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Exporting a descriptor as a Textfile [message #1605]

Mon, 09 May 2022 17:45

Christophe
Messages: 14
Registered: January 2022

Junior Member

Hello everyone,

Is it possible to export descriptors such as Skelspheres or others as a textfile ?

Thanks

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Re: Exporting a descriptor as a Textfile [message #1610 is a reply to message #1605]

Wed, 18 May 2022 14:22

Christophe
Messages: 14
Registered: January 2022

Junior Member

Just to mention that I'd like to use these text files as a part of a matrix to perform diverse ordination techniques not available in DW like UMAP for example.
These files must be stored somewhere since the "Skelsphere" descriptor for example is available when a t-SNE ordination is envisioned.

Thanks

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Re: Exporting a descriptor as a Textfile [message #1611 is a reply to message #1610]

Thu, 19 May 2022 12:42

amorrison
Messages: 25
Registered: March 2016

Junior Member

Hi,
If you use 'add calculated values' and then str(Descriptor Variable) a new column should appear. I think this is what you are looking for.
Angus

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Re: Exporting a descriptor as a Textfile [message #1613 is a reply to message #1611]

Fri, 20 May 2022 16:23

Christophe
Messages: 14
Registered: January 2022

Junior Member

Hi Angus,

Thank you
The columns appear well but the data are unusable (cabalistic signs)
Some descriptors are encoded as a matrix (1024 bits for example), so I suppose this is not the proper way to extract it.

Christophe

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Re: Exporting a descriptor as a Textfile [message #1615 is a reply to message #1613]

Sat, 21 May 2022 18:48

nbehrnd
Messages: 121
Registered: June 2019

Senior Member

Christophe,

for a small set of molecules, I think I'm able to replicate your findings e.g., for the assignment and subsequent display of skelspheres as a string:

/forum/index.php?t=getfile&id=552&private=0

/forum/index.php?t=getfile&id=552&private=0

(observation with DW 5.5.0 for Linux, including the update by May 13th).

On the other hand (now specific to skelspheres); if these are like fingerprints e.g., openbabel offers,[1] what are programs you intend to use which accept these as an input for further computation?

E.g., openbabel reports about DMF:

$ obabel -:"CN(C)C=O" -ofpt -xf FP2
>   5 bits set 
00000000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000000 00200000 00000000 
00008000 00000000 00000000 00000000 00000000 00000000 
00000000 00000000 00000000 00000400 00000000 00000000 
00000000 00000000 00000000 00000000 00000000 00040001 
00000000 00000000 
1 molecule converted

$ obabel -:"CN(C)C=O" -ofpt -xs -xf FP2
>
0 6 1 7 1 6 <693>
0 7 1 6 <82>
0 8 2 6 <623>
0 8 2 6 1 7 <330>
0 8 2 6 1 7 1 6 <64>
1 molecule converted

Norwid

[1] https://open-babel.readthedocs.io/en/latest/FileFormats/Fing erprint_format.html

Attachment: example_str_skelspheres.png
(Size: 62.54KB, Downloaded 13 times)
Attachment: molecules.dwar
(Size: 7.46KB, Downloaded 1 time)

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