Smarts

KNIME Analytics Platform
1

Hi all,

Has anyone managed to get a simple method (node) for pattern matching… I have list of smarts that would like to search my library of molecules with. I’m also keen on finding out if any one ever got the chance to implement a similarity (tanimoto) node for calculating self similarity within a set of compounds…if not how easy (diffucult) would it be to write a node for this.

Thanks Knime users

Chido

PS: Still cannot find where users can contribute and download nodes…

2

We have a SMARTS node on our list since a long time. However, we depend on CDK for almost all chemistry related functionality, and the SMARTS matching code is only available in version 1.2 which, for various reason, we were not able to integrate into KNIME so far. But in principle, writing such a node is fairly straight-forward.

3

Thanks Thor
I will download 1.2 and see how it works… Any advise with the tanimoto (could be any sim measure here) similarity calculator?
regards
Chido

4

With KNIME 2.1 we will also release a plugin containing various node for handling distance matrices. The Distance Matrix Calculator node can compute Tanimoto distances on bit strings (among others). So all you need is a node that creates binary fingerprints for your molecules (there is one in the CDK plugin). For other types of molecular distances you need to write your own node.

5

Thanks again Thor
I have my own binary FP calculator (…encoding interations as well as 2D structural info…) when is this plugin going to be released? LOL (I’m an impatient man)

regards

Chido

6

The plan is in about 2 weeks, but no guarantees on that.

7

Thanks for the the heads up… I will certainly be looking forward to it… I’m still wondering if there is a repository where users can upload/download user contributed nodes…??

Chido