Re: [Cdk-user] Substructure search using ShortestPathFingerprinter

2020-02-25 Thread John Mayfield 
Yes good idea, I added a comment at the bottom but it does explicitly say
that at the top.

On Tue, 25 Feb 2020 at 08:43, nicepeopleproject 
wrote:

> Thank you!
> The documentation for the ShortestPathFingerprinter class says "Fingerprints
> allow for a fast screening step to exclude candidates for a substructure
> search in a database. They are also a means for determining the similarity
> of chemical structures.". Perhaps it’s worth removing so that there are
> no contradictions.
>
> чт, 20 февр. 2020 г. в 18:28, John Mayfield :
>
>> I've added a warning in the doc, there was already a warning on MACCS 166
>> keys.
>>
>> https://github.com/cdk/cdk/commit/82cb4f8d49283e117696f40d09538c70790a18fd
>>
>> On Thu, 20 Feb 2020 at 15:20, John Mayfield 
>> wrote:
>>
>>> *wrote :-)
>>>
>>> On Thu, 20 Feb 2020 at 15:20, John Mayfield 
>>> wrote:
>>>
 Only *Fingerprinter* or *ExtendedFingerprint* obey this transitivity
 property.

 Relevant post I wrong in 2015:
 https://nextmovesoftware.com/blog/2015/02/16/for-every-fingerprint-optimisation-there-is-an-equal-and-opposite-fingerprint-deterioration/

 On Thu, 20 Feb 2020 at 10:44, nicepeopleproject <
 nicepeopleproj...@gmail.com> wrote:

> Hello!
> I'm trying to realize substructure search. As I understand, the
> ShortestPathFingerprinter is suitable for this. I ran into the following
> problem. I attach two file(in molecules.zip). when using butane.mol as
> query, should find ciclopentane.mol. When i found BitSet for butane i got:
> {115, 503, 540, 653, 893}
> {115, 503, 542, 653, 893} - for ciclopentane.
> So i cannot find ciclopentane. Is there a way to make it work?
>
> --
> С уважением,
> Николаев Артём
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>

>
> --
> С уважением,
> Николаев Артём
>
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Re: [Cdk-user] Substructure search using ShortestPathFingerprinter

2020-02-25 Thread nicepeopleproject 
Thank you!
The documentation for the ShortestPathFingerprinter class says "Fingerprints
allow for a fast screening step to exclude candidates for a substructure
search in a database. They are also a means for determining the similarity
of chemical structures.". Perhaps it’s worth removing so that there are no
contradictions.

чт, 20 февр. 2020 г. в 18:28, John Mayfield :

> I've added a warning in the doc, there was already a warning on MACCS 166
> keys.
>
> https://github.com/cdk/cdk/commit/82cb4f8d49283e117696f40d09538c70790a18fd
>
> On Thu, 20 Feb 2020 at 15:20, John Mayfield 
> wrote:
>
>> *wrote :-)
>>
>> On Thu, 20 Feb 2020 at 15:20, John Mayfield 
>> wrote:
>>
>>> Only *Fingerprinter* or *ExtendedFingerprint* obey this transitivity
>>> property.
>>>
>>> Relevant post I wrong in 2015:
>>> https://nextmovesoftware.com/blog/2015/02/16/for-every-fingerprint-optimisation-there-is-an-equal-and-opposite-fingerprint-deterioration/
>>>
>>> On Thu, 20 Feb 2020 at 10:44, nicepeopleproject <
>>> nicepeopleproj...@gmail.com> wrote:
>>>
 Hello!
 I'm trying to realize substructure search. As I understand, the
 ShortestPathFingerprinter is suitable for this. I ran into the following
 problem. I attach two file(in molecules.zip). when using butane.mol as
 query, should find ciclopentane.mol. When i found BitSet for butane i got:
 {115, 503, 540, 653, 893}
 {115, 503, 542, 653, 893} - for ciclopentane.
 So i cannot find ciclopentane. Is there a way to make it work?

 --
 С уважением,
 Николаев Артём
 ___
 Cdk-user mailing list
 Cdk-user@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/cdk-user

>>>

-- 
С уважением,
Николаев Артём
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Re: [Cdk-user] Substructure search using ShortestPathFingerprinter

2020-02-20 Thread John Mayfield 
I've added a warning in the doc, there was already a warning on MACCS 166
keys.

https://github.com/cdk/cdk/commit/82cb4f8d49283e117696f40d09538c70790a18fd

On Thu, 20 Feb 2020 at 15:20, John Mayfield 
wrote:

> *wrote :-)
>
> On Thu, 20 Feb 2020 at 15:20, John Mayfield 
> wrote:
>
>> Only *Fingerprinter* or *ExtendedFingerprint* obey this transitivity
>> property.
>>
>> Relevant post I wrong in 2015:
>> https://nextmovesoftware.com/blog/2015/02/16/for-every-fingerprint-optimisation-there-is-an-equal-and-opposite-fingerprint-deterioration/
>>
>> On Thu, 20 Feb 2020 at 10:44, nicepeopleproject <
>> nicepeopleproj...@gmail.com> wrote:
>>
>>> Hello!
>>> I'm trying to realize substructure search. As I understand, the
>>> ShortestPathFingerprinter is suitable for this. I ran into the following
>>> problem. I attach two file(in molecules.zip). when using butane.mol as
>>> query, should find ciclopentane.mol. When i found BitSet for butane i got:
>>> {115, 503, 540, 653, 893}
>>> {115, 503, 542, 653, 893} - for ciclopentane.
>>> So i cannot find ciclopentane. Is there a way to make it work?
>>>
>>> --
>>> С уважением,
>>> Николаев Артём
>>> ___
>>> Cdk-user mailing list
>>> Cdk-user@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>>
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Re: [Cdk-user] Substructure search using ShortestPathFingerprinter

2020-02-20 Thread John Mayfield 
Only *Fingerprinter* or *ExtendedFingerprint* obey this transitivity
property.

Relevant post I wrong in 2015:
https://nextmovesoftware.com/blog/2015/02/16/for-every-fingerprint-optimisation-there-is-an-equal-and-opposite-fingerprint-deterioration/

On Thu, 20 Feb 2020 at 10:44, nicepeopleproject 
wrote:

> Hello!
> I'm trying to realize substructure search. As I understand, the
> ShortestPathFingerprinter is suitable for this. I ran into the following
> problem. I attach two file(in molecules.zip). when using butane.mol as
> query, should find ciclopentane.mol. When i found BitSet for butane i got:
> {115, 503, 540, 653, 893}
> {115, 503, 542, 653, 893} - for ciclopentane.
> So i cannot find ciclopentane. Is there a way to make it work?
>
> --
> С уважением,
> Николаев Артём
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
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[Cdk-user] Substructure search using ShortestPathFingerprinter

2020-02-20 Thread nicepeopleproject 
Hello!
I'm trying to realize substructure search. As I understand, the
ShortestPathFingerprinter is suitable for this. I ran into the following
problem. I attach two file(in molecules.zip). when using butane.mol as
query, should find ciclopentane.mol. When i found BitSet for butane i got:
{115, 503, 540, 653, 893}
{115, 503, 542, 653, 893} - for ciclopentane.
So i cannot find ciclopentane. Is there a way to make it work?

-- 
С уважением,
Николаев Артём


butane.MOL
Description: Binary data


ciclopentane.MOL
Description: Binary data
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