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
>>
>>
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>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
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