Oh you must be right. I have no knowledge about this.
Just out of curiosity, in topological sense, if a bond order is between 1 and 2
(due to conjugation for example), will it be considered as rotatable?
Best wishes,
James
From: Jens Thomas [mailto:jenstho...@users.sourceforge.net]
Sent: Wednesday, September 17, 2014 3:25 PM
To: avogadro-discuss@lists.sourceforge.net
Subject: Re: [Avogadro-Discuss] How to calculate rotateable bonds?
I think Max meant which bonds are rotatable in a topological sense - i.e. are
not part of a ring and so the two parts of the molecule are free to move.
I think this code lives in openbabel. The following source file might be a good
place to start:
http://sourceforge.net/p/openbabel/code/HEAD/tree/openbabel/trunk/src/rotor.cpp
I've not had a chance to look here myself, but I think the CDK also has code
for ring perception:
http://sourceforge.net/projects/cdk/
Best wishes,
Jens
On 17 September 2014 20:08, James Mao <xjames...@gmail.com> wrote:
Isn’t that you need define “rotatable” first? A rotational barrier below a
limit? Then you need define it is a rigid rotation or relaxed rotation, at what
computational level…
I don’t think this is what Avogadro should consider, but you can do it by
yourself.
James Mao
---------------------------------------
Postdoctoral Research Associate
1207 Chevron Science Center,
Department of Chemistry,
University of Pittsburgh
From: Maxwell Wesley Terban [mailto:mwt2...@columbia.edu]
Sent: Tuesday, September 16, 2014 3:16 AM
To: avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] How to calculate rotateable bonds?
Hi,
I am wondering how Avogadro computes rotateable bonds in a molecule. I want to
write my own code in python to do something similar in which I would input a
molecular structure and then the program would categorize and print out which
bonds in the structure are rotateable.
Thanks,
Max
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191
<http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk>
&iu=/4140/ostg.clktrk
_______________________________________________
Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss
------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Avogadro-Discuss mailing list
Avogadro-Discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-discuss