Re: [Cdk-user] Raw fingerprints impossible to calculate

[John Mayfield]

Okay looking at it the Substructure fingerprint would be easy to adapt...
but it's not hard to just count the substructures. Utility code like that
is difficult to justify, every line is more to maintain.

The other problem is I don't like the fingerprint APIs so it's a toss-up
between using effort to implement something I (or hopefully someone else)
will ultimately rewrite in future. "Deprecated on arrival" I believe Egon
has said before.

On Fri, 21 Feb 2020 at 18:25, John Mayfield 
wrote:

> What do you think the "raw" fingerprint is? Why would you expect it for
> the Substructure one?
>
> On Fri, 21 Feb 2020 at 09:47, Maria Sorokina 
> wrote:
>
>> I tried in total 7 fingerprinters (PubChem, Substructure, MACCS,
>> KlekotaRoth, Circular, ShortestPath and Hybrifization) and none worked. For
>> some, I’m not surprised, but I was really expecting to have the raw
>> fingerprints for the Substructure one
>>
>>
>> Dr. Maria Sorokina
>> Steinbeck Research Group
>> Analytical Chemistry - Cheminformatics and Chemometrics
>> Friedrich-Schiller-University Jena, Germany
>> http://cheminf.uni-jena.de
>>
>> Le 21 févr. 2020 à 10:39, John Mayfield  a
>> écrit :
>>
>> ... I do have some patches for an updated fingerprint API stack that
>> would also add this in to more places. Essentially it was added to the
>> public API but only implemented in a few places and left as a "ToDo"
>> elsewhere. Might be something for the hack-a-thon.
>>
>> I should PubChem fingerprints are binary in nature though so you would
>> probably never want the RAW version. *getBitFingerprint()* it
>> implemented always.
>>
>> John
>>
>> On Fri, 21 Feb 2020 at 09:34, John Mayfield 
>> wrote:
>>
>>> Hi Maria,
>>>
>>> Not all fingerprint support the "RAW" option and Count options.
>>>
>>> John
>>>
>>> On Fri, 21 Feb 2020 at 09:31, Maria Sorokina 
>>> wrote:
>>>
 Dear community,

 It is decidedly substructure search and fingerprinting period of the
 year!

 I want to create (to store) raw fingerprints of a range of different
 fingerprint types for a big number of complex molecules (natural products).

 For example this:

 PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( 
 SilentChemObjectBuilder.getInstance() );

 System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer));

 For all my molecules I am getting an" UnsupportedOperationException",
 which according to the documentation reflects only the fact that the 
 fingerprinter
 cannot produce the raw fingerprint.
 I am using the latest (2.3) version of the CDK.
 Can anybody help me with this issue?


 Kind regards,
 Maria


 Dr. Maria Sorokina
 Steinbeck Research Group
 Analytical Chemistry - Cheminformatics and Chemometrics
 Friedrich-Schiller-University Jena, Germany
 http://cheminf.uni-jena.de

 ___
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 Cdk-user@lists.sourceforge.net
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>>>
>>
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Re: [Cdk-user] Raw fingerprints impossible to calculate

[John Mayfield]

What do you think the "raw" fingerprint is? Why would you expect it for the
Substructure one?

On Fri, 21 Feb 2020 at 09:47, Maria Sorokina 
wrote:

> I tried in total 7 fingerprinters (PubChem, Substructure, MACCS,
> KlekotaRoth, Circular, ShortestPath and Hybrifization) and none worked. For
> some, I’m not surprised, but I was really expecting to have the raw
> fingerprints for the Substructure one
>
>
> Dr. Maria Sorokina
> Steinbeck Research Group
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> http://cheminf.uni-jena.de
>
> Le 21 févr. 2020 à 10:39, John Mayfield  a
> écrit :
>
> ... I do have some patches for an updated fingerprint API stack that would
> also add this in to more places. Essentially it was added to the public API
> but only implemented in a few places and left as a "ToDo" elsewhere. Might
> be something for the hack-a-thon.
>
> I should PubChem fingerprints are binary in nature though so you would
> probably never want the RAW version. *getBitFingerprint()* it implemented
> always.
>
> John
>
> On Fri, 21 Feb 2020 at 09:34, John Mayfield 
> wrote:
>
>> Hi Maria,
>>
>> Not all fingerprint support the "RAW" option and Count options.
>>
>> John
>>
>> On Fri, 21 Feb 2020 at 09:31, Maria Sorokina 
>> wrote:
>>
>>> Dear community,
>>>
>>> It is decidedly substructure search and fingerprinting period of the
>>> year!
>>>
>>> I want to create (to store) raw fingerprints of a range of different
>>> fingerprint types for a big number of complex molecules (natural products).
>>>
>>> For example this:
>>>
>>> PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( 
>>> SilentChemObjectBuilder.getInstance() );
>>>
>>> System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer));
>>>
>>> For all my molecules I am getting an" UnsupportedOperationException",
>>> which according to the documentation reflects only the fact that the 
>>> fingerprinter
>>> cannot produce the raw fingerprint.
>>> I am using the latest (2.3) version of the CDK.
>>> Can anybody help me with this issue?
>>>
>>>
>>> Kind regards,
>>> Maria
>>>
>>>
>>> Dr. Maria Sorokina
>>> Steinbeck Research Group
>>> Analytical Chemistry - Cheminformatics and Chemometrics
>>> Friedrich-Schiller-University Jena, Germany
>>> http://cheminf.uni-jena.de
>>>
>>> ___
>>> Cdk-user mailing list
>>> Cdk-user@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>>
>
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Re: [Cdk-user] Raw fingerprints impossible to calculate

[Maria Sorokina]

I tried in total 7 fingerprinters (PubChem, Substructure, MACCS, KlekotaRoth, 
Circular, ShortestPath and Hybrifization) and none worked. For some, I’m not 
surprised, but I was really expecting to have the raw fingerprints for the 
Substructure one


Dr. Maria Sorokina
Steinbeck Research Group
Analytical Chemistry - Cheminformatics and Chemometrics
Friedrich-Schiller-University Jena, Germany
http://cheminf.uni-jena.de

> Le 21 févr. 2020 à 10:39, John Mayfield  a écrit 
> :
> 
> ... I do have some patches for an updated fingerprint API stack that would 
> also add this in to more places. Essentially it was added to the public API 
> but only implemented in a few places and left as a "ToDo" elsewhere. Might be 
> something for the hack-a-thon.
> 
> I should PubChem fingerprints are binary in nature though so you would 
> probably never want the RAW version. getBitFingerprint() it implemented 
> always.
> 
> John
> 
> On Fri, 21 Feb 2020 at 09:34, John Mayfield  > wrote:
> Hi Maria,
> 
> Not all fingerprint support the "RAW" option and Count options.
> 
> John
> 
> On Fri, 21 Feb 2020 at 09:31, Maria Sorokina  > wrote:
> Dear community,
> 
> It is decidedly substructure search and fingerprinting period of the year!
> 
> I want to create (to store) raw fingerprints of a range of different 
> fingerprint types for a big number of complex molecules (natural products).
> 
> For example this:
> PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( 
> SilentChemObjectBuilder.getInstance() );
> System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer));
> For all my molecules I am getting an" UnsupportedOperationException", which 
> according to the documentation reflects only the fact that the fingerprinter 
> cannot produce the raw fingerprint.
> I am using the latest (2.3) version of the CDK. 
> Can anybody help me with this issue?
> 
> 
> Kind regards,
> Maria
> 
> 
> Dr. Maria Sorokina
> Steinbeck Research Group
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> http://cheminf.uni-jena.de 
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net 
> https://lists.sourceforge.net/lists/listinfo/cdk-user 
> 

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Re: [Cdk-user] Raw fingerprints impossible to calculate

[John Mayfield]

... I do have some patches for an updated fingerprint API stack that would
also add this in to more places. Essentially it was added to the public API
but only implemented in a few places and left as a "ToDo" elsewhere. Might
be something for the hack-a-thon.

I should PubChem fingerprints are binary in nature though so you would
probably never want the RAW version. *getBitFingerprint()* it implemented
always.

John

On Fri, 21 Feb 2020 at 09:34, John Mayfield 
wrote:

> Hi Maria,
>
> Not all fingerprint support the "RAW" option and Count options.
>
> John
>
> On Fri, 21 Feb 2020 at 09:31, Maria Sorokina 
> wrote:
>
>> Dear community,
>>
>> It is decidedly substructure search and fingerprinting period of the year!
>>
>> I want to create (to store) raw fingerprints of a range of different
>> fingerprint types for a big number of complex molecules (natural products).
>>
>> For example this:
>>
>> PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( 
>> SilentChemObjectBuilder.getInstance() );
>>
>> System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer));
>>
>> For all my molecules I am getting an" UnsupportedOperationException",
>> which according to the documentation reflects only the fact that the 
>> fingerprinter
>> cannot produce the raw fingerprint.
>> I am using the latest (2.3) version of the CDK.
>> Can anybody help me with this issue?
>>
>>
>> Kind regards,
>> Maria
>>
>>
>> Dr. Maria Sorokina
>> Steinbeck Research Group
>> Analytical Chemistry - Cheminformatics and Chemometrics
>> Friedrich-Schiller-University Jena, Germany
>> http://cheminf.uni-jena.de
>>
>> ___
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>
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Re: [Cdk-user] Raw fingerprints impossible to calculate

[Egon Willighagen]

Mmm... time to update my book to discuss this :)

Egon

On Fri, Feb 21, 2020 at 10:35 AM John Mayfield 
wrote:

> Hi Maria,
>
> Not all fingerprint support the "RAW" option and Count options.
>
> John
>
> On Fri, 21 Feb 2020 at 09:31, Maria Sorokina 
> wrote:
>
>> Dear community,
>>
>> It is decidedly substructure search and fingerprinting period of the year!
>>
>> I want to create (to store) raw fingerprints of a range of different
>> fingerprint types for a big number of complex molecules (natural products).
>>
>> For example this:
>>
>> PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( 
>> SilentChemObjectBuilder.getInstance() );
>>
>> System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer));
>>
>> For all my molecules I am getting an" UnsupportedOperationException",
>> which according to the documentation reflects only the fact that the 
>> fingerprinter
>> cannot produce the raw fingerprint.
>> I am using the latest (2.3) version of the CDK.
>> Can anybody help me with this issue?
>>
>>
>> Kind regards,
>> Maria
>>
>>
>> Dr. Maria Sorokina
>> Steinbeck Research Group
>> Analytical Chemistry - Cheminformatics and Chemometrics
>> Friedrich-Schiller-University Jena, Germany
>> http://cheminf.uni-jena.de
>>
>> ___
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
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Re: [Cdk-user] Raw fingerprints impossible to calculate

[John Mayfield]

Hi Maria,

Not all fingerprint support the "RAW" option and Count options.

John

On Fri, 21 Feb 2020 at 09:31, Maria Sorokina 
wrote:

> Dear community,
>
> It is decidedly substructure search and fingerprinting period of the year!
>
> I want to create (to store) raw fingerprints of a range of different
> fingerprint types for a big number of complex molecules (natural products).
>
> For example this:
>
> PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( 
> SilentChemObjectBuilder.getInstance() );
>
> System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer));
>
> For all my molecules I am getting an" UnsupportedOperationException",
> which according to the documentation reflects only the fact that the 
> fingerprinter
> cannot produce the raw fingerprint.
> I am using the latest (2.3) version of the CDK.
> Can anybody help me with this issue?
>
>
> Kind regards,
> Maria
>
>
> Dr. Maria Sorokina
> Steinbeck Research Group
> Analytical Chemistry - Cheminformatics and Chemometrics
> Friedrich-Schiller-University Jena, Germany
> http://cheminf.uni-jena.de
>
> ___
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> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
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[Cdk-user] Raw fingerprints impossible to calculate

[Maria Sorokina]

Dear community,

It is decidedly substructure search and fingerprinting period of the year!

I want to create (to store) raw fingerprints of a range of different 
fingerprint types for a big number of complex molecules (natural products).

For example this:
PubchemFingerprinter pubchemFingerprinter = new PubchemFingerprinter( 
SilentChemObjectBuilder.getInstance() );
System.out.println(pubchemFingerprinter.getRawFingerprint(myAtomContainer));
For all my molecules I am getting an" UnsupportedOperationException", which 
according to the documentation reflects only the fact that the fingerprinter 
cannot produce the raw fingerprint.
I am using the latest (2.3) version of the CDK. 
Can anybody help me with this issue?


Kind regards,
Maria


Dr. Maria Sorokina
Steinbeck Research Group
Analytical Chemistry - Cheminformatics and Chemometrics
Friedrich-Schiller-University Jena, Germany
http://cheminf.uni-jena.de

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