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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>>>>>
>>>>>
>>>>
>>>
>>>
>>> --
>>> 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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