Rendering/layout fails.

[Saurabh Srivastava]

Hi Indigo Dev:

I have a complicated reaction that I am rendering, but it fails with a "com.ggasoftware.indigo.IndigoException: layout_graph: attaching cycle with only one vertex drawn" on calling layout. The SMILES output by reaction.smiles() is pasted below.

Could you please advise on what the potential cause is?

To add to the details: If I copy paste this smile and attempt to render in a unit test: it passes! On the other hand, within the larger code (which does a loadReaction -> automap -> unfoldHydrogens -> setAtomMappingNumber on some unmapped atoms -> layout ) the rendering fails. So it is not a trivial example to debug, but I am hoping that the source that outputs the exception above will give some insights.

Thanks a lot.

Saurabh 

[H+:122].O=O.[C:4]([H:96])([H:95])([H:94])[C:5]([O:7][C:8]1([H:93])[C:21]23[C:22]([H:90])([H:89])[C:23]4([H:91])[N:24]5[C:25]([H])([H:97])/[C:26](=[C:27](\[H:80])/[C:28]([H:79])([H:78])[H:77])/[C:10]([H:81])([C:11]([H:83])([H:82])[C:12]5([H:84])[C:13]2=[N:14][C:15]2[C:20]3=[C:19]([H:88])[C:18]([H:87])=[C:17]([H:86])[C:16]=2[H:85])[C:9]14[H:92])=[O:6].C1([H])([H])C(C(N([H])[H])=[O:36])=C([H])[N:98]([C:38]2([H:99])[O:42][C:41]([H:102])([C:43]([H:104])([H:103])[O:44][P:45]([O:48][P:49]([O:52][C:53]([H:108])([H:107])[C:54]3([H:109])[O:58][C:57]([H:112])([N:59]4[C:63]5[N:64]=[C:65]([H:114])[N:66]=[C:67]([N:68]([H:116])[H:115])[C:62]=5[N:61]=[C:60]4[H:113])[C:56]([H:111])([O:69][P:70]([O:73][H:117])([O:72][H:118])=[O:71])[C:55]3([H:110])[O:74][H:119])([O:51][H:106])=[O:50])([O:47][H:105])=[O:46])[C:40]([H:101])([O:75][H:120])[C:39]2([H:100])[O:76][H:121])C([H])=C1[H]>>[O:6]([H])[H:122].[C:28]([H:79])([H:78])([H:77])[C:27]([H:80])=[C:26]1[C:25]([H:97])([O:36][H])[N:24]2[C:12]3([H:84])[C:13]4[C:21]5([C:8]([H:93])([O:7][C:5]([C:4]([H:96])([H:95])[H:94])=[O:6])[C:9]([H:92])([C:10]1([H:81])[C:11]3([H:83])[H:82])[C:23]2([H:91])[C:22]5([H:90])[H:89])[C:20]1[C:15](=[C:16]([H:85])[C:17]([H:86])=[C:18]([H:87])[C:19]=1[H:88])[N:14]=4.[C:21]1([H])[C:20]([H])=[N+:98]([C:38]2([H:99])[O:42][C:41]([H:102])([C:43]([H:104])([H:103])[O:44][P:45]([O:48][P:49]([O:52][C:53]([H:108])([H:107])[C:54]3([H:109])[O:58][C:57]([H:112])([N:59]4[C:63]5[N:64]=[C:65]([H:114])[N:66]=[C:67]([N:68]([H:116])[H:115])[C:62]=5[N:61]=[C:60]4[H:113])[C:56]([H:111])([O:69][P:70]([O:72][H:118])([O:73][H:117])=[O:71])[C:55]3([H:110])[O:74][H:119])([O:51][H:106])=[O:50])([O:47][H:105])=[O:46])[C:40]([H:101])([O:75][H:120])[C:39]2([H:100])[O:76][H:121])[C:10]([H])=[C:9]([C:23]([N:24]([H])[H])=O)[C:8]=1[H]

Exception in thread "main" com.ggasoftware.indigo.IndigoException: layout_graph: attaching cycle with only one vertex drawn

at com.ggasoftware.indigo.Indigo.checkResult(Indigo.java:62)

at com.ggasoftware.indigo.IndigoObject.layout(IndigoObject.java:1030)

[Mikhail Rybalkin]

Hello Saurabh,

Thank you for this bug report! We have fixed this issue and you can download the latest version of Indigo from our website.

Best regards,

Mikhail

[Saurabh Srivastava]

That is great Mikhail!

Thanks for fixing this. I will let you how it works when I try it out.

Saurabh