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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