Molconvert limited to 80 molecules in one SDF file ?

Hi,


while evaluating Marvin, I found that a 1000 molecules MOL file (1 file with 1000 molecules) is stopping coordinates computation after 80 (average, seems to be random).


Any help appreciated.





(cannot put sample file, sorry)





Erwan

More info:





when opening the SDF file with MarvinView, it says:


read error after molecule 80.


Bad Bond type 0.





However, it is not true, since I can delete the 80 first molecules from the file and have the same error message at a different number after


each delete (read error after molecule 84, read error after molecule 74...)





When file goes below 80 molecules (or so), it shows no error...





I have huge files, and I don't want to chunk them to


compute coordinates...





Help.





Erwan








Stack dump:


java.io.IOException: Bad bond type 0


at chemaxon.marvin.modules.MolImport.readBondBlockV2(Unknown Source)


at chemaxon.marvin.modules.MolImport.readCtab(Unknown Source)


at chemaxon.marvin.modules.MolImport.readMol0(Unknown Source)


at chemaxon.marvin.modules.MolImport.readMol(Unknown Source)


at chemaxon.formats.MolImporter.readDoc(Unknown Source)


at chemaxon.marvin.View.readStream(Unknown Source)


at chemaxon.marvin.View.main(Unknown Source)


at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)


at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)


at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)


at java.lang.reflect.Method.invoke(Unknown Source)


at com.zerog.lax.LAX.launch(Unknown Source)


at com.zerog.lax.LAX.main(Unknown Source)

I have checked SD file loading but I have not found any problem. Perhaps, your SD file is not correct. Can you send us to check it?

Hi,





I don't want to publish the files here, but I can send it to you...


could you send me you email ?





The files will also be blured (all atoms replaced by C), to avoid


confidentiality issues...





Erwan

OK, I will send you an email.


Tamas

Erwan,


Your SDfile is not correct. This is a small section of the Bond Block in your file, which belongs to molecule 70:

Code:

9  7  1  0  0  0  0  10  7  0  0  0  0  0  11  3  4  0  0  0  0

The third column is for the bond type. Legal values are between 1 and 8. There is a 0 in the second row, which causes the error.


See the specification of the Bond Block in this document:


http://www.mdli.com/downloads/public/ctfile/ctfile.jsp


Ferenc

Thanks for your help.





My molecule generator must have a bug somewhere.





Best regards