openmolecules.org Forum: Cheminformatics » Exporting a descriptor as a Textfile

Home » DataWarrior » Cheminformatics » Exporting a descriptor as a Textfile

Show: Today's Messages :: Polls :: Message Navigator

Re: Exporting a descriptor as a Textfile [message #1616 is a reply to message #1615]

Tue, 24 May 2022 15:24

Christophe
Messages: 31
Registered: January 2022

Member

Hi Norwid,

Thank you

It looks you managed to convert the structure DW column into one of the finger print managed by open babel.

I am not sure this procedure captures the native information of the skelspheres descriptor. It generated a FP2 (by default) FP descriptor.

I know how to generate a lot of different FP from structures. For example PaDEL (free java program, http://www.yapcwsoft.com/dd/padeldescriptor Wink

does a very good job. It provides a matrix (.csv file) with structures (in rows) and bits (binary or count, depending on the FP you select) (in columns).

If you know how bits (or series of bits) are organized you can try to trace the source that causes the differences in distribution by multidimension reduction methods in R for example.

with DW, when I apply a similarity (or activity cliff) with Skelspheres and/or OrgFunctions, I have data sets that cluterize very well but it is quite challenging then to relate the resulting clusters to the distributional differences in term of structure (SkelSpheres) or functionalization (Orgfunctions). If these two descriptors are different from the one I used so far such as ExtFP, MACCSFP .... may be I could gain more information. But I need the "matrix formalism" into a text file.
Christophe

Report message to a moderator

[Message index]

		Exporting a descriptor as a Textfile By: Christophe on Mon, 09 May 2022 17:45
		Re: Exporting a descriptor as a Textfile By: Christophe on Wed, 18 May 2022 14:22
		Re: Exporting a descriptor as a Textfile By: amorrison on Thu, 19 May 2022 12:42
		Re: Exporting a descriptor as a Textfile By: Christophe on Fri, 20 May 2022 16:23
		Re: Exporting a descriptor as a Textfile By: nbehrnd on Sat, 21 May 2022 18:48
		Re: Exporting a descriptor as a Textfile By: Christophe on Tue, 24 May 2022 15:24
		Re: Exporting a descriptor as a Textfile By: thomas on Thu, 02 June 2022 09:46
		Re: Exporting a descriptor as a Textfile By: Christophe on Thu, 02 June 2022 17:24
		Re: Exporting a descriptor as a Textfile By: thomas on Wed, 13 July 2022 17:29
		Re: Exporting a descriptor as a Textfile By: Christophe on Mon, 18 July 2022 13:35
		Re: Exporting a descriptor as a Textfile By: nbehrnd on Tue, 19 July 2022 07:54
		Re: Exporting a descriptor as a Textfile By: Christophe on Tue, 19 July 2022 09:32

Previous Topic:	Find similars using Flexophore
Next Topic:	t-SNE

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Sun Nov 24 18:12:37 CET 2024

Total time taken to generate the page: 0.03836 seconds