Okay,
Hmm - I didn’t think UIT would choose one structure as a base, cool. Anyways,
as the only difference is the H’s you could add hydrogens (i.e. atom type +
CDKHydrogenManipulator) to make them the same.
J
On 19 Feb 2014, at 15:02, Rajarshi Guha <gu...@mail.nih.gov> wrote:
> Yes, it's the same set of heavy atoms and switching the target and query does
> give the other MCS based on the query molecule.
>
> Using the UIT gives me [CH2]CNC independent of the order of the target and
> query molecules
>
>
> On Wed, Feb 19, 2014 at 9:52 AM, John May <john...@ebi.ac.uk> wrote:
> It’s now an instance class - not sure why though as it was before I started
> contributing. I think it’s to do with the timeout.
>
>> UniversalIsomorphismTester.getOverlaps uit = new
>> UniversalIsomorphismTester();
>> uit.getOverlaps(...);
>
>
> Also, ‘Pattern’ is for substructure/identity checking.
>
> Just looking at this again, N([CH2])CC and [CH2]CN[CH2] are same heavy atoms
> right? The different is one is from the query and one is from the target
> (i.e. hydrogen counts from truncated part).
>
> J
>
> On 19 Feb 2014, at 14:48, Rajarshi Guha <gu...@mail.nih.gov> wrote:
>
>> No I haven't tried with the UIT. How does that work in the latest CDK?
>> UniversalIsomorphismTester.getOverlaps no longer exists (?)
>>
>>
>> On Wed, Feb 19, 2014 at 9:36 AM, John May <john...@ebi.ac.uk> wrote:
>> Do you get the correct answer with the UIT?
>>
>> The SMSD code hasn’t been maintained in a long time and I’ve seen quite a
>> few bugs.
>>
>> J
>>
>> On 19 Feb 2014, at 14:06, Rajarshi Guha <gu...@mail.nih.gov> wrote:
>>
>>> Hi, I'm using the latest master and have a question about an MCS
>>> calculation. Given the two molecules CCCNCC & CNCCS the MCS returned is
>>> N([CH2])CC which is correct. But it could also have been [CH2]CN[CH2]
>>>
>>> The code to get the MCS is getMcsAsNewContainer in
>>> https://github.com/rajarshi/cdkr/blob/master/rcdkjar/src/org/guha/rcdk/util/Misc.java
>>>
>>> Given that various permutations of the SMILES lead to the same MCS, I
>>> assume there is some deterministic rule being used. is that correct?
>>>
>>> --
>>> Rajarshi Guha | http://blog.rguha.net
>>>
>>> NIH Center for Advancing Translational Science
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>>
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>> Rajarshi Guha | http://blog.rguha.net
>>
>> NIH Center for Advancing Translational Science
>
>
> ------------------------------------------------------------------------------
> Managing the Performance of Cloud-Based Applications
> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
> Read the Whitepaper.
> http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
> _______________________________________________
> Cdk-user mailing list
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>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
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