Home » DataWarrior » Functionality » Saving 2D-structure with labels
| Saving 2D-structure with labels [message #1614] |
Fri, 20 May 2022 17:04  |
vijaymasand
Messages: 6
Registered: May 2022
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Junior Member |
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Dear all
Recently, I started using Datawarrior for research work, especially for QSAR and allied areas. It is really wonderful and useful for cheminformatics. I have three requirements from developers.
(1) I want to save the 2D-structure along with the labels, please see the ‘structure view’ panel in the attached image. I tried ‘copy view image’ but it copied only the structure and not the data labels. Is there any method to copy and paste (or save) the structure along with labels?
(2) Right now, it is providing data from Chembl 28. Recently, Chembl 30 was released. Is possible to force it to download data from Chembl 30?
(3) In ‘Look and Feel’ menu could you please add ‘white’ as an option.
Thanks in advance.
From
Vijay
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| Re: Saving 2D-structure with labels [message #1629 is a reply to message #1624] |
Mon, 06 June 2022 19:14  |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Dear Vijay,
lacking access to Windows 11, I'm unable to replicate your findings. Thus, the operation system, or/and the executable of DW specifically released for Windows might contribute to this.
However, because DW* does not provide a progress bar when generating a .png or .svg from the array / structure view, a (perhaps hasty) perception may be anywhere between «the request to export the table wasn't yet launched» and «because of the computational load, the computer froze». In my case, it takes some time i) before an icon about the new file is displayed in the file browser, ii) the CPU monitor records a significant increase in computation, iii) the new file starts to be written, iv) writing all the data into the new file is completed. Do you consider a library of 5k random molecules DW generated a lager one (attached below)? The annotated structure array, exported as .svg is larger than 100 MB; for inkscape, this represents a larger file.
Difficult to tell if a sequential generation of these small illustrations (one frame with one molecular structure & selected description) as individual .png/.svg in a pattern like 001.png, 002.png, 003.png, etc. (or their .svg analogues) would be an advantage for you.
Norwid
*) tested with DW 5.5.0 for Linux including the update by 2022-06-04 in Debian 12/bookworm (branch testing)
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| Re: Saving 2D-structure with labels [message #1632 is a reply to message #1631] |
Tue, 07 June 2022 19:30 |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Dear Vijay,
indeed, the «print to pdf» is an attractive alternative. Not only that the depictions don't pixelate as in the .png bitmap, the .pdf retains a searchable text layer. This then allows to identify /the/ entry of particular interest by a label set (SMILES string, catalogue number, etc.) after the document was exported.
Norwid
[Updated on: Tue, 07 June 2022 19:30] Report message to a moderator |
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| Re: Saving 2D-structure with labels [message #1663 is a reply to message #1657] |
Thu, 30 June 2022 20:03 |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Dear Vijay,
congratulations to your publication.
Note, table 1 includes some examples of «counting patterns» which indeed exceed DW's set of pre-set statistics (e.g., counting small saturated carbon-only cycles) available via chemistry -> from chemical structure -> calculate properties. However, the development version of DW offers an additional functionality via chemistry -> from chemical structure -> add substructure count. Assisted by the program's sketcher, you may define countable pattern matching your needs like «excluding S of sulfone, the eighth atom should be an aromatic carbon atom»
By selection (lasso) and double click, the properties of the atoms in question may be specified further. The documentation calls this «substructure count»,[1] just prior to the section header «The Structure Filter».
With best regards,
Norwid
[1] https://openmolecules.org/help/chemistry.html#StructureFilte r
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| Re: Saving 2D-structure with labels [message #1665 is a reply to message #1663] |
Sat, 02 July 2022 04:36 |
vijaymasand
Messages: 6
Registered: May 2022
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Junior Member |
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Thank you, dear Norwid
I am aware about the 'substructure count' and 'calculate properties' functionalities, which are really excellent and useful. I will definitely use them in future work.
Have a nice day.
Vijay
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, I used molecular descriptors calculated by Datawarrior. The paper is full of mechanistic interpretations and new findings. 
