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Re: name vs score 2D plot [message #1867 is a reply to message #1864] |
Tue, 07 March 2023 15:52 ![Go to previous message Go to previous message](/forum/theme/myThemeWithHFCSS/images/up.png) ![Go to next message Go to next message](/forum/theme/myThemeWithHFCSS/images/down.png) |
nbehrnd
Messages: 215 Registered: June 2019
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Senior Member |
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Hi sublimeuser,
is it possible for you to share a typical, yet not confidential .sdf presenting the problems to you? I speculate perhaps the problem correlates with the syntax in the input file.
In an instance of Linux Debian 12/bookworm with openbabel (vesion 3.1.1) I created two .sdf files where the «compound name» is the standard InChI key
``` shell
$ obabel -:"O" -:"CCOCC" -:"c1ccncc1" -h --gen3d --append "inchikey" -O testV2000.sdf
$ obabel -:"O" -:"CCOCC" -:"c1ccncc1" -h --gen3d --append "inchikey" -x3000 -O testV3000.sdf
```
This is to cover both the elder V2000 format, as well as the contemporary V3000 one DW prefers on file I/O as .sdf. The reading from the CLI was in pattern of
``` shell
$ datawarrior ./testV3000.sdf &
```
run without noticeable difficulty, nor the adjust the header "compound name" by "InChI key" - there was a prompt (automatic) update in the 2D and 3D plot on abscissa and ordinate.
The four tests run DataWarrior 5.5.0 in said Debian, either the one provided by a pristine installation with the installer fetched by 2022-05-18 (i.e., the state by 2021-04-03), or by subsequent application of the update fetched today (2023-03-07) about the state reached by 2024-02-24.
With regards,
Norwid
[Updated on: Tue, 07 March 2023 15:53] Report message to a moderator
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Re: name vs score 2D plot [message #1875 is a reply to message #1871] |
Sat, 18 March 2023 17:55 ![Go to previous message Go to previous message](/forum/theme/myThemeWithHFCSS/images/up.png) |
thomas
Messages: 696 Registered: June 2014
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Senior Member |
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Hi Norwid and Sublimeuser,
there are a couple of defined maxima applied to graphical views in DataWarrior to prevent an explosion of in-memory-data. Usually, these limits are meant to be high enough to not restrict any reasonable graph drawing. For instance category columns can be assigned to an axis if they have not more than 256 distinct categories (your compound name column should be classified as category column). The idea was that more than 256 distinct objects on an axis cannot be displayed well anymore. Admittedly, 256 seems very low, especially considering that the limitation stays in place when zooming in. I will increase the limit to 10000.
Thomas
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