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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)
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 previous message
thomas is currently offline  thomas
Messages: 655
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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