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Noel,
Thank you for your email. I appreciate your help on this.
Let me start with a little more background on the problem. I am using Pybel to extract the information I need about a set of ~875 PAH molecules (including alkyl substituted and radical PAHs). I gave the openbabel molreport output in my email as it shows the problem and is easier to reproduce. I am attaching an archive containing 8 molecules that we have found are not correctly identified by openbabel. The "signature" of an error is typically that a C atom is labelled as sp3 hybridized when it only has three atoms attached. (I have since learned that I can correct the labeling of one of the molecules by reordering the C atoms.)
In the attached archive (test.tar.bz2) are the 8 molecules in Xmol format and a file called output. The output file contains the results of my python code to extract information on the C atoms in the molecules. I have labelled the errors in the file.
I have worked quite a bit with two of the molecules, azulene and 2175908. I have tried to reorder the atoms, convert to 2d, create a mol file using openbabel, remove hydrogens and then convert to 2d, etc. None of these things has helped. However, when I create the same molecule in ChemDraw, openbabel does label the aromaticity correctly.
I hope that all of this is clear and helpful in creating a clear bug report. Again, I am very grateful for your help. Please feel free to email me if I can be of any further assistance.
Best,
Tom |
test.tar.bz2
Description: BZip2 compressed data
On Apr 10, 2012, at 8:25 AM, Noel O'Boyle wrote: As you've found, the aromacticity detection algorithm is not 100% foolproof. If you could collect samples of failure, I'll file a bug report on your behalf.
- Noel
On 6 April 2012 22:30, Tom Allison <thomas.alli...@nist.gov> wrote:
Hi all:
When I use the following file named ("2175908.xyz")
32
C -0.0000291523 0.3160533892 0.0000391375
C -0.0001205266 1.6897724142 -0.0000354856
C -1.1476732403 2.5783557540 -0.2608024912
C -0.7134957259 3.8662394928 -0.1740293423
C 0.7129989228 3.8663434783 0.1737218341
C 1.1473141698 2.5785212088 0.2606887592
C -1.2644704298 -0.4669809214 -0.0452676405
C -1.3842734724 -1.5748302555 -0.9092111725
C -2.5671655274 -2.3121439686 -0.9674254281
C -3.6482201199 -1.9753081246 -0.1450833664
C -3.5369915676 -0.8931744203 0.7330960347
C -2.3586383931 -0.1441061301 0.7818485083
C 1.2645222956 -0.4667992671 0.0453076719
C 1.3845170526 -1.5745972058 0.9092922448
C 2.5675194722 -2.3117317314 0.9675038733
C 3.6485034257 -1.9747635145 0.1451230867
C 3.5370868080 -0.8926841387 -0.7330993315
C 2.3586202924 -0.1437917456 -0.7818487405
H -2.1411960222 2.2431146601 -0.5485969616
H 2.1408663145 2.2434246253 0.5485503630
H -0.5431393751 -1.8455762282 -1.5506763815
H -2.2681816578 0.6873079580 1.4827257348
H 0.5434416788 -1.8454371687 1.5507951627
H 2.2680166731 0.6875666639 -1.4827732159
H -1.3135614066 4.7603046291 -0.3472070119
H 1.3129633051 4.7604990947 0.3467837936
H -2.6449018560 -3.1564972331 -1.6566520117
H -4.3702438297 -0.6335492646 1.3906685655
H 2.6454009422 -3.1560463895 1.6567616751
H 4.3702800277 -0.6329621345 -1.3907082265
H -4.5706652438 -2.5597893522 -0.1828188830
H 4.5710368348 -2.5591054801 0.1828592980
with the command "obabel 2175908.xyz -o molreport" I get the following output
TITLE: 2175908.xyz
FORMULA: C18H14
MASS: 230.3038
ATOM: 1 C TYPE: C2 HYB: 2 CHARGE: -0.0323
ATOM: 2 C TYPE: C2 HYB: 2 CHARGE: -0.0234
ATOM: 3 C TYPE: C2 HYB: 2 CHARGE: -0.0546
ATOM: 4 C TYPE: C2 HYB: 2 CHARGE: -0.0612
ATOM: 5 C TYPE: C2 HYB: 2 CHARGE: -0.0612
ATOM: 6 C TYPE: C2 HYB: 2 CHARGE: -0.0546
ATOM: 7 C TYPE: C3 HYB: 3 CHARGE: 0.0461
ATOM: 8 C TYPE: C2 HYB: 2 CHARGE: -0.0720
ATOM: 9 C TYPE: C2 HYB: 2 CHARGE: -0.0791
ATOM: 10 C TYPE: C3 HYB: 3 CHARGE: 0.0049
ATOM: 11 C TYPE: C2 HYB: 2 CHARGE: -0.0791
ATOM: 12 C TYPE: C2 HYB: 2 CHARGE: -0.0720
ATOM: 13 C TYPE: C3 HYB: 3 CHARGE: 0.0461
ATOM: 14 C TYPE: C2 HYB: 2 CHARGE: -0.0720
ATOM: 15 C TYPE: C2 HYB: 2 CHARGE: -0.0791
ATOM: 16 C TYPE: C3 HYB: 3 CHARGE: 0.0049
ATOM: 17 C TYPE: C2 HYB: 2 CHARGE: -0.0791
ATOM: 18 C TYPE: C2 HYB: 2 CHARGE: -0.0720
ATOM: 19 H TYPE: HC HYB: 0 CHARGE: 0.0623
ATOM: 20 H TYPE: HC HYB: 0 CHARGE: 0.0623
ATOM: 21 H TYPE: HC HYB: 0 CHARGE: 0.0581
ATOM: 22 H TYPE: HC HYB: 0 CHARGE: 0.0581
ATOM: 23 H TYPE: HC HYB: 0 CHARGE: 0.0581
ATOM: 24 H TYPE: HC HYB: 0 CHARGE: 0.0581
ATOM: 25 H TYPE: HC HYB: 0 CHARGE: 0.0618
ATOM: 26 H TYPE: HC HYB: 0 CHARGE: 0.0618
ATOM: 27 H TYPE: HC HYB: 0 CHARGE: 0.0575
ATOM: 28 H TYPE: HC HYB: 0 CHARGE: 0.0575
ATOM: 29 H TYPE: HC HYB: 0 CHARGE: 0.0575
ATOM: 30 H TYPE: HC HYB: 0 CHARGE: 0.0575
ATOM: 31 H TYPE: HC HYB: 0 CHARGE: 0.0394
ATOM: 32 H TYPE: HC HYB: 0 CHARGE: 0.0394
BOND: 0 START: 27 END: 9 ORDER: 1
BOND: 1 START: 21 END: 8 ORDER: 1
BOND: 2 START: 24 END: 18 ORDER: 1
BOND: 3 START: 30 END: 17 ORDER: 1
BOND: 4 START: 9 END: 8 ORDER: 2
BOND: 5 START: 9 END: 10 ORDER: 1
BOND: 6 START: 8 END: 7 ORDER: 1
BOND: 7 START: 18 END: 17 ORDER: 2
BOND: 8 START: 18 END: 13 ORDER: 1
BOND: 9 START: 17 END: 16 ORDER: 1
BOND: 10 START: 19 END: 3 ORDER: 1
BOND: 11 START: 25 END: 4 ORDER: 1
BOND: 12 START: 3 END: 4 ORDER: 2
BOND: 13 START: 3 END: 2 ORDER: 1
BOND: 14 START: 31 END: 10 ORDER: 1
BOND: 15 START: 4 END: 5 ORDER: 1
BOND: 16 START: 10 END: 11 ORDER: 1
BOND: 17 START: 7 END: 1 ORDER: 1
BOND: 18 START: 7 END: 12 ORDER: 1
BOND: 19 START: 2 END: 1 ORDER: 2
BOND: 20 START: 2 END: 6 ORDER: 1
BOND: 21 START: 1 END: 13 ORDER: 1
BOND: 22 START: 13 END: 14 ORDER: 1
BOND: 23 START: 16 END: 32 ORDER: 1
BOND: 24 START: 16 END: 15 ORDER: 1
BOND: 25 START: 5 END: 6 ORDER: 2
BOND: 26 START: 5 END: 26 ORDER: 1
BOND: 27 START: 6 END: 20 ORDER: 1
BOND: 28 START: 11 END: 12 ORDER: 2
BOND: 29 START: 11 END: 28 ORDER: 1
BOND: 30 START: 12 END: 22 ORDER: 1
BOND: 31 START: 14 END: 15 ORDER: 2
BOND: 32 START: 14 END: 23 ORDER: 1
BOND: 33 START: 15 END: 29 ORDER: 1
The carbon atoms in the two benzene rings should be labelled aromatic.
Can anyone explain why these carbons are not correctly labeled. Note that I have converted a number of similar molecules, and I have only a few cases where the assignment of aromaticity is incorrect.
Thanks in advance,
Tom
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