Allow non-ligand, non-protein atoms to move beyond min_cutoff

proteneer / timemachine

Differentiate all the things!

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Allow non-ligand, non-protein atoms to move beyond min_cutoff #1248

Closed proteneer closed 9 months ago

proteneer commented 9 months ago

During minimization, water molecules can spuriously move beyond the specified min_cutoff. This PR restricts the movement to that of only ligand and protein atoms. InitialState is now modified to include also protein_idxs.