Another exception in custom amino acid use

User ee508a317e

30-11-2010 11:34:54

Hello,

I am trying to define "Ahx", aminohexanoic acid, as a custom amino acid. When I do this I get the following exception:

Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException

at chemaxon.marvin.sketch.swing.SketchPanel.molLoaded(Unknown Source)

at chemaxon.marvin.sketch.swing.SketchPanel.molLoaderFinished(Unknown Source)

at chemaxon.marvin.util.MolLoader.run(Unknown Source)

at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)

Here is the line from my <userhome>/.chemaxon/custom_aminoacids.dict file:

X(Ahx) X(Ahx) [NH2][CH2][CH2][CH2][CH2][CH2]C=O 1 7

X(Aib) X(Aib) [CH3][CX4]([CH3])([NX3])C=O 4 5

I have also specified Aib (aminoisobutyric acid) as a custom amino acid and this works fine. But with Ahx I get the exception above.

Can anyone explain why this should occur? Although I am a novice with Smarts format it looks okay to me. I did wonder whether in the API code there is any chemical intelligence like checking that the amino group is adjacent to the acyl carbon?

I should mention that I am setting MSketchPane via:

MSketchPane.setMol (String mol, String format) and using "peptide" as the format

Thanks,

Tim

ChemAxon 990acf0dec

30-11-2010 12:45:18

Hi Tim,

Although I am not an expert in the custom aminoacid definitions, I tested it, and it seems that the second "x" character causes the issue. If you change the name to X(Ahz) for example, then it works fine.

Best regards,

Akos

User ee508a317e

30-11-2010 17:04:41

Hi Akos,

Okay yes worked around the issue as you described. Thank you.

I guess strictly this is a bug as there doesn't seem to be any intrinsic reason why this restriction should exist.

Regards,

Tim

ChemAxon 990acf0dec

30-11-2010 21:52:40

Hi Tim,

Yes, I think so too. We will fix this issue.

Best regards,

Akos

ChemAxon d9100dae53

13-12-2010 12:52:01

Hi Tim,

Thanks for the report. The names with "x" will work in the next version of Marvin (5.4.1)

Regards,

Rita