SMILES 2D tp SDF 3D conversion

Hi,


I got a StringIndexOutOfBoundsException using

Code:

molconvert sdf -3:"c2E" test.smi

but converting to sdf first and then using above commando solved the issue. Example from http://www.chemaxon.com/conf/Advanced_automatic_generation_of_3D_molecular_structures.pdf

Code:

molconvert sdf -3:"c2E" test.sdf

Code:

test.smi:1: error: String index out of range: -1 java.lang.StringIndexOutOfBoundsException: String index out of range: -1         at java.lang.String.substring(Unknown Source)         at chemaxon.marvin.modules.MolExport.appendEnergy(MolExport.java:439)         at chemaxon.marvin.modules.MolExport.appendHeader(MolExport.java:417)         at chemaxon.marvin.modules.MolExport.convert(MolExport.java:334)         at chemaxon.formats.MolExporter.write(MolExporter.java:216)         at chemaxon.formats.MolConverter.write(MolConverter.java:708)         at chemaxon.formats.MolConverter.convert0(MolConverter.java:684)         at chemaxon.formats.MolConverter.convert(MolConverter.java:594)         at chemaxon.formats.MolConverter.main(MolConverter.java:1245)

Tobias

Hi Tobias!





First of all thanks for reporting this problem.





We've tested the molconverter of the current release with some random molecules as input file with the same parameteres you used after your report. Because the molconverter didn't throw us this exeption, we'd like to ask you to send the test.smi file, and the Marvin version you use for us.





Best regards,


Istvan Fajth

Hi,


sorry I forgot the version numbers:


Molecule File Converter, version 4.1.13, (C) 1999-2007 ChemAxon Ltd.





The smiles file is any smiles like


C


CC


CCC


CCCC





I first thought its because I have a property field attached to the SMILES,


but this is not the case. Example 3 files attached. Only the SDF works.





I will upgrade to version 5 today.


Thank you.


Tobias

Hi!





I've found information about your problem, it was a known issue until the 5.0.3 release of Marvin. So Marvin 5.0.3 and the later versions will work fine.





The related bugfix note in the changelog is:


MOL/SDF export caused a null pointer exception when energy field was corrupted (NaN or Infinity)





Best regards,


Istvan Fajth

Hi Istvan,


thank you for checking.


I just upgraded to 5.0.X


Tobias