Hi Everyone, Greg, I am basically replacing part of an existing molecule using ReplaceSubstructs. The replaced parts do not have any coordinate information (as these are SMILES/SMART patterns really). If I use AllChem.Compute2DCoords(...) the new "added" atoms get 2D co-ordinates, but the rest of the atoms in the molecule have new co-ordinates (but I want to keep that info). I would like to generate 2D coordinates for the newly added (replaced) atoms only, but doing so in the already existing co-ordinate frame.
In order to illustrate my point further I am attaching a test script which exhibits this problem. Please note the last two atoms (freshly replaced): ... 11.2046 9.1283 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8452 8.2597 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 4.9633 5.4306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 (And if I enable Compute2DCoords, I get different co-ordinates for the first 3 atoms, and last 2 of course (this last part I don't mind)) Does anyone have any ideas how to go about implementing this? Or, wishfully, is there out of the box functionality for this? Even quick dirty fixes would do. Jean-Paul Ebejer Early Stage Researcher
test.py
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