The above link is code to get bond length matrix from smiles.
Now are we able to convert to an XYZ file?
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$\begingroup$ From that, you can generate a set of internal coordinates. All computational software can work also with that kind of input $\endgroup$– Andrea PellegriniCommented Feb 12, 2023 at 9:32
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1$\begingroup$ Here is a question and answer that explains how to do this if you have the full set of distances. In general though, it may not be possible to reconstruct the full 3-D geometry from just the bond lengths. For instance, in methane, there will only be four bond lengths in your weighted adjacency matrix, which is insufficient to get the 9 degrees of freedom necessary to embed the molecule in 3-D space. math.stackexchange.com/questions/156161/… $\endgroup$– jheindelCommented Feb 19, 2023 at 19:45
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$\begingroup$ @jheindel do you think you can write a full answer so that this question can be cleared from our unanswered queue? $\endgroup$– Nike Dattani - No Free TimeCommented Oct 21, 2023 at 15:57
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$\begingroup$ I think it's easier to first get the xyz and then build the adjacency matrix. In any case, either rdkit or OpenBabel are able to generate xyz coordinates from smiles. $\endgroup$– AnonCommented Nov 5, 2023 at 20:04
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1 Answer
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jheindel's comment points to an answer:
"Here is a question and answer that explains how to do this if you have the full set of distances. In general though, it may not be possible to reconstruct the full 3-D geometry from just the bond lengths. For instance, in methane, there will only be four bond lengths in your weighted adjacency matrix, which is insufficient to get the 9 degrees of freedom necessary to embed the molecule in 3-D space. https://math.stackexchange.com/q/156161/202425"
If someone would like to write an answer, I can delete this Community Wiki answer (you can just ask me in a comment on this answer, or click "flag" and "In need of moderator intervention" and explain yourself).