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Home » DataWarrior » Bug Reports » 3D coordinates of hydrogen atom lost for structures containing positive charged nitrogen (3D coordinate of hydrogen is expected to be kept)
3D coordinates of hydrogen atom lost for structures containing positive charged nitrogen [message #824] Mon, 23 March 2020 11:47 Go to next message
zhentg is currently offline  zhentg
Messages: 25
Registered: March 2020
Junior Member
Dear developers,

When I load SDF with 3D coordinates, I found if a structure contains positively charged nitrogen, then its hydrogen atom will disppear in DataWarrior. Furthermore, if the structure is exported to a new SDF file, the hydrogen atoms are still missing.
index.php?t=getfile&id=162&private=0
Could you help to check this?

Attached is the original SDF, a DataWarrior file created from the SDF, and a snapshot to highlight the issue.

Thanks!

Datawarrior is a good tool

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Re: 3D coordinates of hydrogen atom lost for structures containing positive charged nitrogen [message #829 is a reply to message #824] Tue, 24 March 2020 17:09 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 716
Registered: June 2014
Senior Member
thank you for sending the detailled description and the sample files. The problem is caused by a (probably) wrong interpretation of a field in the molfile part of your SD-file, that is meant to store (unusual) atom valences,
but is typically not used for atoms with usual valences. For charged atoms RDKit populates this value and DataWarrior
used to interpret this in a conflicting way causing wrong implicit hydrogen counts.
The issue is fixed now and you may download replacements files from
openmolecules.org/datawarrior/dw521x.zip (Linux or Mac) and openmolecules.org/datawarrior/dw521win.zip (for Windows).

Thomas

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Re: 3D coordinates of hydrogen atom lost for structures containing positive charged nitrogen [message #832 is a reply to message #829] Wed, 25 March 2020 09:50 Go to previous message
zhentg is currently offline  zhentg
Messages: 25
Registered: March 2020
Junior Member
Thanks a lot, Thomas.
Just tested the new DataWarrior.exe, and the bug is fiexed.
With that, I can visualize 3D conformations better in DataWarrior.

Datawarrior is a good tool

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