sense. Thank you for the clarification!
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________________________________
From: Geoffrey Hutchison
<geoff.hutchi...@gmail.com<mailto:geoff.hutchi...@gmail.com>>
Sent: Wednesday, June 6, 2018 5:55:40 PM
To: John Michael Bruning
Cc:
openbabel-discuss@lists.sourceforge.net<mailto:openbabel-discuss@lists.sourceforge.net>
Subject: Re: [Open Babel] obfit question
Am I incorrectly running obfit, or am I misinterpreting what obfit does? Thanks
for any help!
You're mis-interpreting what obfit does. It operates in 3D coordinates. So what
you're doing is okay - but if you then generate a PNG, you've thrown away the
3D coordinates.
If you want to see if obfit is operating correctly, open the resulting file in
PyMol or Avogadro or some similar 3D viewer.
If you want to highlight a SMARTS pattern in a depiction, you want something
different:
http://open-babel.readthedocs.io/en/latest/Command-line_tools/Rosetta.html#align-the-depiction-using-a-fixed-substructure
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu<mailto:geo...@pitt.edu>
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/
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