Re: [Rdkit-discuss] generating scaffold trees

2017-03-31 Thread Axel Pahl 

Hi Markus,

to my knowledge, there is no implementation in RDKit available yet.

Kind regards,
Axel

On 31.03.2017 16:55, Markus Metz wrote:

Dear Axel and all:

I have come across an older discussion about Ansgar Schuffenhauer's 
work on scaffolds:

--

Axel Pahl 
 
Fri, 22 May 2015 04:39:33 -0700 



Dear RDKitters,

has someone used the RDKit to generate scaffold trees from molecules as
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58
I know that this is possible with ScaffoldHunter and that there is a
Pipeline Pilot component for it, but being able to do it in RDKit would
fit especially well in my workflow...

Kind regards and have a nice weekend,
Axel
--
Has there been any update regarding this matter?
Thank you very much and cheers,
Markus


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot


___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss


--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] generating scaffold trees

2017-03-31 Thread Markus Metz 
Dear Axel and all:

I have come across an older discussion about Ansgar Schuffenhauer's work on
scaffolds:
--

Axel Pahl 

Fri, 22 May 2015 04:39:33 -0700


Dear RDKitters,

has someone used the RDKit to generate scaffold trees from molecules as
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58

I know that this is possible with ScaffoldHunter and that there is a
Pipeline Pilot component for it, but being able to do it in RDKit would
fit especially well in my workflow...

Kind regards and have a nice weekend,
Axel


--

Has there been any update regarding this matter?

Thank you very much and cheers,
Markus
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] generating scaffold trees

2015-09-02 Thread Axel Pahl 
Hi Nick,

are there any news on this?
It would still be very interesting.

Kind regards,
Axel
(and a great UGM to all attendees!)

On 22.05.2015 17:31, Nicholas Firth wrote:
> We have an as yet unpublished method which is similar (but performs better) 
> implemented in RDKit. However we use MOE for the scaffold tree. It would be 
> quite easy to implement in RDKit , but I have a thesis to write!
>
> My suggestion would be to ask Nathan to write up the paper and then give you 
> guys the code.
>
> Best,
> Nick
>
> Nicholas C. Firth | PhD Student | Cancer Therapeutics
> The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | 
> Surrey | SM2 5NG
> T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter 
> @ICRnews
>
> 
> From: George Papadatos [gpapada...@gmail.com]
> Sent: 22 May 2015 16:27
> To: Axel Pahl
> Cc: RDKit Discuss
> Subject: Re: [Rdkit-discuss] generating scaffold trees
>
> Hi all,
>
> Coincidentally, we had a chat about this with James the other day.
> Maybe the good colleagues at the ICR have implemented this already with 
> RDKit? Nick?
>
> Cheers,
>
> g
>
>
> On 22 May 2015 at 13:38, Axel Pahl <axelp...@gmx.de<mailto:axelp...@gmx.de>> 
> wrote:
> Dear RDKitters,
>
> has someone used the RDKit to generate scaffold trees from molecules as
> described in this paper:
> Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
> Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58
>
> I know that this is possible with ScaffoldHunter and that there is a
> Pipeline Pilot component for it, but being able to do it in RDKit would
> fit especially well in my workflow...
>
> Kind regards and have a nice weekend,
> Axel
>
>
> --
> One dashboard for servers and applications across Physical-Virtual-Cloud
> Widest out-of-the-box monitoring support with 50+ applications
> Performance metrics, stats and reports that give you Actionable Insights
> Deep dive visibility with transaction tracing using APM Insight.
> http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
> ___
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net>
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
> Limited by Guarantee, Registered in England under Company No. 534147 with its 
> Registered Office at 123 Old Brompton Road, London SW7 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If 
> the message is received by anyone other than the addressee, please return the 
> message to the sender by replying to it and then delete the message from your 
> computer and network.
>


--
Monitor Your Dynamic Infrastructure at Any Scale With Datadog!
Get real-time metrics from all of your servers, apps and tools
in one place.
SourceForge users - Click here to start your Free Trial of Datadog now!
http://pubads.g.doubleclick.net/gampad/clk?id=241902991=/4140
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] generating scaffold trees

2015-05-23 Thread Axel Pahl 
That would be awesome.
Kind regards,
Axel

On 22.05.2015 17:31, Nicholas Firth wrote:
 We have an as yet unpublished method which is similar (but performs better) 
 implemented in RDKit. However we use MOE for the scaffold tree. It would be 
 quite easy to implement in RDKit , but I have a thesis to write!

 My suggestion would be to ask Nathan to write up the paper and then give you 
 guys the code.

 Best,
 Nick

 Nicholas C. Firth | PhD Student | Cancer Therapeutics
 The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | 
 Surrey | SM2 5NG
 T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter 
 @ICRnews

 
 From: George Papadatos [gpapada...@gmail.com]
 Sent: 22 May 2015 16:27
 To: Axel Pahl
 Cc: RDKit Discuss
 Subject: Re: [Rdkit-discuss] generating scaffold trees

 Hi all,

 Coincidentally, we had a chat about this with James the other day.
 Maybe the good colleagues at the ICR have implemented this already with 
 RDKit? Nick?

 Cheers,

 g


 On 22 May 2015 at 13:38, Axel Pahl axelp...@gmx.demailto:axelp...@gmx.de 
 wrote:
 Dear RDKitters,

 has someone used the RDKit to generate scaffold trees from molecules as
 described in this paper:
 Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
 Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58

 I know that this is possible with ScaffoldHunter and that there is a
 Pipeline Pilot component for it, but being able to do it in RDKit would
 fit especially well in my workflow...

 Kind regards and have a nice weekend,
 Axel


 --
 One dashboard for servers and applications across Physical-Virtual-Cloud
 Widest out-of-the-box monitoring support with 50+ applications
 Performance metrics, stats and reports that give you Actionable Insights
 Deep dive visibility with transaction tracing using APM Insight.
 http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.netmailto:Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

 The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
 Limited by Guarantee, Registered in England under Company No. 534147 with its 
 Registered Office at 123 Old Brompton Road, London SW7 3RP.

 This e-mail message is confidential and for use by the addressee only.  If 
 the message is received by anyone other than the addressee, please return the 
 message to the sender by replying to it and then delete the message from your 
 computer and network.



--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

[Rdkit-discuss] generating scaffold trees

2015-05-22 Thread Axel Pahl 
Dear RDKitters,

has someone used the RDKit to generate scaffold trees from molecules as 
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A., 
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58

I know that this is possible with ScaffoldHunter and that there is a 
Pipeline Pilot component for it, but being able to do it in RDKit would 
fit especially well in my workflow...

Kind regards and have a nice weekend,
Axel


--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] generating scaffold trees

2015-05-22 Thread George Papadatos 
Hi all,

Coincidentally, we had a chat about this with James the other day.
Maybe the good colleagues at the ICR have implemented this already with
RDKit? Nick?

Cheers,

g


On 22 May 2015 at 13:38, Axel Pahl axelp...@gmx.de wrote:

 Dear RDKitters,

 has someone used the RDKit to generate scaffold trees from molecules as
 described in this paper:
 Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
 Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58

 I know that this is possible with ScaffoldHunter and that there is a
 Pipeline Pilot component for it, but being able to do it in RDKit would
 fit especially well in my workflow...

 Kind regards and have a nice weekend,
 Axel



 --
 One dashboard for servers and applications across Physical-Virtual-Cloud
 Widest out-of-the-box monitoring support with 50+ applications
 Performance metrics, stats and reports that give you Actionable Insights
 Deep dive visibility with transaction tracing using APM Insight.
 http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
 ___
 Rdkit-discuss mailing list
 Rdkit-discuss@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

Re: [Rdkit-discuss] generating scaffold trees

2015-05-22 Thread Nicholas Firth 
We have an as yet unpublished method which is similar (but performs better) 
implemented in RDKit. However we use MOE for the scaffold tree. It would be 
quite easy to implement in RDKit , but I have a thesis to write! 

My suggestion would be to ask Nathan to write up the paper and then give you 
guys the code. 

Best,
Nick

Nicholas C. Firth | PhD Student | Cancer Therapeutics
The Institute of Cancer Research | 15 Cotswold Road | Belmont | Sutton | Surrey 
| SM2 5NG
T 020 8722 4033 | E nicholas.fi...@icr.ac.uk | W www.icr.ac.uk | Twitter 
@ICRnews


From: George Papadatos [gpapada...@gmail.com]
Sent: 22 May 2015 16:27
To: Axel Pahl
Cc: RDKit Discuss
Subject: Re: [Rdkit-discuss] generating scaffold trees

Hi all,

Coincidentally, we had a chat about this with James the other day.
Maybe the good colleagues at the ICR have implemented this already with RDKit? 
Nick?

Cheers,

g


On 22 May 2015 at 13:38, Axel Pahl axelp...@gmx.demailto:axelp...@gmx.de 
wrote:
Dear RDKitters,

has someone used the RDKit to generate scaffold trees from molecules as
described in this paper:
Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A.,
Waldmann, H., J. Chem. Inf. Model. 2007, 47, 47-58

I know that this is possible with ScaffoldHunter and that there is a
Pipeline Pilot component for it, but being able to do it in RDKit would
fit especially well in my workflow...

Kind regards and have a nice weekend,
Axel


--
One dashboard for servers and applications across Physical-Virtual-Cloud
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.netmailto:Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.

--
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss