Thanks! I think I can take it from here, but a few more questions, as I
looked at the OBFit source and I am pretty confused on how it works. Isn't
there a superimpose method? What is the benefit to qtrfit? Also how do I
use these in Python? I tried feeding superimpose two obmol objects but it
apparently requires doubles and a size parameter but it's very unclear why
or what these are from the documentation. What I want to do is just take
two molecules and align them on a single fragment, then add a third one on
top of those. I don't know if this is necessarily simple but it definitely
seems doable if I just call OBFit using subprocess, but that seems like a
poor kludge. I just don't want to have to reimplement OBFit in python in my
little script here because that just seems like overkill, I think I am just
missing how to use superimpose and qtrfit really...
Thanks again for your time!
-- Raj
On Wed, Jun 19, 2013 at 8:01 PM, Geoffrey Hutchison <
[email protected]> wrote:
> > 1. Can I superimpose more than two molecules using OBFit? How would this
> be done if it is possible?
>
> I'm not sure what you mean. The obfit program can take one scaffold and
> align many molecules in a multi-molecule file.
>
> I think you're asking if you can put say 3 fragments all on top of each
> other. Yes, but you'd have to do it stepwise -- align two, then add the
> next, etc.
>
> > 2. If not, or even if so, how would I superimpose molecules using the
> OpenBabel base classes and methods, in a program, as opposed to using OBFit
> externally?
>
> The code for obfit is open source. I'd check tools/obfit.cpp:
> https://github.com/openbabel/openbabel/blob/master/tools/obfit.cpp
>
> Hope that helps,
> -Geoff
------------------------------------------------------------------------------
This SF.net email is sponsored by Windows:
Build for Windows Store.
http://p.sf.net/sfu/windows-dev2dev
_______________________________________________
OpenBabel-discuss mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
