‘Morgan’ descriptor : Draw a curve showing the maximum property predictions obtained vs. iteration number.

#1

Hi

I have a second problem I would like modify the RetroPath2.0-Mods-iQSAR-v2 such that molecules are represented by the ‘Morgan’ descriptor. I want to draw the curve showing the maximum property predictions obtained vs. iteration number. I must to set up the maximum
number of iteration to 50 as it takes time to run. Finally I would like to draw the molecules having the highest predicted value at the first iteration and the last iteration.

I have to use RetroPath2.0-Mods-iQSAR-v2 workflow (downloadable via this link): https://www.myexperiment.org/workflows/5029.html
To the Input Node it is necessary to have:
-Should one consider explicit Hs? No
-Number of iteration : 100
-Maximum molecular weight for compounds: 1,000
-Source file (.csv) is: " source.csv " . It is in this file https://www.myexperiment.org/files/1927.html
-Rules files (.csv) is : “rules-chemistry-switch.csv”. It is in this file https://www.myexperiment.org/files/1927.html
-Number of subsets for the tournament selection : 10
-Number of best structures to keep in each subset : 2
All boxes must be ticked.

To the Output Node it is necessary to put
-Path to the result folder : choose a folder
-Name of the global result file (will be written inside the result folder) “result.csv”.

The training set for CSV Reader is in this file https://www.myexperiment.org/files/1927.html. It’s is name : "setny-training-set "

It is an interesting workflow. The output of results can take up to 15 minutes.

I do not understand too much the sequences.

Thank you very much if you have an idea !

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Draw a curve showing the maximum property predictions iteration number
#2

Hi David,

could you please specify what is your output (format, properties etc.) which you want then use to draw the curve?

Best,
Martyna

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#3

Hi Martyna !

I want just do running the RetroPath2.0-Mods-iQSAR-v2 workflow and obain a curve. In output, all files formats suit me, as long as the curve drawing the molecules having the highest predicted value at the first iteration and at the last iteration is readable. I would like to put the iteration on the abscissa and maximum ATC predicted on the ordinate.
Do you know which node can make me put out a curve?

Best regards

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#4

Hi David,

this should work with a Line Plot (JavaScript) Node.
Here you can check the examples how the node can be used in a workflow:
knime://EXAMPLES/03_Visualization/02_JavaScript/02_Example_for_JS_Line_Plot_Basic
knime://EXAMPLES/03_Visualization/02_JavaScript/03_Example_for_JS_Line_Plot_Advanced

Best,
Martyna

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#5

Hey Martyna !

Thank you for these examples, I will try for my case !

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