# RDKit Chemical Transformation node

**URL:** <https://forum.knime.com/t/rdkit-chemical-transformation-node/90119>\
**Category:** Community Extensions\
**Tags:** rdkit\
**Created:** [October 2, 2025, 11:58pm UTC](https://forum.knime.com/t/rdkit-chemical-transformation-node/90119 "2025-10-02T23:58:31Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![ChemMitch](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/c/7ba0ec/32.png) [@ChemMitch](https://forum.knime.com/u/ChemMitch)\
**Post date:** [October 2, 2025, 11:58pm UTC](https://forum.knime.com/t/rdkit-chemical-transformation-node/90119/1 "2025-10-02T23:58:31Z")

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Is there a way to use the chemical transformation node to serially process one match at a time instead of serially applying the transformation multiple times for the same starting molecule?

For example, consider this SMARTS:

[N;H1;X3:1]\>\>[N;X3:1][N]=O

to turn secondary amines into N-nitrosamines.

One of the input structures is this

CC1=C([C@H](c2ccccc2[N+](=O)[O-])N[C@H](c3ccccc3[N+](=O)[O-])N1)C(=O)OC

Which has 2 matching secondary amines.  
As far as I can tell, the RDKit Chemical Transformation node gives you the option of getting either a single mono-nitrosamine or the dinitrosamine.

**Is there a way to get both mono-nitrosamines?**

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**Author:** ![ScottF](https://forum-cdn.knime.com/user_avatar/forum.knime.com/scottf/32/61316_2.png) [@ScottF](https://forum.knime.com/u/ScottF)\
**Post date:** [October 30, 2025, 3:23pm UTC](https://forum.knime.com/t/rdkit-chemical-transformation-node/90119/2 "2025-10-30T15:23:17Z")

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Pinging @greglandrum here to see if he knows some RDKit chemistry magic 🙂

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<div class="post-metadata">

**Author:** ![ChemMitch](https://forum-cdn.knime.com/letter_avatar_proxy/v4/letter/c/7ba0ec/32.png) [@ChemMitch](https://forum.knime.com/u/ChemMitch)\
**Post date:** [October 30, 2025, 3:44pm UTC](https://forum.knime.com/t/rdkit-chemical-transformation-node/90119/3 "2025-10-30T15:44:18Z")

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In the meantime, I wrote a standalone Python script to perform the transformations.

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**Author:** ![Alice\_Krebs](https://forum-cdn.knime.com/user_avatar/forum.knime.com/alice_krebs/32/43061_2.png) [@Alice\_Krebs](https://forum.knime.com/u/Alice_Krebs)\
**Post date:** [November 6, 2025, 8:33am UTC](https://forum.knime.com/t/rdkit-chemical-transformation-node/90119/4 "2025-11-06T08:33:55Z")

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Hi @ChemMitch

Sorry for the (too) late reply, but for future reference, the **One Component Reaction** node is the one you are looking for 🙂

 ![image](https://forum-cdn.knime.com/uploads/default/original/3X/f/1/f1c7f3b897ae853d6d0ce8421c738f3ee6884f38.png)

> **[Serial transformation of a molecule – alice\_krebs](https://hub.knime.com/alice_krebs/spaces/Public/Serial%20transformation%20of%20a%20molecule~vW4XiLYZuu325zys/current-state)**
>
> Solutions for data science: find workflows, nodes and components, and collaborate in spaces.

Best,  
Alice

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**Author:** ![system](https://forum-cdn.knime.com/uploads/default/original/1X/ab3ccf34482a0329361734a18199390177204f15.png) [@system](https://forum.knime.com/u/system)\
**Post date:** [November 13, 2025, 8:34am UTC](https://forum.knime.com/t/rdkit-chemical-transformation-node/90119/5 "2025-11-13T08:34:19Z")

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