[OpenBabel-Devel] [ openbabel-Bugs-2033843 ] SMARTS "X" primitive is wrong for radicals

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Bugs item #2033843, was opened at 2008-07-31 13:04
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Category: None
Group: 2.2
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Stephen Pascoe (donquix2003)
Assigned to: Nobody/Anonymous (nobody)
Summary: SMARTS "X" primitive is wrong for radicals

Initial Comment:
According to the Daylight SMARTS website "[#6;X3v3+0]" should match a carbon radical.  (http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#RAD)

This doesn't work, instead the radical is treated as a connection:

$ echo 'C[CH2]' | babel -ismi -s'[#6;X3v3+0]' -osmi
0 molecules converted
12 audit log messages
$ echo 'C[CH2]' | babel -ismi -s'[#6;X4v4+0]' -osmi
C[CH2]
1 molecule converted
31 audit log messages

Similarly for the less constrained match "[#6;X3]"

$ echo 'C[CH2]' | babel -ismi -s'[#6;X3]' -osmi
0 molecules converted
12 audit log messages

I'd like to see this work consistently for heteroatoms too:

$ echo 'CCO[O]' | babel -ismi -s'[O;X1]' -osmi
0 molecules converted
18 audit log messages

Cheers,
Stephen.

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