Re: [Rdkit-discuss] chair vs boat detection

2021-03-12 Thread Ling Chan 
Thank you Sunhwan and Geoff, I shall take a look.
Ling


Geoffrey Hutchison  於 2021年3月12日週五 下午1:48寫道：

> Yes, you can detect chair / boat (etc.) using Cremer-Pople parameters
> (particularly the angles).
>
> There is a bunch of related RDKit code from our recent ring-puckering
> paper:
> https://doi.org/10.1021/acs.jcim.0c01144
> https://github.com/lucianlschan/RING
>
> In particular - you want to call GetRingPuckerCoords(coordinates)
> https://github.com/lucianlschan/RING/blob/master/Ring_Analysis.py
>
> Hope that helps,
> -Geoff
>
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geo...@pitt.edu 
> twitter: @ghutchis
> web: https://hutchison.chem.pitt.edu/
>
> On Mar 12, 2021, at 1:10 PM, Paul Emsley 
> wrote:
>
>
> On 12/03/2021 05:11, Ling Chan wrote:
>
>
>
> Just wonder if there is any function to distinguish between a chair ring
> and a boat ring?
>
> Don't worry if there is no such utility. I can write my own geometry
> detection. Just that I don't want to reinvent the wheel.
>
>
> Isn't this Cremer Pople?
>
> http://enzyme13.bt.a.u-tokyo.ac.jp/CP/
>
> https://smb.slac.stanford.edu/facilities/software/ccp4/html/privateer.html
>
>
> Paul.
>
>
>
>
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Re: [Rdkit-discuss] chair vs boat detection

2021-03-12 Thread Geoffrey Hutchison 
Yes, you can detect chair / boat (etc.) using Cremer-Pople parameters 
(particularly the angles).

There is a bunch of related RDKit code from our recent ring-puckering paper:
https://doi.org/10.1021/acs.jcim.0c01144 

https://github.com/lucianlschan/RING

In particular - you want to call GetRingPuckerCoords(coordinates)
https://github.com/lucianlschan/RING/blob/master/Ring_Analysis.py

Hope that helps,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
twitter: @ghutchis
web: https://hutchison.chem.pitt.edu/

> On Mar 12, 2021, at 1:10 PM, Paul Emsley  wrote:
> 
> 
> On 12/03/2021 05:11, Ling Chan wrote:
>> 
>> 
>> Just wonder if there is any function to distinguish between a chair ring and 
>> a boat ring?
>> 
>> Don't worry if there is no such utility. I can write my own geometry 
>> detection. Just that I don't want to reinvent the wheel.
>> 
> 
> Isn't this Cremer Pople?
> 
> http://enzyme13.bt.a.u-tokyo.ac.jp/CP/
> 
> https://smb.slac.stanford.edu/facilities/software/ccp4/html/privateer.html
> 
> 
> Paul.
> 
> 
> 
> 
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Re: [Rdkit-discuss] chair vs boat detection

2021-03-12 Thread Ling Chan 
Thank you for the pointers, Paul.
Ling


Paul Emsley  於 2021年3月12日週五 上午10:12寫道：

>
> On 12/03/2021 05:11, Ling Chan wrote:
> >
> >
> > Just wonder if there is any function to distinguish between a chair
> > ring and a boat ring?
> >
> > Don't worry if there is no such utility. I can write my own geometry
> > detection. Just that I don't want to reinvent the wheel.
> >
>
> Isn't this Cremer Pople?
>
> http://enzyme13.bt.a.u-tokyo.ac.jp/CP/
>
> https://smb.slac.stanford.edu/facilities/software/ccp4/html/privateer.html
>
>
> Paul.
>
>
>
>
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Re: [Rdkit-discuss] chair vs boat detection

2021-03-12 Thread Paul Emsley 



On 12/03/2021 05:11, Ling Chan wrote:



Just wonder if there is any function to distinguish between a chair 
ring and a boat ring?


Don't worry if there is no such utility. I can write my own geometry 
detection. Just that I don't want to reinvent the wheel.




Isn't this Cremer Pople?

http://enzyme13.bt.a.u-tokyo.ac.jp/CP/

https://smb.slac.stanford.edu/facilities/software/ccp4/html/privateer.html


Paul.




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Re: [Rdkit-discuss] chair vs boat detection

2021-03-11 Thread Greg Landrum 
Hi Ling,

The RDKit does not currently have such a function (at least not that I'm
aware of).

-greg


On Fri, Mar 12, 2021 at 6:13 AM Ling Chan  wrote:

> Hello colleagues,
>
> Just wonder if there is any function to distinguish between a chair ring
> and a boat ring?
>
> Don't worry if there is no such utility. I can write my own geometry
> detection. Just that I don't want to reinvent the wheel.
>
> Thank you.
>
> Ling
>
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[Rdkit-discuss] chair vs boat detection

2021-03-11 Thread Ling Chan 
Hello colleagues,

Just wonder if there is any function to distinguish between a chair ring
and a boat ring?

Don't worry if there is no such utility. I can write my own geometry
detection. Just that I don't want to reinvent the wheel.

Thank you.

Ling
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