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cLogD [message #955] Tue, 16 June 2020 15:46 Go to next message
thurow.sam@gmail.com is currently offline  thurow.sam@gmail.com
Messages: 1
Registered: June 2020
Location: Brazil
Junior Member
Hi everybody!

the option that calculate logD is unclickcable, is there a way to activate that button?

thanks

Sam
Re: cLogD [message #956 is a reply to message #955] Tue, 16 June 2020 22:15 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 412
Registered: June 2014
Senior Member
cLogD requires a pKa prediction, which DataWarrior cannot do itself yet. However, DataWarrior may use the commercial ChemAxon pKa-plugin to do the prediction. If the DataWarrior installation folder contains a capka.jar file, which contains the needed ChemAxon software, then cLogD and pKa prediction are enabled.
Re: cLogD [message #1207 is a reply to message #955] Tue, 02 February 2021 22:15 Go to previous messageGo to next message
bruce is currently offline  bruce
Messages: 2
Registered: February 2021
Junior Member
I am about to purchase the chemaxon cLogD plugin for datawarrior-

are there any procedures written up so i can install this functionality into the program?

thanks!
Re: cLogD [message #1208 is a reply to message #1207] Tue, 02 February 2021 22:47 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 412
Registered: June 2014
Senior Member
No, unfortunately, there is no easily reproducible procedure described. DataWarrior checks for a file called 'capka.jar' among its jar files. If it finds it and if the accessed classes and their dependencies are inside it in the proper folder hierarchy representing the package names, then it should work. You should also place the license file where the ChemAxon documentation expects it to be. I did it only once many years ago. At that time it was a cumbersome procedure, because the original pKa-plugin contained many jar files with altogether more than 100MB content. To add this to a DataWarrior installation was prohibitive, even though it was an in-house Actelion installation. Therefore, I unpacked all jar files into one root directory and intended to remove everything that was not needed for the pKa-calculation. I tried various Java obfuscators, because they have a mode to not obfuscate Java bytecode, but just remove unused dependencies. None of them could handle this amount of Java stuff. Finally I ended up removing one file after another with a script and checking after every step that the pKa calculation still works. Problematic was that the code often uses the reflection API and that required classes depend on certain features of the molecule (really a mess). Different molecules needed different classes added via classForName()!!! My procedure finally reduced the size from >100MB to 0.72MB.

Of course, if you unpack all jars into one root directory and pack everything again into one large capka.jar, it should work. However, I didn't try this with the current pKa-plugin.

The classes required by DataWarrior are:
chemaxon.formats.MolFormatException;
chemaxon.formats.MolImporter;
chemaxon.marvin.calculations.pKaPlugin;
chemaxon.marvin.plugin.PluginException;

I also attach a list of all files that I have added and that seems to be complete...

If your are successful with the current ChemAxon plugin, then please let other users know.

Thomas
  • Attachment: capka.txt
    (Size: 13.82KB, Downloaded 7 times)

[Updated on: Tue, 02 February 2021 22:48]

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Re: cLogD [message #1210 is a reply to message #1208] Wed, 03 February 2021 18:29 Go to previous message
bruce is currently offline  bruce
Messages: 2
Registered: February 2021
Junior Member
thanks Thomas. Very much appreciate all of the work you have done on this program
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