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

Reply via email to