Mapping .xyz to atoms in SMILES #3800
Replies: 2 comments 2 replies
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The RDKit doesn't have code to guess bond orders from geometry, so if you really don't have any idea what the atom ordering in the XYZ file is, then I think you're probably going to have to use something like xyz2mol: https://github.com/jensengroup/xyz2mol |
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To add on, besides the One step further, to match atom order in the smiles to the atom order in the perceived molecules, you can use |
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Hi everyone,
Do any of you know whether there's an easy way to map from an
.xyz
file with 3D coordinates to atoms in a given SMILES after usingMolFromxyz
? I would like to be able to associate every atom in the.xyz
file with an atom index in a mol.Beta Was this translation helpful? Give feedback.
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