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Molecule Displayed Incorrectly [message #959] Thu, 18 June 2020 22:48 Go to next message
sbembenek18 is currently offline  sbembenek18
Messages: 32
Registered: April 2019
Member
I've noticed in certain cases, DW will not correctly display the molecule. This appears to happen for 'non conventional' protomers mostly but not always. I've included an example. The attached molecule should appear as in the image. However, if you load the SDF in DW, you see that it does not appear this way.

  • Attachment: mol.png
    (Size: 13.15KB, Downloaded 31 times)
  • Attachment: mol_dw_error.sdf
    (Size: 1.71KB, Downloaded 23 times)
Re: Molecule Displayed Incorrectly [message #963 is a reply to message #959] Sun, 21 June 2020 14:11 Go to previous messageGo to next message
thomas is currently offline  thomas
Messages: 341
Registered: June 2014
Senior Member
Thank you for reporting this issue. There was indeed a bug in the charge neutralization part of the structure normalization, which takes place when importing structures from SD-Files or SMILES. This is fixed in the current development update. However, still DataWarrior doesn't show the structure as in mol.png, because DataWarrior normalizes and canonicalizes structures during the import. Part of the normalization is to neutralize charges as much as possible, meaning to move protons from protonated and positively charged atoms (e.g. ammonium) to negatively charged hetero atoms where possible.
Re: Molecule Displayed Incorrectly [message #981 is a reply to message #963] Fri, 03 July 2020 23:26 Go to previous message
sbembenek18 is currently offline  sbembenek18
Messages: 32
Registered: April 2019
Member
thanks. I appreciate why it is doing it. it could be useful to allow the user to change this default behavior so that DW displays the molecule "as is"
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