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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