Excise and repaint #143
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Excise and repaint #143
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rousseab
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src/diffusion_for_multi_scale_molecular_dynamics/active_learning_loop/excisor/base_excisor.py
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...on_for_multi_scale_molecular_dynamics/active_learning_loop/sample_maker/base_sample_maker.py
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...cale_molecular_dynamics/active_learning_loop/sample_maker/excise_and_repaint_sample_maker.py
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In this PR, I introduce the "sample maker" class, which is a generator but with a different name to avoid overloading terms.
Given an input structure (AXL), the sample maker generates new candidates. The BaseExciseSampleMaker uses an excisor under the hood to find the initial problematic substructure. The ExciseAndRepaintSampleMaker inherits from this and uses an axl score network for repainting the structure.
I added a tutorial, which is probably the best entry point to get an overview of the method.
Note that I defined a filter method, which does nothing for now. We will be able to override them later if we want to add heuristics (such as no two atoms on top of each other)