| Merge File Issues [message #2163] |
Wed, 17 April 2024 10:39  |
amorrison
Messages: 38
Registered: March 2016
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Member |
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Hi,
I recently updated to v6.01.03 and now seem to have an issue with merging data from another file.
The workflow I have is as follows. I have a DataWarrior file that I update with new compounds weekly in DataWarrior I use the advanced stereochemistry flags to indicate chirality. I then export this as an SDF file to calculate properties in another programme, which is then exported as a new SDF file.
As this application does not handle v3000 file format I lose the chiral flags in the structures. When I open the new annotated SDF file (which has the additional compounds) I have been replacing the structures (via merge) with the previously prepared ones in DW with chiral flag annotations. This has worked great until today. Now when I do this all the column filters are lost I can see from the row count they are there but the new compounds I have just added are hidden. Disabling all row filters and resetting all row filters has no effect.
Any help on this one?
Many thanks,
Angus
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| Re: Merge File Issues [message #2172 is a reply to message #2164] |
Tue, 23 April 2024 18:55  |
amorrison
Messages: 38
Registered: March 2016
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Member |
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Hi Norwid,
Many thanks for the very useful suggestion. I'm trying to keep the chiral annotations (&, or, abs). To be fair, I have not tried exporting it as a v2000 file format and trying the merge in this case.
Best wishes,
Angus
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| Re: Merge File Issues [message #2173 is a reply to message #2171] |
Tue, 23 April 2024 19:16 |
amorrison
Messages: 38
Registered: March 2016
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Member |
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Hi Thomas,
Was not sure how to do this as a macro, so apologies but hopefully you can follow what I am doing. I've attached some files for a small set of compounds from ChEMBL.
Step 1 - Export DataWarrior file CDK2_Dwar.dwar to an sdf file (v3000).
Step 2 - Calculate properties in another program (ACD) and export as a SDF file (CDK2_Export_ACD.sdf)
Step 3 - Open CDK2_Export_ACD.sdf in DataWarrior - Say no to the racemate warning
Step 4 - Merge CDK2_Dwar.dwar in to CDK2_Export_ACD.sdf with Compound_ID as merge key and Structure 'replace with new'
All row filters are then lost and only 3 structures are visible, although the row count is 26. As part of this test I (have just) saved the resulting file and have just reopened it and the structures are now visible although all the row filters are still missing.
Apologies for the long winded explanation but hopefully you get the gist of what I am trying to do.
Best wishes,
Angus
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| Re: Merge File Issues [message #2179 is a reply to message #2173] |
Wed, 24 April 2024 13:49 |
thomas
Messages: 716
Registered: June 2014
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Senior Member |
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Hi Angus,
many thanks for the files. I could now reproduce the issue, which was caused by an old bug where existing columns were not re-analyzed after merging, when their values updated. Then, DataWarrior used outdated category lists for these columns resulting in Exceptions, when a category filter was applied.
This is now fixed and will be deployed in the next online-update.
Best wishes,
Thomas
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