Hmm.. should we deprecate one of LargestChainDescriptor
or LongestAliphaticChainDescriptor? Same purpose as far as I can set.
John
Regards,
John W May
john.wilkinson...@gmail.com
On 11 February 2016 at 17:58, Rajarshi Guha <rajarshi.g...@gmail.com> wrote:
> 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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