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lewisacidic / scikit-chem

A high level cheminformatics package for the Scientific Python stack, built on RDKit.
http://scikit-chem.readthedocs.io/en/latest/index.html
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Implement a plugin infrastructure #47

Open lewisacidic opened 8 years ago

lewisacidic commented 8 years ago

We could have a plugin infrastructure, for each of the external tools, and for example the interact module.

lewisacidic commented 8 years ago

To be a lot more concrete, the plugin/extension architecture I see as allowing third party packages to register Featurizers, Standardizers, GeometryOptimizers etc. that can then be imported as part of the library if they are installed.

We spin out the ChemAxon wrappers into skchem_chemaxon, which are untestable in CI and provide a hard to satisfy dependency.

The directory structure might be

skchem_chemaxon
├── README.md
├── setup.py
└── skchem_chemaxon
    ├── features
    │   ├── atom.py
    │   ├── fingerprint.py
    │   └── mol.py
    └── standardizers
        └── standardizer.py

As an example, we could find any top level packages matching skchem_* and import the relevant packages/modules, allowing the project structure to be extended by third parties without having to get things from different top level packages.


>>> mf = skchem.features.MorganFeaturizer()
>>> type(mf)
skchem.features.fingerprints.MorganFeaturizer
>>> cxf = skchem.features.ChemAxonFeaturizer()
>>> type(cxf)
skchem_chemaxon.features.mol.ChemAxonFeaturizer

>>> skchem.standardizers.get('cx_feat')

And probably more things.

This might be a bit unnecessary on reflection, as it isn't that hard to just import from the correct module, just saw this was what they do with flask extensions.