#1116 Inconsistent errror messages for aromatic boron

cdk-1.4.x
closed
nobody
None
9
2014-04-15
2011-01-18
No

Reported by Andrew on the BO ML:

"CDK says:

from cinfony import cdk
cdk.readstring("smi", "c1cc2c3cc1.c1cb23cc1")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/dalke/jython2.5.1/Lib/site-packages/cinfony/cdkjython.py", line 122, in readstring
raise IOError, ex
IOError: org.openscience.cdk.exception.InvalidSmilesException: Found element which is not a 'organic subset' element. You must use [b].

and when I try using [b]

cdk.readstring("smi", "c1cc2c3cc1.c1c[b]23cc1")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/dalke/jython2.5.1/Lib/site-packages/cinfony/cdkjython.py", line 122, in readstring
raise IOError, ex
IOError: org.openscience.cdk.exception.InvalidSmilesException: Expected element symbol, found null!
"

Discussion

  • Rajarshi Guha

    Rajarshi Guha - 2011-06-20

    I don't see the patch applied to cdk 1.4?

     
  • Egon Willighagen

    Correct. I left a comment in the patch report as to why...

     
  • Rajarshi Guha

    Rajarshi Guha - 2011-06-25

    Applied the patch, but is this correct? Isn't boron part of the orgnaic subset?

     
  • Egon Willighagen

    Yes, but I see that as a separate problem (and we have your patch in the pipeline for that). This lower casing happens not just for boron, but for any other element too, and the problem is more generic.

     

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