Yes, 5 should be the value for this
On Thu, Feb 11, 2016 at 12:57 PM, John M <john.wilkinson...@gmail.com>
wrote:
> Cheers for patch Rajarshi, added some clean up the code:
> https://github.com/cdk/cdk/pull/195 but get a test failure on,
> "CC=CC(C)=O" expected longest path is 6 but I get 5?
>
> 5 looks correct to me?
>
> John
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 11 February 2016 at 17:03, Rajarshi Guha <rajarshi.g...@gmail.com>
> wrote:
>
>> 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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>
--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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