Is there a way to use the RDKIT nodes to attach attachement/R sites on molecules? This functionality of adding R and A arises frequently if one were to construct combinatorial libraries.
For a fragment database containing several thousand data, it is simply not possible to do it by hand.
Software that generate combilibs however do require SMILES strings with A and R defined.
It's actually somewhat straightforward with the RDKit to do this.
Suppose I want to attach a marker to an oxadiazole ring. I would use a one-component reaction node and the following reaction:
[$(c1ncno1):1]>>[1*][c:1]
This attaches a dummy atom with isotopic-label 1 to one of the carbons.
The corresponding SMILES generated for oxadiazole itself (generated from either the RDKit canonical smiles or RDKit -> molecule nodes with the output format set to SMILES) is: [1*]c1oncn1
The SDF output (from the RDKit->molecule node with the output format set to SDF) is:
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
2.7760 0.0000 0.0000 R 1 0 0 0 0 0 0 0 0 0 0 0
1.2760 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3943 1.2135 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3943 -1.2135 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.0323 0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.0323 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
3 2 1 0
2 4 2 0
5 3 1 0
4 6 1 0
6 5 2 0
M END
$$$$
This should probably get you close to what you need. If you need to attach multiple R groups, you'll need to use multiple reactions (each defining a particularly attachement point) and if you want R1/A1 labels in the SMILES (definitely not part of the SMILES spec), you can use the knime String Replacer node to replace the [1*], [2*], etc. labels with [R1], [R2], etc.
hope this helps,
-greg
thanks. Not very familiar with the reaction node and syntax but time to learn!
cheers
This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.