On Fri, Sep 16, 2011 at 8:39 AM, Martin Guetlein <
martin.guetl...@googlemail.com> wrote:
>
>
> On Fri, Sep 16, 2011 at 8:33 AM, Nina Jeliazkova <
> jeliazkova.n...@gmail.com> wrote:
>
>>
>>
>> On 16 September 2011 09:29, Martin Guetlein <
>> martin.guetl...@googlemail.com> wrote:
>>
>>>
>>>
>>> On Thu, Sep 15, 2011 at 12:33 PM, Fredrik Wallner <fred...@wallner.nu>wrote:
>>>
>>>> Hi again,
>>>> (I realized i forgot to cc the list in my last reply)
>>>> 15 sep 2011 kl. 12:29 skrev Martin Guetlein:
>>>>
>>>> On Thu, Sep 15, 2011 at 12:21 PM, Fredrik Wallner
>>>> <fred...@wallner.nu>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Since the fp2 fingerprint is a path-based hashed fingerprint, there is
>>>>> no such list.
>>>>>
>>>>
>>>> But the bit at positon <i> is always the same fragent, right? So it
>>>> would it general be possible to create such a list?
>>>>
>>>> Martin
>>>>
>>>>
>>>> No it's not. The same fragment is always mapping to the same position,
>>>> but multiple fragments can map to the same bit, that's what happens with a
>>>> hashed fingerprint
>>>>
>>>> /Fredrik
>>>>
>>>
>>>
>>> I see, but multiple fragments mapping at the same bit would be fine as
>>> well, as smarts strings allows the logical or. This means the list is still
>>> possible, isnt it?
>>>
>>
>> The list may turn to be almost infinite ... it's a hash function,
>> one-way.
>>
>> Nina
>>
>
> Understand, all possible fragments of length 7 is quite a lot. I will try
> the -xs.
>
> Thanks,
> Martin
>
I went with the -xs and am currently working on the to-smarts conversion.
First question:
I got those lines:
0 16 5 6 5 7 5 6 1 6 2 7 1 8 <7>
0 16 5 6 5 7 5 6 5 6 <668>
1 7 1 6 1 6 1 6 <544>
1 16 1 6 1 7 1 6 1 6 1 6 <633>
2 6 1 7 1 6 1 16 1 6 1 6 <514>
2 6 2 6 1 16 1 6 1 7 1 6 <651>
2 7 1 6 1 16 1 6 1 6 2 6 <428>
5 7 5 7 5 6 5 7 5 6 5 6 <294>
5 16 5 6 5 7 5 6 5 6 <272>
According to here
http://openbabel.org/docs/dev/FileFormats/Fingerprint_format.html, "the
first digit indicates whether the fragment is linear (0) or cyclic (1)".
What does a 5 or a 2 at the beinning mean?
Second question:
Are the bond numbers the same as in the SDF spec?
This would be:
http://www.symyx.com/downloads/public/ctfile/ctfile.jsp
ctfile.pdf , page 16
Bond type
Integer:
1 = single
2 = double
3 = triple
4 = aromatic
5 = single or double
6 = single or aromatic
7 = double or aromatic
8 = any
Best regards,
Martin
>
>
>
>
>>
>>> My problem with the -xs command is, that I would have to do the
>>> conversion dynamically, that would be quite inefficient...
>>>
>>> Martin
>>>
>>>
>>>>
>>>>
>>>>
>>>>
>>>>> The -xs option (note that it's not -s) is your best alternative. You
>>>>> can then convert these lines into a smart string with string substitutions
>>>>> if you would like, but it really comes down to what you need them for.
>>>>>
>>>>> Kind regards,
>>>>> Fredrik
>>>>>
>>>>> 15 sep 2011 kl. 12:01 skrev Martin Guetlein:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I would like to have the corresponding fragment for each bit of the fp2
>>>>> fingerprint.
>>>>> Using the -s param (as described by Noel here:
>>>>> http://forums.openbabel.org/Need-help-in-calculationg-tanimoto-coefficient-td3233604.html)
>>>>> is not very practical for what I want to do, I would prefer a list of 1024
>>>>> smarts strings.
>>>>> Is this available somewhere?
>>>>>
>>>>> Cheers,
>>>>> Martin
>>>>>
>>>>> --
>>>>> Dipl-Inf. Martin Gütlein
>>>>> Phone:
>>>>> +49 (0)761 203 7633 (office)
>>>>> +49 (0)177 623 9499 (mobile)
>>>>> Email:
>>>>> guetl...@informatik.uni-freiburg.de
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>>>>
>>>>
>>>> --
>>>> Dipl-Inf. Martin Gütlein
>>>> Phone:
>>>> +49 (0)761 203 7633 (office)
>>>> +49 (0)177 623 9499 (mobile)
>>>> Email:
>>>> guetl...@informatik.uni-freiburg.de
>>>>
>>>>
>>>>
>>>
>>>
>>> --
>>> Dipl-Inf. Martin Gütlein
>>> Phone:
>>> +49 (0)761 203 7633 (office)
>>> +49 (0)177 623 9499 (mobile)
>>> Email:
>>> guetl...@informatik.uni-freiburg.de
>>>
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>>
>
>
> --
> Dipl-Inf. Martin Gütlein
> Phone:
> +49 (0)761 203 7633 (office)
> +49 (0)177 623 9499 (mobile)
> Email:
> guetl...@informatik.uni-freiburg.de
>
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 7633 (office)
+49 (0)177 623 9499 (mobile)
Email:
guetl...@informatik.uni-freiburg.de
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