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Use of calculated column functions [message #814]

Wed, 11 March 2020 11:09

sansun
Messages: 50
Registered: April 2019

Member

I have a file with the bioactivity column for several molecules.

I want to create a new column so that molecules with IC50 less than value 'x' are annotated as '1' while those with more than 'y' value labelled as '0'.

I understand that it can be done bey 'Calculated column' but I am not able to figure out the exact formula.
Any help is appreciated.

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Re: Use of calculated column functions [message #815 is a reply to message #814]

Wed, 11 March 2020 22:25

nbehrnd
Messages: 229
Registered: June 2019

Senior Member

To showcase this function with a minimal working example (attached below), I set up
a new file with benzene, toluene, and the xylenes in the first column, and their then
molecular masses calculated by DW in the second column. Subsequently, a third column
was generated (Data -> Add Calculated Values). Instead of an IC50 value, the MW was
used as threshold criterion -- available from the pull-down menu next to «Add Variable»
-- which was combined into

(TotalMolweight < 80) == 1

as test condition.

index.php?t=getfile&id=160&private=0

Page http://www.openmolecules.org/help/jep.html offers additional insight about the
functions and syntax available.

Attachment: minimum_test.dwar
(Size: 1.64KB, Downloaded 496 times)
Attachment: photo.png
(Size: 52.11KB, Downloaded 936 times)

[Updated on: Wed, 11 March 2020 22:35]

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Re: Use of calculated column functions [message #816 is a reply to message #815]

Thu, 12 March 2020 11:43

sansun
Messages: 50
Registered: April 2019

Member

Thanks a lot.

However, with your example molecules with Mwt = 80 are labelled as 0 but all others are labelled as 1.

My problem is slightly different. For example, I want '1' only for the molecules with Mwt > 100.

I don't want any value (or want some distinct value e.g. '3' Wink

for molecules with Mwt between 80-100.

I am trying to find other ways. Let me know if you get some idea.

Thanks again!

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Re: Use of calculated column functions [message #817 is a reply to message #816]

Thu, 12 March 2020 22:03

nbehrnd
Messages: 229
Registered: June 2019

Senior Member

Your observation is true because I understood your question as aiming for a (Boolean) on/off or True / False categorical two-level criterion. Please clarify if this was misunderstood by mine.

So far, I did not mind that instead categorical "1" and "0" strings the calculated column reads like floating numbers "1.0", and "0.0" instead and seems to be limited to two levels. To label molecules of molecular weight greater than 100, the computation would be adjusted to (TotalMolweight > 100 ) == 1. If searching for molecules with a molecular weight either below 80 .OR. greater 100, a plausible instruction were (TotalMolweight > 100 || TotalMolweight < 80) == 1; and the toluene molecule as an example for the range of 80 < MW < 100 is identified by (TotalMolweight > 80 && TotalMolweight < 100) == 1.

I see that attributing a string as a result of such a computation may be useful, or to extend the Boolean two-level perspective for, e.g. annotating members of a compound list as basic / neuter / acidic. Even more so as such an attribution by Add Calculated Values may consider multiple criteria from multiple columns at once. For both however, I do not know if DW contains such a functionality.

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