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 <chicago...@gmail.com
<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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