Refactoring structural modeling pipelines

[schallerdavid]

Description

This PR will refactor and implement new structural modeling pipelines. It will focus on a more fine-grained inheritance and lessons learned from the kinase docking benchmark. Please create a new PR targeting the refactor_modeling_featurizers branch when implementing a new featurizer. Modify the Todo list if needed.

Todos

kinoml.features.core

• [x] OEBaseModelingFeaturizer

kinoml.features.protein

• [x] OEProteinStructureFeaturizer

kinoml.features.complexes

• [x] OEComplexFeaturizer
• [x] OEDockingFeaturizer

Other

• [x] switch to new OEDocking API #78
• [x] test OEDocking module #79
• [x] add support for CIF format (important when PDB format is not available, e.g. 6z1q)

Status

• [x] Ready to go

[codecov-commenter]

Codecov Report

Merging #85 (b12d703) into master (66d0ee7) will increase coverage by 6.39%. The diff coverage is 33.88%.

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