LayerDesign fix to allow ligand-containing pdbs to run
Original layerdesign didn't work on ligands. Our old fix added "L" to the ddsp secstruct string for each ligand molecule. Rocco's recent, better, fix, puts a " " for each ligand, which broke our old, hacky and un-integration-tested fix. This commit gits rid of the hacky fix and works with Rocco's fix. All Unit tests pass and integration tests pass. We should still make a LayerDesign integration test.