[Cdk-devel] [ cdk-Bugs-716259 ] Wrong aromaticity detection

[SourceForge.net <no...@so...>]

Bugs item #716259, was opened at 2003-04-06 18:53
Message generated for change (Comment added) made by steinbeck
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=120024&aid=716259&group_id=20024

Category: None
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Submitted By: Christoph Steinbeck (steinbeck)
Assigned to: Christoph Steinbeck (steinbeck)
Summary: Wrong aromaticity detection

Initial Comment:
Once again a bug in the aromaticity detection. 

In the molecule

7-Hydroxy-2-methoxy-1,4-phenanthrenedione; Densiflorol

B; from www.nmrshiftdb.org the the quinone ring is

detected as aromatic.

----------------------------------------------------------------------

>Comment By: Christoph Steinbeck (steinbeck)
Date: 2003-09-03 10:39

Message:
Logged In: YES 
user_id=54358

This is fixed. A test was added for that.

----------------------------------------------------------------------

Comment By: Kai Hartmann (kaihartmann)
Date: 2003-08-20 14:41

Message:
Logged In: YES 
user_id=743500

Fix has been commited.

To do:



- Add additional tests for more complex ringsystems

- Write API docu

----------------------------------------------------------------------

Comment By: Kai Hartmann (kaihartmann)
Date: 2003-06-13 10:05

Message:
Logged In: YES 
user_id=743500

Before we forget it, some bugfixes:



AromaticityCalculator 1.5:

(77) if (bond.getOrder() == 2 && ring.contains(bond))

lines 91-95 should be placed after line 86



HueckelAromaticityDetector 1.13:

(104) INSERT: ring.setFlag(CDKConstants.ISAROMATIC, true);

method isAromatic is obsolete because whole ringsystem of

molecule has to be checked. Use ring-flags instead.



HueckelAromaticityDetectorTest 1.8:

Revise porphyrin test at positions 15 & 19;

add test for quinone



Still, the aromaticity test doesn't work. Maybe a

fundamentally other algorithm has to be found that checks

each separate ringsystem.

----------------------------------------------------------------------

Comment By: Christoph Steinbeck (steinbeck)
Date: 2003-04-08 13:51

Message:
Logged In: YES 
user_id=54358

Here's another one:

Interiotherin D

In this molecule, the dioxo ring is falsly detected as aromatic.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=120024&aid=716259&group_id=20024