you can ignore the patch since I've just made a pull request with this fix
On Thu, Feb 11, 2016 at 10:47 AM, Rajarshi Guha <rajarshi.g...@gmail.com>
wrote:
> 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
>>>>
>>>>
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>>>
>>>
>>> --
>>> Rajarshi Guha | http://blog.rguha.net
>>> NIH Center for Advancing Translational Science
>>>
>>
>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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