openmolecules.org

 
Home » DataWarrior » Cheminformatics » Lipinski's rule (flag non-compliant molecules)
Lipinski's rule [message #975] Mon, 29 June 2020 04:33 Go to next message
sansun is currently offline  sansun
Messages: 49
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'

Report message to a moderator

Re: Lipinski's rule [message #977 is a reply to message #975] Mon, 29 June 2020 09:19 Go to previous messageGo to next message
nbehrnd is currently offline  nbehrnd
Messages: 224
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

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

Report message to a moderator

Re: Lipinski's rule [message #978 is a reply to message #977] Tue, 30 June 2020 07:58 Go to previous messageGo to next message
sansun is currently offline  sansun
Messages: 49
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")

Report message to a moderator

Re: Lipinski's rule [message #979 is a reply to message #978] Wed, 01 July 2020 10:11 Go to previous message
nbehrnd is currently offline  nbehrnd
Messages: 224
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

Report message to a moderator

Previous Topic: TFA salts
Next Topic: Box plots
Goto Forum:
  

[ Syndicate this forum (XML) ] [ RSS ] [ PDF ]

Current Time: Wed Oct 30 20:58:21 CET 2024

Total time taken to generate the page: 0.00576 seconds
openmolecules.org