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Not with SMILES. Your template then must be a drawing in the orientation you prefer that must be conserved when loading. So you need to use a format that support coordinates most notably:
If you really need SMILES then CXSMILES is the suggested option. You will probbaly be able to create them, if you don't have Marvin license, by loading a molfile into RDKit and then writing it as cxsmiles with |
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Hi there,
I am relatively new to RDKit. I would like to rotate a substructure of a set of melucules, so I can align all the other molecules on that rotated substructure. All molecules are provided as smiles.
My molecules are dipenylethers, so I selected a phenol as substructure. The examples I found for this worked just fine for another set of molecules I tested. But for the diephenylethers I want to have the substrucre oriented differently.
Again, the code pasted above does its work, but for my purpose I would like to have the molecule rotated, that the hydoxyl group is shown at the top position. Or in other words, the OH group shall be shown at the highlighted position:
Are there any suggestions, how I could do this?
Best,
Gerald
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