Re: [Rdkit-discuss] How does rdkit cartridge work?

2020-01-26 Thread Greg Landrum 
On Mon, Jan 27, 2020 at 6:13 AM Thomas Strunz  wrote:

>
> about your comment on custom fingerprints:
>
> "*I'm not sure what you mean by substructures, but you can, from Python,
> use custom fingerprints in the cartridge. That's explained
> here: 
> http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html
> *
> "
>
>
> For me and I suspect this is what Changge actually was asking if one can
> add a custom fingerprint for the substructure search part (the screen-out)
> and not just the similarity search (the blog post linked looks like it is
> only for similarity search). And with "custom substructure" I would assume
> a fully or partial substructure fingerprint.
>

Unfortunately the way the pattern fingerprints are used with the index
makes it impossible to change this without building and installing your own
version of the cartridge. There's now way that I know of to get this setup
so that one can provide the fingerprints externally.

In some cases the Patternfingerprint doesn't have very good screenout rates
> and layeredfingerprint is much better.
>

If/when you come across cases like this, I would be interested to hear
about them so that I can think about improving the pattern fingerprint
(adding new patterns isn't that hard at the C++ level).

Best,
-greg



> (Not really an issue for me just an obeservation).So from that point I can
> see and understand the need for using a custom fingerprint for the
> screenout step.
>
> Best Regards,
>
> Thomas
> --
> *Von:* Greg Landrum 
> *Gesendet:* Samstag, 25. Januar 2020 06:11
> *An:* Chicago Ji 
> *Cc:* rdkit-discuss 
> *Betreff:* Re: [Rdkit-discuss] How does rdkit cartridge work?
>
> Hi Changge,
>
> On Fri, Jan 24, 2020 at 5:14 PM Chicago Ji  wrote:
>
>
> I find that rdkit cartridge is quite efficient in substructure searching.
>
>
> Glad to hear that! :-)
>
>
> Is there any paper or similar paper that describes things behind rdkit
> cartridge?
>
>
> No, just the documentation.
>
>
> For example, what kind of substructures were indexed?
>
>
> The Pattern fingerprint is what's used to build the index for substructure
> searching. That fingerprint is described in the RDKit documentation here:
> https://www.rdkit.org/docs/RDKit_Book.html#pattern-fingerprints
>
>
> Is there a way that the users can add custom defined fingerprints and
> substructures?
>
>
> I'm not sure what you mean by substructures, but you can, from Python, use
> custom fingerprints in the cartridge. That's explained here:
> http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html
>
> Best,
> -greg
>
>
>
> Many thanks for your help!
>
> Best,
> Changge
>
>
>
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Re: [Rdkit-discuss] How does rdkit cartridge work?

2020-01-26 Thread Thomas Strunz 
Hi Greg,

about your comment on custom fingerprints:

"I'm not sure what you mean by substructures, but you can, from Python, use 
custom fingerprints in the cartridge. That's explained here: 
http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html;


For me and I suspect this is what Changge actually was asking if one can add a 
custom fingerprint for the substructure search part (the screen-out) and not 
just the similarity search (the blog post linked looks like it is only for 
similarity search). And with "custom substructure" I would assume a fully or 
partial substructure fingerprint. In some cases the Patternfingerprint doesn't 
have very good screenout rates and layeredfingerprint is much better. (Not 
really an issue for me just an obeservation).So from that point I can see and 
understand the need for using a custom fingerprint for the screenout step.

Best Regards,

Thomas

Von: Greg Landrum 
Gesendet: Samstag, 25. Januar 2020 06:11
An: Chicago Ji 
Cc: rdkit-discuss 
Betreff: Re: [Rdkit-discuss] How does rdkit cartridge work?

Hi Changge,

On Fri, Jan 24, 2020 at 5:14 PM Chicago Ji 
mailto:chicago...@gmail.com>> wrote:

I find that rdkit cartridge is quite efficient in substructure searching.

Glad to hear that! :-)

Is there any paper or similar paper that describes things behind rdkit 
cartridge?

No, just the documentation.

For example, what kind of substructures were indexed?

The Pattern fingerprint is what's used to build the index for substructure 
searching. That fingerprint is described in the RDKit documentation here: 
https://www.rdkit.org/docs/RDKit_Book.html#pattern-fingerprints

Is there a way that the users can add custom defined fingerprints and 
substructures?

I'm not sure what you mean by substructures, but you can, from Python, use 
custom fingerprints in the cartridge. That's explained here: 
http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html

Best,
-greg


Many thanks for your help!

Best,
Changge



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Re: [Rdkit-discuss] How does rdkit cartridge work?

2020-01-26 Thread Tim Dudgeon 
Greg is too modest to mention it, but he recently blogged on performance 
aspects of the cartridge which covers many aspects of how it works:

http://rdkit.blogspot.com/2020/01/some-thoughts-on-performance-of-rdkit.html

On 25/01/2020 05:11, Greg Landrum wrote:

Hi Changge,

On Fri, Jan 24, 2020 at 5:14 PM Chicago Ji > wrote:



I find that rdkit cartridge is quite efficient in substructure
searching.


Glad to hear that! :-)

Is there any paper or similar paper that describes things behind
rdkit cartridge?


No, just the documentation.

For example, what kind of substructures were indexed?


The Pattern fingerprint is what's used to build the index for 
substructure searching. That fingerprint is described in the RDKit 
documentation here: 
https://www.rdkit.org/docs/RDKit_Book.html#pattern-fingerprints


Is there a way that the users can add custom defined fingerprints
and substructures?


I'm not sure what you mean by substructures, but you can, from Python, 
use custom fingerprints in the cartridge. That's explained here: 
http://rdkit.blogspot.com/2017/04/using-custom-fingerprint-in-postgresql.html


Best,
-greg

Many thanks for your help!

Best,
Changge


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