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> wrote:
> Ahhh, that makes sense. Thank you for the clarification!
>
> Get Outlook for iOS <https://aka.ms/o0ukef>
> ------------------------------
> *From:* Geoffrey Hutchison <geoff.hutchi...@gmail.com>
> *Sent:* Wednesday, June 6, 2018 5:55:40 PM
> *To:* John Michael Bruning
> *Cc:* 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 <geo...@pitt.edu>
> twitter: @ghutchis
> web: https://hutchison.chem.pitt.edu/
>
>
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