[Cdk-devel] [ cdk-Patches-3554480 ] Extended Nplanar3 perception

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Patches item #3554480, was opened at 2012-08-05 02:33
Message generated for change (Comment added) made by egonw
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Category: cdk-1.4.x
>Group: Needs Revision
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: John May (jwmay)
Assigned to: Nobody/Anonymous (nobody)
Summary: Extended Nplanar3 perception

Initial Comment:
Patch from Stephan Biesken - posted on cdk-devel:

...

The reason why the atom perception fails is because, in this particular case, it relies on aromaticity flags being already perceived for the atom bonds, which we get automatically from reading a SDF with bond order 4. The algorithm then checks the implicit hydrogen count and defaults (null) to N.sp2, which is incorrect. Obviously this issue can be solved with a few lines of code (patch attached, please review).

...

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>Comment By: Egon Willighagen (egonw)
Date: 2012-08-05 02:43

Message:
These nitrogens are indeed very difficult... I need to see a unit test,
with a small(-est possible) structure with the N.planar3 which fails and
find N.sp2 instead...

Also, it is not clear to my why the if clause checks if there is a charge
value set, but not actually tests what the charge is...

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