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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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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>
>
> --
> Rajarshi Guha | http://blog.rguha.net
>
> NIH Center for Advancing Translational Science
>
>
>
>
> ------------------------------------------------------------------------------
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> 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
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--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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