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SEDenmarkLab / molli_firstgen

In silico library generation tool box
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Extending compatibility of Molecule class instantiation from other file types #11

Open ianrinehart opened 3 years ago

ianrinehart commented 3 years ago

As a normal part of doing any computations, a bunch of structures that I was working with had some errors. I could easily get xyz files, triage the problems, and make the necessary edits so that they will work.

Unfortunately, I have xyz files and there is not a clear way to create molecule class instances. If there were, then I would easily be able to reenter the workflow with these "special" cases.

In other words, can there be a ml.Molecule.from_xyz() and a condition for the .from_file() function to accomodate xyz?

esalx commented 3 years ago

This can be handled already using OpenBabelDriver, but I was definitely hoping to get a from_file() function going that would just use the openbabel backend.

The problem with .xyz files is that the connectivity table has to be guessed, which openbabel can do. But so far I have been trying to avoid it.