subject:"\[Cdk\-user\] Raw fingerprints impossible to calculate"

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

2020-02-25 Thread John Mayfield

Okay,

I'm going to presume you want to search the data.. to retrieve similar
compounds or substructures. If not then just store the hexadecimal
fingerprint.

It's not impossible to do searching in MongoDB, see a talk from Matt Swain
,
... and my follow ups:
http://efficientbits.blogspot.com/2014/11/memory-mapped-fingerprint-index-part-i.html
,
http://efficientbits.blogspot.com/2014/12/memory-mapped-fingerprint-index-part-ii.html
.

However my view is (as I make clear in those blog posts) MongoDB is the
wrong technology for this, but you could convert your the binary
fingerprint to a vector. In fact to *toString* works well:

System.out.println(new
> Fingerprinter().getBitFingerprint(mol).asBitSet().toString());


{43, 46, 51, 60, 65, 70, 72, 86, 95, 99, 111, 114, 123, 128, 144, 157, 158,
161, 166, 174, 185, 188, 204, 213, 222, 253, 271, 275, 278, 311, 315, 320,
335, 364, 371, 379, 390, 409, 446, 449, 463, 486, 498, 520, 523, 535, 540,
565, 574, 586, 588, 611, 628, 632, 637, 647, 649, 655, 667, 725, 742, 756,
770, 793, 845, 859, 865, 918, 951, 954, 959, 1015}

You could then use and/or queries to find fingerprint subsets or computer
Tanimotos etc.

John

On Mon, 24 Feb 2020 at 13:44, Maria Sorokina 
wrote:

> I see the problem.
>
> Well, originally, I wanted to checkout how the raw fingerprints look like.
> I am storing all the data (and the fingerprints) in MongoDB, and I am still
> not sure if in case I save the BitFingerprints directly in there (with is
> possible when the field has an Object type), if they will be parseable by
> the mongo engine as fingerprints (without retrieving them to be read with
> CDK). So this is why I wanted to check the raw fingerprints, as they should
> be more JSON-friendly format, and mongo engine would be able to read those
> integers and strings for further similarity search.
>
> Kind regards,
> Maria
>
>
> 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 19:31, John Mayfield  a
> écrit :
>
> 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,
>

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

2020-02-24 Thread Maria Sorokina

I see the problem.

Well, originally, I wanted to checkout how the raw fingerprints look like. I am 
storing all the data (and the fingerprints) in MongoDB, and I am still not sure 
if in case I save the BitFingerprints directly in there (with is possible when 
the field has an Object type), if they will be parseable by the mongo engine as 
fingerprints (without retrieving them to be read with CDK). So this is why I 
wanted to check the raw fingerprints, as they should be more JSON-friendly 
format, and mongo engine would be able to read those integers and strings for 
further similarity search.

Kind regards,
Maria 


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 19:31, John Mayfield  a écrit 
> :
> 
> 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 
>> ___
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net 
>> https://lists.sourceforge.net/lists/listinfo/cdk-user 
>> 
> 

___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

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

2020-02-21 Thread 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

 ___
 Cdk-user mailing list
 Cdk-user@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/cdk-user

>>>
>>
___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

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

2020-02-21 Thread 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
>>>
>>
>
___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

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

2020-02-21 Thread 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 
> 

___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

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

2020-02-21 Thread 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
>>
>
___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

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

2020-02-21 Thread 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
>>
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>


-- 
Hi, do you like citation networks? Already 51% of all citations are
available  available for innovative new uses
. Join me in asking the American
Chemical Society to join the Initiative for Open Citations too
.
SpringerNature,
the RSC and many others already did .

-
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: -0001-7542-0286 
ImpactStory: https://impactstory.org/u/egonwillighagen
___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

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

2020-02-21 Thread 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
>
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

[Cdk-user] Raw fingerprints impossible to calculate

2020-02-21 Thread 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

___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

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

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

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

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

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

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

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

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

[Cdk-user] Raw fingerprints impossible to calculate

9 matches

Site Navigation

Mail list logo

Footer information