openkinome / kinoml

Structure-informed machine learning for kinase modeling
https://openkinome.org/kinoml/
MIT License
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IO handling #23

Closed schallerdavid closed 3 years ago

schallerdavid commented 4 years ago

How should we handle reading and writing, e.g. molecules? Would it be good to have an io subpackage? Also, loop modeling and system preparation with OE tk will benefit from reading the original pdb file, since openeye uses information stored in the HEADER section. So we would need an OpenEye specific io module.

jaimergp commented 4 years ago

Core objects in kinoml.core are responsible of importing from several formats. A kinoml.io subpackage might be useful to implement more loaders, but those should only be used from kinoml.core.ObjectModel.from_* classmethods.

That's my initial idea, but we might need to revisit how we adapt because there might be edge cases that makes this more difficult than I thought (e.g. lazy loading smiles).