OK, thank you for the clarification!
Cheers
On Fri, Feb 12, 2016 at 8:52 PM, John M <john.wilkinson...@gmail.com> wrote:
> Hi Gio,
>
> Next release is 1.5.13. Probably do it soon, not a huge number of changes
> but I know a few patches people are waiting (this now being added as one of
> them).
>
> Please can you also confirm me that the purpose
>> of the LargestChainDescriptor is to provide the longest path that contains
>> non-aromatic, non-ring atoms?
>
>
> Yes... but it now no longer checks aromaticity. Since an atom is only
> aromatic if it's in a ring we just need to check the non-ring atoms.
>
> John
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 12 February 2016 at 19:20, Giovanni Cincilla <gcinci...@gmail.com>
> wrote:
>
>> Very good guys! You are great. So I suppose the bug-free version will be
>> available in the next CDK release, isn't it? Can you please me specify
>> which version it will be?
>> Please can you also confirm me that the purpose
>> of the LargestChainDescriptor is to provide the longest path that contains
>> non-aromatic, non-ring atoms? In other words: should the parameter
>> *checkRingSystem* always be set = true in this description. I'm asking
>> you this because it seems that in the current KNIME-CDK version this is
>> currently not the case.
>> Thank you in advance for your feedback!
>> Gio
>>
>> On Thu, Feb 11, 2016 at 7:10 PM, Rajarshi Guha <rajarshi.g...@gmail.com>
>> wrote:
>>
>>> well the first looks at all atoms, the other only considers carbon
>>> chains.
>>>
>>> I'd say keep them both in for now (though the first could be
>>> parametrized on element, in which case we'd only need one)
>>>
>>> On Thu, Feb 11, 2016 at 1:06 PM, John M <john.wilkinson...@gmail.com>
>>> wrote:
>>>
>>>> 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
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> 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
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>>>>>>> _______________________________________________
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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
>>>
>>
>>
>
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