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
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> 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
>>>>>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>>>>>> _______________________________________________
>>>>>>> Cdk-user mailing list
>>>>>>> Cdk-user@lists.sourceforge.net
>>>>>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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
>>> Troubleshoot faster and improve end-user experience. Signup Now!
>>> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
>>> _______________________________________________
>>> Cdk-user mailing list
>>> Cdk-user@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>>>
>>
>>
>> --
>> 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
> Troubleshoot faster and improve end-user experience. Signup Now!
> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
> _______________________________________________
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
------------------------------------------------------------------------------
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
Troubleshoot faster and improve end-user experience. Signup Now!
http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
