Problem with molconvert

Hello,

I have a problem with document to structure.

If I try and run molconvert on a PDF I get the following (truncated)...

$ molconvert smiles:a test.pdf -o test.smi
Jun 25, 2015 1:53:03 PM chemaxon.naming.document.TesseractProcessOCR isAvailable
WARNING: Tesseract could not be installed, OCR is disabled
java.io.IOException: I'm sorry, I could not find tesseract-unknown-3.01.jar
	at chemaxon.marvin.util.InstalledComponent.findLocalJar(InstalledComponent.java:195)
	at chemaxon.marvin.util.InstalledComponent.nonAppletInstall(InstalledComponent.java:171)

MarvinBeans: marvinbeans-15.6.15.0-macos

OS: Mac OS X Yosemite (10.10.3).

Java: 1.6.0.jdk

tesseract (via Homebrew): tesseract-3.02.02_3

Is it that this functionality is not supported on OS X? I see 'tesseract-X-3.01.jar' files for Windows and Linux but not Mac.

Thanks,

Francis

Hi Francis,

This should work on Mac OS. However there might be a few issues to solve to get it working. The first thing is, I suspect you are actually running an older version of marvin. Could you please check what this command says:

molconvert | head -1

Oh dear, I *was* an old version (/Applications/MarvinBeans/bin/molconvert) by mistake and not the new version I'd installed.

However, now that's fixed, I have a slightly different problem...

$ whence molconvert

/Applications/ChemAxon/MarvinBeans/bin/molconvert

$ molconvert -h | head -1

Molecule File Converter, version 15.6.15.0, (C) 1999-2015 ChemAxon Ltd.

$ molconvert smiles:a test.pdf -o test.smi

Jun 25, 2015 3:09:55 PM chemaxon.naming.document.TesseractProcessOCR isAvailable

WARNING: Tesseract could not be installed, OCR is disabled

java.io.IOException: Missing resource: /tesseract-macosx-3.01.zip

at chemaxon.util.InstalledComponent.installInto(InstalledComponent.java:224)

I do have an Mac OSX jar now, though...

-rw-r--r--  1 francis  admin  1451901 15 Jun 13:32 /Applications/ChemAxon/MarvinBeans/lib/tesseract-macosx-3.01_1.jar

Good, we're making progress :) There is indeed an issue with tesseract on Mac OS in our current version. This should be fixed in next week's version. Is this OK for you, or would you need a workaround sooner?

Next week would be fine! Any particular release number I should look out for?

This fix should be included in version 15.06.29.

Version 15.06.29 is now released. Francis, could you please confirm if it fixes the issue for you?

I think that's fixed, yes: I've no problems with any of the PDFs I've tried it on so far. Many thanks!

Great! Thanks for your report and your patience.