I wonder if we should simply write the original bond orders to CML instead of aromatic ones. Not sure how this is handled anyway? Does the CML written by this test have both (aromaticity flag as well as bond orders?) Did not have time to run it.
Cheers, Chris Egon Willighagen wrote: > On Friday 27 April 2007, Nina Jeliazkova wrote: >> Here is the story. >> 1) Create (somehow) a structure as IMolecule (e.g. benzene with >> alternating single/double bonds) >> 2) Run HueckelAromaticityDetector to perceive aromaticity >> 3) Write the structure into CML >> 4) Read the structure back from CML into a new IMolecule >> 5) Now the new IMolecule has bond orders 1.5 , while the origin one as in >> 1) has bond orders 1.0 and 2.0 > > Ah... that sounds like a bug. CDK in the early days used 1.5 bond order == an > aromatic bond, but drop that in favour of > IBond.setFlag(CDKConstancs.ISAROMATIC). Seems that the CMLReader has not been > updated. > >> This doesn't break isomorphism test and fingerprints, but does break atom >> types recognition as per HybridizationStateATMatcher. In this example, >> atom types of the original molecule will be C.sp2, while in the new >> molecule will be Caromatic.sp2. > > Atom type perception is a tricky thing indeed. What suprises me that the > first > type is not aromatic too! Because you did do atomiticity detection. Actually, > since the atom type list contains the the concept of aromaticity, it must be > done prior to calling the perception tool. Maybe a second bug? > >> Not sure this breaks anything else than my atom environments code, but I am >> wondering what's the best way to handle the issue. >> >> Attached is JUnit test. > > Thanx! I have filed it in the bug track system, so that it can soon be fixed > (by the first who has time for it). > > Egon > -- PD Dr. Christoph Steinbeck ([EMAIL PROTECTED]) Gastdozent für Chemieinformatik Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071-29-78978 Fax (+49/0) 7071-29-5091 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
