It's a simple change but it makes sense to me a chain is length>1
John
Regards,
John W May
john.wilkinson...@gmail.com
On 18 February 2016 at 14:52, 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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