Very good! I'm happy to hear that.
Cheers
On Thu, Feb 18, 2016 at 6:44 PM, John M <john.wilkinson...@gmail.com> wrote:
> Hopefully soon, I'm in the process of moving house this/next month but one
> that's settled I'll make it ASAP.
>
> John
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 18 February 2016 at 16:40, Giovanni Cincilla <gcinci...@gmail.com>
> wrote:
>
>> Guys,
>> Thanks for your quick answers. More than quick they were in "real-time"!
>> Amazing ;-)
>> OK, so if we base on the Javadocs definition where "a chain exists only
>> if there are two or more atoms" then the current implementation is correct.
>> This is great as you solved all the inconsistencies I pointed out. Congrats!
>> Please, I would have one last question: do you have idea about when the
>> new official version (1.5.13) will be released?
>>
>>
>> On Thu, Feb 18, 2016 at 4:00 PM, Rajarshi Guha <rajarshi.g...@gmail.com>
>> wrote:
>>
>>> From the Javadocs, it says
>>>
>>> "Note that a chain exists if there are two or more atoms. Thus single
>>> atom molecules will return 0"
>>>
>>> So based on the definition, both your examples should have the value 0.
>>>
>>> I don't know if this is a descriptor implemented based on an official
>>> reference/description or whether this was custom designed by the author.
>>>
>>> In my mind, a chain should require >= 2 atoms and so the current values
>>> are correct.
>>>
>>> But happy to see what others think
>>>
>>> On Thu, Feb 18, 2016 at 9:52 AM, Giovanni Cincilla <gcinci...@gmail.com>
>>> wrote:
>>>
>>>> Hi guys,
>>>> I just had the possibility to test the corrected version. In general
>>>> the inconsistencies were solved, but I still have doubt.
>>>> Molecules from Row2 to Row8 now have all the correct values for
>>>> LargestChainDescriptor. Anyway I think that Row0 and Row1 molecules should
>>>> have (given its definition) a LargestChainDescriptor = 1 because they do
>>>> have one atom in a non cyclic system. In my opinion LargestChainDescriptor
>>>> should distinguish between these cases and those where no atoms are present
>>>> in non cyclic system. While with the current implementation seems it is not
>>>> possible to have a LargestChainDescriptor = 1.
>>>>
>>>> I my mind:
>>>>
>>>> 1. "Cc1nn(c(N)c1)-c2nc3c(s2)cccc3" should have a
>>>> LargestChainDescriptor = 1
>>>> 2. "s1c2c(cccc2)nc1-n3cccn3" should have a LargestChainDescriptor =
>>>> 0
>>>>
>>>>
>>>> What do you think about this? Do I am missing something?
>>>> Thanks in advance for your help and support.
>>>> Gio
>>>>
>>>> On Thu, Feb 11, 2016 at 4:47 PM, 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
>>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>
>>>
>>> --
>>> Rajarshi Guha | http://blog.rguha.net
>>> NIH Center for Advancing Translational Science
>>>
>>
>>
>>
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