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Lipinski's rule [message #975]

Mon, 29 June 2020 04:33

sansun
Messages: 50
Registered: April 2019

Member

Is there a way to filter/mark compounds that do not comply to 2 or more parameters of the Lipinski's rule of 5 in datawarrior?

Probably it can be done using 'calcualated values'

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Re: Lipinski's rule [message #977 is a reply to message #975]

Mon, 29 June 2020 09:19

nbehrnd
Messages: 233
Registered: June 2019

Senior Member

Your are right, this may achieved by addition of a new column from the menu Data -> Add
Calculated Values. This equally extends the scope of an earlier question by you, too.[1]

Assuming you already have a table with the Lipinski criteria computed, you may then mark
the entries where simultaneously the molecular weight exceeds 500 g/mol and a number of
HAcceptors is greater than 10 by a test condition of

if(TotalMolweight > 500 && HAcceptors > 10, "reject", "admit")

index.php?t=getfile&id=226&private=0

And indeed, there are drugs which do not meet these screening criteria.

index.php?t=getfile&id=227&private=0

DW's manual describes in detail the syntax to apply here.[2] A minimal example .dwar
file is attached below, too.

[1] http://openmolecules.org/forum/index.php?t=msg&goto=817& amp; amp;#msg_817
[2] http://www.openmolecules.org/help/jep.html

Attachment: conditional-or8.png
(Size: 6.14KB, Downloaded 1107 times)
Attachment: example-or8.png
(Size: 7.52KB, Downloaded 1013 times)
Attachment: test_list.dwar
(Size: 3.96KB, Downloaded 521 times)

[Updated on: Mon, 29 June 2020 09:23]

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Re: Lipinski's rule [message #978 is a reply to message #977]

Tue, 30 June 2020 07:58

sansun
Messages: 50
Registered: April 2019

Member

Thanks nbehrnd

However, your equation considers only two parameters at a time while I want to have combination of any 2 parameters at a time (6 possible combinations). Based on your answer I came up with the following equation that takes care of all possible combinations of 2 parameters and it seems to work:

if(TotalMolweight > 500 && HAcceptors > 10 || TotalMolweight > 500 && HDonors > 5 || TotalMolweight > 500 && cLogP > 5 || HAcceptors > 10 && HDonors > 5 || HAcceptors > 10 && cLogP > 5 || cLogP > 5 && HDonors > 5, "reject", "admit")

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Re: Lipinski's rule [message #979 is a reply to message #978]

Wed, 01 July 2020 10:11

nbehrnd
Messages: 233
Registered: June 2019

Senior Member

Hello Sansun,

you are correct, the answer provided by me only intended to serve a springboard / minimal
working example about using two parameters in one .AND. conditional. Thus the indication
of the manual page presenting the syntax in greater detail, including an .OR. clause to
expand the scope of the test beyond that example. I'm happy for you your derived, more
advanced scrutiny works for you, and for any future user who may see this as a as a source
of inspiration and reference.

Norwid

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