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Replicating tautomers generated by version 4.0.3
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Jason

Joined: 04 Mar 2015
Posts: 5

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Link to postPosted: Thu Apr 09, 2015 1:45 amPost subject: Replicating tautomers generated by version 4.0.3 Reply with quote

Hi everyone,

I’m currently attempting to replicate the results of a paper that used the ChemAxon suite back in 2008. It appears that the current software is generating different tautomers for some chemicals to those in the paper. The paper is quotes “MarvinBeans pKa estimation plug-in, ver. 4.0.3” as their source. I currently have an academic licence for using the software. Is it possible for me to get this earlier version of the software so that I can replicate the results? Or is there a way to change the output in a way that will replicate the tautomers of the earlier software. I'm working with smiles so I can make simple changes to the output structure.

 Thanks,

Jason Jooste     

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
Posts: 315

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Link to postPosted: Thu Apr 09, 2015 3:52 pmPost subject: Reply with quote

Dear Jason, 

You can download the old Marvin versions from the link below. You can use the corresponding applet version as well. 

The links are:

https://www.chemaxon.com/marvin-archive/

and 

https://www.chemaxon.com/download.php?d=/data/download/marvin/archives

Best regards, 

Daniel

Jason

Joined: 04 Mar 2015
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Link to postPosted: Fri Apr 10, 2015 2:40 amPost subject: Reply with quote

Thanks for your help Daniel, that was just what I needed!

I'm having a strange problem though, when I import the jmarvin.jar file and try to use tautomerization plugin the method and field names are all alphabetic instead of corresponding to the names in the examples. Are the JAR files protected in some way? Am I using them incorrectly? I'm sorry if I'm being a bit dense, I've tried to find a tutorial on how to use the MarvinBeans packages but I haven't been able to find anything.

The autocomplete I am getting in eclipse (I confirmed the methods with reflection so this isn't an Eclipse issue):

 

Thanks, 

Jason

László
ChemAxon personnel
Joined: 14 Jan 2011
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Link to postPosted: Mon Apr 13, 2015 9:22 pmPost subject: Reply with quote

Dear Jason,

In marvin-all and marvin-bin packages the methods are obfuscated.
You have to download marvinbeans-4.0.3.zip, and use MarvinBeans.jar from lib directory.

Best regards,
Laszlo 

Jason

Joined: 04 Mar 2015
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Link to postPosted: Tue Apr 14, 2015 1:50 amPost subject: Reply with quote

Thanks for your help Laszlo, that worked perfectly!

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