Yes, it does appear to be a bug. Inspeting the code the LargestChainDescriptor is looking for the longest path that contains non-aromatic, non-ring atoms.
For Row0, there are only two non-ring, non-aromatic atoms and so there are two possible chains with a single atom, hence each chain has the value of 0. For Row2, the longest chain according to the definition is the C#N substructure, hence the value should be 2 For Row5 and Row6, the values should also be 2. I've attached a patch against master that fixes this (I wasn't sure how to make a pull request from a local branch) On Thu, Feb 11, 2016 at 7:50 AM, Giovanni Cincilla <gcinci...@gmail.com> wrote: > Thank you for your quick reply. > Examples are provided in the original KNIME forum thread ( > https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502), > anyway I can report those here: > > 2. In some cases terminal atoms seems not to be counted as part of the > largest chain LC (LC Row0 = 0; LC Row2 = 1), while in other cases they are > (LC Row5 = 2; LC Row6 =2). > 3. In some cases iso terminal groups are countes as 2 (Row4) while in > other cases are counted as 3 (Row8). > > *Molecules:* > "Row0","Cc1nn(c(c1)N)c1nc2c(s1)cccc2" > "Row1","Clc1cnn(c(=O)c1Cl)Cc1[nH]c(=O)c2c(n1)c1ccccc1o2" > "Row2","Nc1c(cn[nH]1)C#N" > "Row3","Fc1ccc(cc1)C(=O)c1ccc(cc1)Oc1ncc(cn1)Br" > "Row4","[O-][n+]1ccc(cc1)[N+](=O)[O-]" > "Row5","OCc1ccccc1CN" > "Row6","COc1ccc(cc1)c1noc(c1)Cn1nc(C)c(c(c1=O)C#N)C" > "Row7","Cc1nc(SCc2nc3ccsc3c(=O)[nH]2)c2c(n1)scc2c1cccs1" > "Row8","CC(=O)c1cccc(c1)Nc1nc(nc2c1cccc2)c1cccnc1" > > I hope the examples are quite clear. > > On Thu, Feb 11, 2016 at 1:18 PM, Rajarshi Guha <rajarshi.g...@gmail.com> > wrote: > >> Could you provide an example where issues 2 & 3 show up? >> >> The descriptor is meant to compute the length of the longest aliphatic >> chain in a molecule >> >> On Thu, Feb 11, 2016 at 4:29 AM, Giovanni Cincilla <gcinci...@gmail.com> >> wrote: >> >>> Dear all, >>> I use CDK mainly through KNIME and I found some supposed inconsistencies >>> using the LargestChainDescriptor. I originally posted my doubt in KNIME-CDK >>> forum where I also provided examples: >>> >>> >>> https://tech.knime.org/forum/cdk/cdk-largest-chain-descriptor-inconsistencies#comment-41502 >>> >>> I'm not sure about the purpose of such descriptor. Essentially my doubts >>> are the following: >>> >>> 1. The LargestChainDescriptor count atoms that belong to aliphatic >>> rings. Is that correct or it is a bug? The word "chain" in my opinion can >>> seems opposed to the word "ring". >>> 2. In some cases terminal atoms seems not to be counted as part of >>> the largest chain, while in other cases they are. >>> 3. In some cases iso terminal groups are counted as 2 while in other >>> cases are counted as 3 >>> 4. Atoms between rings in some case to be correctly counted, while >>> in other cases they are not >>> >>> Please, can anybody provide some clarification about these issues? >>> Thanks, >>> Gio >>> >>> >>> ------------------------------------------------------------------------------ >>> Site24x7 APM Insight: Get Deep Visibility into Application Performance >>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month >>> Monitor end-to-end web transactions and take corrective actions now >>> Troubleshoot faster and improve end-user experience. Signup Now! >>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >>> _______________________________________________ >>> Cdk-user mailing list >>> Cdk-user@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >>> >> >> >> -- >> Rajarshi Guha | http://blog.rguha.net >> NIH Center for Advancing Translational Science >> > > -- Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science
0001-Ensure-that-we-reset-visited-flag-each-time-we-start.patch
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