bug or difference in aromaticringcount

Hi,

I have molecules which are reported in a column all with aromaticringcount = 3

however If I run cxcalc some of them have 1 and some have 3

Also if I double click to open the molecule and perform a topology analysis, some of them

have 3 and some of them have 1.

Tobias

aromaticringcount Instant-JCHEM (last 4 mols)

O\N=C1/N2C=CN(C=C2)C1=O 3
OC(=O)C1=NN2C=CN1C=C2 3
CC1=NN2C=CN1C(=O)C2=O 3
C\N=C1/OC2=CN=C1C(=N)O2 3

CXCALC aromaticringcount (last 4 mols)

2200 1
2201 3
2202 1
2203 3

Instant JChem Version: 2.4.3.1 (build: 090319)
JChem Version: 5.2.0
JChem Table Version: 5020005
Marvin Version: 5.2.0 (build date: 2009-03-11)
Java: 1.6.0_10-beta; Java HotSpot(TM) Client VM 11.0-b12
System: Windows XP version 5.1 running on x86; Cp1252; en_US (instantjchem)
NetBeans build: 200711261600

Hi,

that bug or calc error seems to be solved with the 2.5 update,

but still assuming that the versions before were stable versions its abit mindboggling.

I am also not updating to every new IJChem version, never change a a running system,

 

Another problem was that certain calculations (Dreiding) failed or did not update the values in the column, that seems to be resolved with the current version too.

Another remark, just for the records is, that having field names (aromaticbondcount etc) in the sdf file during import seems to update the calculations. That makes the import very slow. Not sure if this is a bug or feature. I would rather import as static field and do the calculation inside. But thats debatable.

Cheers

Tobias

 

OK, please let us know if there is still a problem with the aromaticringcount.

During import values in the file are just imported as they are. No values will be recalculated. THis only happens when you specifically add a chemical terms column.

Tim

TobiasKind wrote:

Hi, I have molecules which are reported in a column all with aromaticringcount = 3 however If I run cxcalc some of them have 1 and some have 3

It seems the calculation gives different results if the molecules are aromatized (IJC performs the calculations on the standardized molecules).

JChem 5.2

$ standardize -c aromatize c6h5n3o2-130k-ARATICRINGCOUNT3-PROBLEM.sdf | cxcalc aromaticringcount | tail -n 4
2200 3
2201 3
2202 3
2203 3

$ cxcalc aromaticringcount c6h5n3o2-130k-AROMATICRINGCOUNT3-PROBLEM.sdf | tail -n 4
2200 1
2201 3
2202 1
2203 3

JChem 5.2.2

$ standardize -c aromatize c6h5n3o2-130k-AROMATICRINGCOUNT3-PROBLEM.sdf | cxcalc aromaticringcount | tail -n 4
2200 0
2201 3
2202 1
2203 0

$ cxcalc aromaticringcount c6h5n3o2-130k-AROMATICRINGCOUNT3-PROBLEM.sdf | tail -n 4
2200 1
2201 3
2202 1
2203 3

We will fix these bugs.

Zsolt

Thank you.

There was another related topic in the cxcalc forum;

http://www.chemaxon.com/forum/ftopic4915.html

 

Tobias

 

This was fixed in IJC 5.3.1. See the link above for more details.

Filip