ConformerPlugin

I can't find the ConformerPlugin class- with JChem 3.1.7 installed, my javac keeps complaining about ConformerPlugin not found although I have the following includes:





import chemaxon.struc.*;


import chemaxon.formats.*;


import chemaxon.marvin.modules.*;


import java.io.*;


import java.util.*;


import java.lang.*;


import chemaxon.marvin.calculations.*;


import chemaxon.marvin.plugin.*;


import chemaxon.reaction.Standardizer;





What am I missing?

Hi Dragos,





You are not missing anything. The ConformerPlugin will be available only in the Marvin 4.1 release (coming soon) and in the JChem 3.2 release (coming in few months). For the meantime you can use Marvin 4.1 alpha release, which can be downloaded from http://www.chemaxon.com/shared/alpha/ .





You need to import chemaxon.marvin.calculations.ConformerPlugin to use it, so your imports are OK.





Best regards,


Zsolt

Hi, Zsolt - for some obscure reasons, clicking on the download links of the alpha version throws my browser (fireFox) back to the chemaxon home page!

Hi Dragos,





Please try this link: http://www.chemaxon.com/shared/alpha/marvin/do-download-marvinbeans.html





Which one Marvin Beans installer package (platform) you tried to download?





Clear your browser's cache, maybe it can help.





Regards,


Zsolt

Hi, Zsolt


I have the same pb when trying to download the marvinapplets (not the beans)


http://www.chemaxon.com/shared/alpha/marvin/do-download-marvinapplets.html


Back to the home page...


Cheers,


Nicolas

done:


http://www.chemaxon.com/download.php?d=/data/download/marvin/alpha/marvin-all-4_1_0alpha19.tar.gz


works...

We have corrected the link on our download page. Thank you for reporting.

OK, got my marvin_alpha installed and the conformer generation (joined file) compiles properly - if I modify the CLASSPATH to include marvin_alpha marvin.jar jmarvin.jar sjars/batik-core.jar and sjars/plugin/ConformerPlugin.jar. However, when I try to make it run I get:


Generating conformers of molecule 1... -> so far, so good! that's my println





Exception in thread "main" java.lang.NoSuchMethodError: chemaxon.marvin.plugin.CalculatorPlugin.f(Lchemaxon/struc/Molecule;)V


at chemaxon.marvin.calculations.ConformerPlugin.standardize(Unknown Source)


at chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(CalculatorPlugin.java:760)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:694)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:673)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:656)


at Utils.Conformers.<init>(Conformers.java:50)


at Utils.Conformers.main(Conformers.java:221)





It does not appear to be a molecule-specific issue!

Sorry, this is a bug ( related to switching between new and old conformer calculation algorithm) that only affects API usage. In the next alpha release (coming this week, probably tomorrow) it will be fixed.

The new alpha release (Marvin 4.1.0alpha20) is available.


http://www.chemaxon.com/shared/alpha/marvin

OK - so we made it past the compilation phase, ConformerPlugin being well available now (we're in marvin 4.1.1 and jchem 3.1.7). We get however a





Exception in thread "main" java.lang.AbstractMethodError


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:704)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:673)


at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:656)


at Utils.Conformers.<init>(Conformers.java:50)


at Utils.Conformers.main(Conformers.java:221)





Huh - AbstractMethodError??? Joined the code & the unlucky molecules (but since it happened at the first, I suppose any molecules would cause the error). Our CLASSPATH included jchem.jar and ALL the jars in the marvin directory. Good luck!

Please, do not mix the code of Marvin Applets and JChem package: it can cause unexpected errors.


There are several classes that both packages include. But the two packages are compiled with different tools. Furthermore, they can include different version of the same file.


"jchem.jar" also includes Marvin API. Thus, please remove Marvin jars from the CLASSPATH.

yeah, that's what I tried at the first ... but then it says ConformerPlugin not found! The only way to make it find ConformerPlugin was to add Marvin to CLASSPATH!

JChem 3.1.7 includes Marvin 4.0.6. This Marvin release does not contain ConformerPlugin. ConformerPlugin is available since Marvin 4.1. The new JChem major release are going to include Marvin 4.1.x. Try the latest test release of JChem that already includes ConformerPlugin and other new Marvin features.


Download JChem test releases