WARN

Hello,

I just started KNIME and I get the warning below:

WARN SdfValue$SdfUtilityFactory Unknown preferred renderer class "jp.co.infocom.cheminfo.marvin.renderer.MarvinRenderer" - ignoring. 

It seems to me that it is referring to a Marvin component.  I have MarvinSketch, MarvinView, MarvinSpace and MolConverter nodes; but I do not have a MarvinRenderer. 

What could be causing the warning?

Thank you,

Giuseppa

Is this referring to how they are displayed in a KNIME table. You can right click on the structure column header and choose different renderer options, one of which is Marvin.

However, that really should be working with Marvin Renderer.

Simon.

Hi,

Under the following menu: 

             File -> Preferences -> KNIME -> Chemistry

do you have the KNIME preffered renderer set to marvin? 

 

What rendered is being used when you view a table (right click the column header for an SDF column, select available renderers as Simon said)?

 

Sam 

 

Hi Sam,

Thank you for your eply.

I lokked under File -> Preferences ->KNIME -> Chemistry, and I do not find preffered renderer; but Erl Wook Cheminfo.  Marvin Shows under KNIME outside of chemistry and it lists marvin Renderer Option and Marvin Renderer Preference.  I am using an interactive table to display the dat ra.all file read by a filereader.  The available renderers are: Standard Double, Full Precission, Percentage, Gray Scale and Bars. But the WARN message does not appear when I create these protocol; it appears when I open KNIME for the first time with not protocol on the screen at all.

 

Giuseppa

Hi Sam,

Thank you for your eply.

I lokked under File -> Preferences ->KNIME -> Chemistry, and I do not find preffered renderer; but Erl Wook Cheminfo.  Marvin Shows under KNIME outside of chemistry and it lists marvin Renderer Option and Marvin Renderer Preference.  I am using an interactive table to display the dat ra.all file read by a filereader.  The available renderers are: Standard Double, Full Precission, Percentage, Gray Scale and Bars. But the WARN message does not appear when I create these protocol; it appears when I open KNIME for the first time with not protocol on the screen at all.

 

Giuseppa

Hi Sam,

Thank you for your response.

I did not find a preffered rendered label under File -> Preferences -> KNIME -> Chemistry; but only a Earl Wood Cheminfo abel.  I found MArvin under KNIME outside of Chemistry and contains two labels: Marvin Renderer Option and marvin Renderer Preference. 

I am using a file reader to read a data.all table and interactive table for display.  The interactive table available readers are : Standard Double, Full Precision. Percentage, Gray Scale and Bars.  The message below does not appear when I am creating the protocol; but immediately after I open KNIME while tere is still no created protocol.

WARN MolValue$MolUtilityFactory Unknown preferred renderer class "jp.co.infocom.cheminfo.marvin.renderer.MarvinRenderer" - ignoring

Giuseppa

 

Hi Simon,

Thank you for your response.

I am not using any display table at all.  The message below occurs when I open KNIME while there is not protocol at all on the screen.

WARN MolValue$MolUtilityFactory Unknown preferred renderer class "jp.co.infocom.cheminfo.marvin.renderer.MarvinRenderer" - ignoring

Giuseppa

Have you installed the chemistry nodes as well as the Marvin nodes? 

 

When it is working correctly you should get options like those displayed in my attachments. 

Thank you,

Available renderers for molecule in the tab of the does not display any of the choices below.

 

MOE Molecule 3D (+H)

MOE Molecule 3D (-H)

Mol String

Indigo Renderer

Multiline String

SDF String

 It only dislays Mvr String and String.  Is there may be any Chemistry extension that I should install in addition to the default installaion?

Giuseppa

So it looks like you have a marvin structure in that cell (or should do hidden in there) that it can't render. 

 

You should install: "KNIME Base Chemistry Types & Nodes" as well as "KNIME Chemistry Add-Ons" to display things correctly I believe. Both are available in the KNIME update site. But I would guess you have installed these already.

 

MOE Molecule 3D (+H)
MOE Molecule 3D (-H)
Mol String
Indigo Renderer
Multiline String
SDF String

Wouldn't apply to a marvin structure. 

 

Regards

 

Sam