InCHi to a SMILES

Groups Cheminformatics
1

Hello,

Do you know how to go from an InCHi to a SMILES, then a selection of the top ten molecules from a list of SMILES. I will then build a table showing the molecular weight, the SMILES of each molecule.

Thank you very much!

2

Hi David32,

There are actually two ways to convert InCHi to SMILES in KNIME.

  1. OpenBabel node
  2. RDKit From Inchi node -> RDKit Canon SMILES node

Please be aware that converting InChi back into a molecule is almost always a bit risky. You can get different results when you convert a molecule -> Canonical SMILES and molecule -> InChi -> Canonical SMILES.

To select the top ten molecules from a list you can use the Row Filter node. In the configuration settings you should select Include rows by number and select a range from 1 to 10 to receive the first 10 rows from your list.
If you need to calculate the molecular weight you could use the Molecular Properties or the RDKit Descriptor Calculation node.
To select then the columns of your interest you can use the Column filter node and connect a Table View (JavaScript) for the visualization.

Best,
Martyna

3

Dear David32,
in addition to Martyna suggestions, in order to convert InChi to SMILES you can use the CIR (Chemical Identifier Resolver) node.
It is available both in KNIME as community contributions:
https://www.knime.com/book/chemical-identifier-resolver-for-knime-trusted-extension
and in NodePit:


Best,
Andrea

4

Hello,

Thank you very much Martyna and Andrea.mauri !

But when I’m linking Molecular Properties after the Row filter node. I get the message “Dialog cannot be opened” : the dialog cannot be opened for the following reason: No column in spec compatible with “CDKValue” “SdfValue” “SmilesValue” “CMLValue” or “InchiValue”.

Note : I use a .csv file containing a Row ID column and a InchI column

Best regards

5

Everything it’s ok ! I put OpenBable at the end.

6

But I have a problem when I try to put a SMART reaction rule.

I read my .cvs file

I have a SMART reaction without atom like this : ([$([]-[!R]):1]-[$([!R]-[:1]):2]).([$([]-[!R]):3]-[$([!R]-[:3]):4])>>([:1]-[:4]).([:3]-[:2])
and when I try to read on MarvinSketch I do not get a correct reaction.

Is this normal?

7

I correctly re-write the reaction:
([$([]-[!R]):1]-[$([!R]-[:1]):2]).([$([]-[!R]):3]-[$([!R]-[:3]):4])>>([:1]-[:4]).([:3]-[:2])

Marvin Sketch does not translate it well. Do you have an idea ?

Thank you so much

8

Hi David,

It’s difficult to figure out what you’re trying to do here without more information.
Could you please post a workflow that demonstrates the problem you are having?

-greg

9

Hi Greglandrum

I am trying to draw a SMART reaction rule with Knime for this rule-chemistry-switch file in this folder: https://www.myexperiment.org/files/1927.html. When I open it with CSV Reader then I read the rule by Marvin Sketch. My reaction seems to have discrepancies. I do not know if I read it with the right node.

Thank you so much

10

I am trying to draw a SMART reaction rule for this file: https://1drv.ms/u/s!Ahn2LmAio_hFiUHRX5JgdcRzDx0R.