So I create a DepictionGenerator instance within a class, which is then
called repeatedly for depicting IAtomContainers. My original usage was
something like this;
DepictionGenerator generator = new DepictionGenerator()
.withOuterGlowHighlight()
.withParam(StandardGenerator.Visibility.class,
SymbolVisibility.iupacRecommendationsWithoutTerminalCarbon())
.withParam(StandardGenerator.AnnotationColor.class, Color.BLUE);
and for every call to depict molecules I do this;
generator
.depict(mol)
.writeTo(imgFile.getAbsolutePath());
And as said in the original post, I've also removed all calls to
"with"-methods and used the parameterless constructor only, and tried to
depict the molecules as pair the second snippet, still the same Error. The
Error is thrown in the second snippet, where every new molecule should be
depicted.
Even more interestingly is that I created a runnable jar with just an
example application that uses the class that has a DepictionGenerator. It
works to run the runnable jar on the command line, but the exact same jar
does not work when adding it to a different project and running basically
the same main-class of code. Also, if I use the jar, but do not use the
DepictionGenerator within it, everything else works as it should..
Regards,
Staffan
2016-08-22 20:13 GMT+02:00 John M <[email protected]>:
> Okay, how are you interacting with the depiction generator?
>
> John
>
> Regards,
> John W May
> [email protected]
>
> On 22 August 2016 at 14:37, Staffan Arvidsson <[email protected]
> > wrote:
>
>> Hi John,
>>
>> I'm not using any other depiction-depending stuff in the other projects
>> that I've pulled in the jar-file in. Created a empty project and just
>> pulled in a fatjar of the first project (so there should not be any
>> different versions lying around), still the same problem..
>>
>> Here's the output for mvn dependency:tree;
>>
>> [INFO] se.uu.farmbio:PDFGenerator:jar:0.0.1-SNAPSHOT
>> [INFO] +- org.openscience.cdk:cdk-depict:jar:1.5.13:compile
>> [INFO] | +- org.openscience.cdk:cdk-renderextra:jar:1.5.13:compile
>> [INFO] | | +- javax.vecmath:vecmath:jar:1.5.2:compile
>> [INFO] | | +- org.openscience.cdk:cdk-interfaces:jar:1.5.13:compile
>> [INFO] | | +- org.openscience.cdk:cdk-core:jar:1.5.13:compile
>> [INFO] | | +- org.openscience.cdk:cdk-standard:jar:1.5.13:compile
>> [INFO] | | \- org.openscience.cdk:cdk-render:jar:1.5.13:compile
>> [INFO] | +- org.openscience.cdk:cdk-renderawt:jar:1.5.13:compile
>> [INFO] | | \- com.google.guava:guava:jar:17.0:compile
>> [INFO] | +- org.openscience.cdk:cdk-renderbasic:jar:1.5.13:compile
>> [INFO] | +- org.openscience.cdk:cdk-smiles:jar:1.5.13:compile
>> [INFO] | | +- uk.ac.ebi.beam:beam-core:jar:0.9.1:compile
>> [INFO] | | +- uk.ac.ebi.beam:beam-func:jar:0.9.1:compile
>> [INFO] | | +- org.openscience.cdk:cdk-ioformats:jar:1.5.13:compile
>> [INFO] | | +- org.openscience.cdk:cdk-io:jar:1.5.13:compile
>> [INFO] | | | +- xpp3:xpp3:jar:1.1.4c:compile
>> [INFO] | | | \- org.openscience.cdk:cdk-atomtype:jar:1.5.13:compile
>> [INFO] | | \- org.openscience.cdk:cdk-valencycheck:jar:1.5.13:compile
>> [INFO] | +- org.openscience.cdk:cdk-smarts:jar:1.5.13:compile
>> [INFO] | | \- org.openscience.cdk:cdk-isomorphism:jar:1.5.13:compile
>> [INFO] | +- org.openscience.cdk:cdk-sdg:jar:1.5.13:compile
>> [INFO] | +- org.openscience.cdk:cdk-silent:jar:1.5.13:compile
>> [INFO] | +- org.freehep:freehep-graphicsio-svg:jar:2.4:compile
>> [INFO] | | +- org.freehep:freehep-graphics2d:jar:2.4:compile
>> [INFO] | | | \- junit:junit:jar:4.10:compile
>> [INFO] | | | \- org.hamcrest:hamcrest-core:jar:1.1:compile
>> [INFO] | | +- org.freehep:freehep-graphicsio:jar:2.4:compile
>> [INFO] | | | \- org.freehep:freehep-io:jar:2.2.2:compile
>> [INFO] | | +- org.freehep:freehep-graphicsio-tests:jar:2.4:compile
>> [INFO] | | \- org.freehep:freehep-graphicsbase:jar:2.4:compile
>> [INFO] | \- org.freehep:freehep-graphicsio-pdf:jar:2.4:compile
>> [INFO] +- org.javatuples:javatuples:jar:1.2:compile
>> [INFO] +- com.itextpdf:itextpdf:jar:5.5.9:compile
>> [INFO] \- org.apache.directory.studio:org.apache.commons.io:jar:2.4:co
>> mpile
>> [INFO] \- commons-io:commons-io:jar:2.4:compile
>>
>> Regards,
>> Staffan
>>
>> 2016-08-22 15:00 GMT+02:00 John M <[email protected]>:
>>
>>> Hi Staffan,
>>>
>>> RendererModel$Padding is a global option: https://github.com/cdk
>>> /cdk/blob/master/display/render/src/main/java/org/openscienc
>>> e/cdk/renderer/RendererModel.java#L106
>>>
>>> Could you possibly have an old version of the RendererModel lying
>>> around? using JChemPaint.
>>>
>>> Since you're using maven, can you run:
>>> $ mvn dependency:tree
>>>
>>> And list the output.
>>>
>>> J
>>>
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>>> ------------------
>>>
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>>>
>>>
>>
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>>
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>>
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