Re: [Cdk-user] ICountFingerprint usage question

[John M <joh...@gm...>]

Unfortunately I don't think it's possible at the moment. The current
fingerprint API has

*Map<String,Int> getRawFingerprint
<http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/fingerprint/CircularFingerprinter.html#getRawFingerprint(org.openscience.cdk.interfaces.IAtomContainer)>*

Which some what fits with the lingos/path/smarts based fingerprints that
have string ready to hand (path is actually bad using strings) but not for
circular. Could do some sort of coding e.g. 'Idx:5,Rad:3' means atom at
index 5 encoded with radius 3. I've been thinking a better way to
associated hashed with substructures is by using the bond set.

*Map<Set<IBond>,Int> features;*

Another alternative is to use the signature fingerprint, that will
definitely provide the associations and should perform similarly to the
circular.

J

Regards,
John W May
joh...@gm...

On 3 February 2016 at 10:43, Nina Jeliazkova <jel...@gm...>
wrote:

> Hi John,
>
> Thanks!
>
> While on this, I am currently looking on how to extract the substructure
> patterns corresponding to the circular fingerprints hashes. Any chance if
> you already have thoughts on this ?   Supporting this on the interface
> level would be nice as well .  (I have a different use case and not
> particularly interested in the index building capabilities at the moment ).
>
> Best regards,
> Nina
>
>
>
>
>
> On 3 February 2016 at 12:17, John M <joh...@gm...> wrote:
>
>> Hi Nina,
>>
>> I think it's this:
>>
>>
>>>
>>>
>>>
>>>
>>> *ICountFingerprint fp;int numBins = fp.numOfPopulatedbins();for (int i =
>>> 0; i < numBins; i++) {  int hash = fp.getHash(i);  int freq =
>>> fp.getCount(i);}*
>>
>>
>> https://gist.github.com/johnmay/1cc17ff6280f308e015b
>>
>> On a side note this will likely change in the near future. I've ben
>> drafting/prototyping a new fingerprint API (nfp akin to nio in java) that
>> will hide some of this munging and make the abstractions better and more
>> efficient. You can see some early draft of my thoughts but nothing formal
>> yet: https://github.com/cdk/cdk/wiki/New-Fingerprint
>>
>> John
>>
>> Regards,
>> John W May
>> joh...@gm...
>>
>> On 3 February 2016 at 06:39, Nina Jeliazkova <jel...@gm...>
>> wrote:
>>
>>> Hello All,
>>>
>>> I am wondering what is the intended usage of the ICountFingerprint
>>> interface, and more specifically, how does one iterates over the available
>>> hashes using this interface.
>>>
>>> The obvious way of using the size() and for loop is impractical in cases
>>> as CircularFingerprint, where the size is declared = 4294967296l .  On the
>>> other hand the CircularFingerprint internal structure has all the
>>> information available in a more convenient way, but it is not accessible
>>> outside of the class.
>>>
>>> Any ideas? I am willing to provide a patch exposing the info in more
>>> convenient (sparse) way than ICountFingerprint, but not sure how it fits
>>> the CDK interfaces.
>>>
>>> Best regards,
>>> Nina
>>>
>>>
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>>
>