| polycyclic molecule displaying issue [message #2332] |
Tue, 29 October 2024 10:11  |
yunforce
Messages: 11
Registered: May 2024
|
Junior Member |
|
|
I copied the same SMILES string (CC[C@@]12CCC(=O)N3CC[C@]4(C5=CC=CC=C5N[C@@H]4CC1)[C@H]32) into both DataWarrior and ChemDraw. In DataWarrior, the structure displayed had many overlapping bonds, making it difficult to discern the true structure of the molecule. However, when I pasted this SMILES into ChemDraw, it displayed a clearer structure. I wonder if this is due to an issue with the software itself or differences in the structure generation algorithms. If improvements could be made in this area, it would certainly make DataWarrior more popular.
[Updated on: Tue, 29 October 2024 10:16] Report message to a moderator |
|
|
|
| Re: polycyclic molecule displaying issue [message #2335 is a reply to message #2332] |
Tue, 29 October 2024 22:35  |
nbehrnd
Messages: 224
Registered: June 2019
|
Senior Member |
|
|
Hello,
With DW you don't have leverage to alter DataWarrior's attempt to identify by itself the best 2D projection of a 3D molecule. If you copied the SMILES string to the clipboard memory of the computer, then double clicked into a field of the DW spreadsheet, a click with the right mouse button allows to paste the SMILES string already as structure. With the lasso, it is possible to move a little bit the atoms and bonds (as in the video attached), or iron out some oddities with the star button; but that's all. In this regard, DW is not like ChemDraw or Marvin where you can somewhat optimize and reorient the structure formula, or toggle on/off the descriptors of stereochemistry.
An idea for future versions of DataWarrior could be to let the user choose for each .dwar file for structure formulae either with the current 3D projection approach, or a "flattened" one as e.g., by CDKDepict (example attached). But I have no idea how much work this were to provide this choice.
Best regards,
Norwid
|
|
|
|
|
|
Search
Help
Members
Register
Login
Home
