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How to generate MrvCell output in KNIME node?
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Christian

Joined: 28 Feb 2011
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Link to postPosted: Wed Apr 04, 2012 10:10 pmPost subject: How to generate MrvCell output in KNIME node? Reply with quote

Hi,

I am trying to code a KNIME node that generates optional MRV output (I presume the type would be "MrvCell.TYPE").

Is there any publicly available sample code for such a node (e.g., MolConverter code)?

Also, how can I get the necessary packages with MrvCell definitions etc. for Eclipse development?

Thanks in advance,

Christian

Takahiro

Joined: 07 Mar 2005
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Link to postPosted: Thu Apr 05, 2012 1:34 amPost subject: Reply with quote

Hi Christian,

If you would like to use the MrvCell in KNIME, you have to install the Marvin Extensions into your Eclipse.
The Marvin Extensions can be downloaded from http://www.knime.org/downloads/update

Then, you can generate the MrvCell by the following method.

public static DataCell jp.co.infocom.cheminfo.marvin.type.MrvCellFactory#create(chemaxon.struc.Molecule mol)
public static DataCell jp.co.infocom.cheminfo.marvin.type.MrvCellFactory#create(java.lang.String mol)

In case of String argument, the String must represent Mrv format.
Also, you can use the MrvCellFactory.TYPE to determine the DataType of a DataCell.

NOTE:
The MrvCell automatically clears their properties to reduce their data usage.
Instead, I always extract their properties to other columns before generating MrvCell.

Best,
Taka

Christian

Joined: 28 Feb 2011
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Link to postPosted: Thu Apr 05, 2012 2:18 amPost subject: Reply with quote

Hi Taka,

thanks for the quick reply.

I had already installed the Marvin Extensions but I cannot see any package that starts with "jp...".

I have installed "ChemAxon/Infocom Marvin Extensions Feature" (version 2.5.1.v0129). Is there anything else I need to install? Do you know what the Jar name is that should show up in the dependencies?

Thanks,

Christian

Takahiro

Joined: 07 Mar 2005
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Link to postPosted: Thu Apr 05, 2012 3:08 amPost subject: Reply with quote

Hi Christian,

I am sorry for my poor explanation.
You have to add "jp.co.infocom.cheminfo.marvin" plugin into "Required Plug-ins" on "Dependencies".
Also, if you would like to use ChemAxon libraries, add "jp.co.infocom.cheminfo.jchemlib" plugin as well.

Best,
Taka

Christian

Joined: 28 Feb 2011
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Link to postPosted: Thu Apr 05, 2012 5:44 amPost subject: Reply with quote

Hi Taka,

I'm sorry, I am not sure I am following. I am using Eclipse SDK 3.6.1 (that came with Knime). Are you suggesting to add some jar file to the dependencies of the project? Where do I find "Required Plug-ins"? When I right-click on "Plug-in Dependencies" in my project, I can only import/export jars...

Thanks for helping,

Christian

Takahiro

Joined: 07 Mar 2005
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Link to postPosted: Thu Apr 05, 2012 6:08 amPost subject: Reply with quote

Hi Christian,

I am sorry again...
You can use the Plug-in Manifest Editor by opening your Manifest file in your project.
Could you please refer to the following site?

http://help.eclipse.org/helios/topic/org.eclipse.pde.doc.user/guide/tools/editors/manifest_editor/dependencies.htm

If you also have feature project for your plugin, I suggest that you add "jp.co.infocom.cheminfo.marvin.feature" feature into your feature project.

http://help.eclipse.org/helios/topic/org.eclipse.pde.doc.user/guide/tools/editors/feature_editor/dependencies.htm

Best,
Taka

Christian

Joined: 28 Feb 2011
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Link to postPosted: Thu Apr 05, 2012 7:47 pmPost subject: Reply with quote

Hi Taka,

after adding both jp.co.infocom.cheminfo.marvin and jp.co.infocom.cheminfo.jchemlib to the plug-in dependencies, it worked.

Thanks a lot for your help. Much appreciated.

Christian

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