Create CMILES object directly from a molecule - Githubissues

openforcefield / openff-qcsubmit

Automated tools for submitting molecules to QCFractal

https://openff-qcsubmit.readthedocs.io/en/latest/index.html

MIT License

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Create CMILES object directly from a molecule #105

Closed SimonBoothroyd closed 3 years ago

SimonBoothroyd commented 3 years ago

Description

This PR adds a convenience method to create a CMILES containing MoleculeAttributes object from an OpenFF molecule. This allows the object to be created directly without first needing to create a dataset factory first.

Questions

[x] I named this method from_openff_molecule to make it explicit that this method creates from an OpenFF molecule rather than say a QCElemental molecule, but it may be better to just have a from_molecule method and handle the molecule type in the method itself, maybe making private _from_openff_molecule, _from_qcel_molecule, _from_XXX_molecule methods to handle the different molecule cases.

Status

[ ] Ready to go

jthorton commented 3 years ago

@SimonBoothroyd thanks for putting this together this is great and helps with the awkwardness of using a factory to make the CMILS objects. WRT to the naming let's stick with from_openff_molecule for now I think only an openff molecule is safe to use as input due to missing information in the likes of qcelemental molecules and I like the idea of making it very clear that we are using a openff molecule as our goto structure which users might not expect when working with qcfractal.

Please feel free to merge tests are broken due to fragmenter and an rdkit update which I will work on separately.