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