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Table 2 Select optional Scoria functions available when third-party libraries are installed

From: Scoria: a Python module for manipulating 3D molecular data

Features Optional dependencies
Module Definition Notes NumPy SciPy MDAnalysis
fileio load_pym_into Load PYM file   
fileio load_via_MDAnalysis Load from file(s) via MDAnalysis  
fileio load_MDAnalysis_into Load from MDAnalysis Universe object  
fileio save_pym   
selections select_all_atoms_bound_to_selection Select atoms bound to user-specified selection   
selections select_branch Selects an individual branch of a molecule   
selections select_atoms_from_same_molecule Select atoms belonging to same molecule   
selections selections_of_constituent_molecules Gets a list of all selections based on their molecule   
selections select_atoms_near_other_selection  
selections select_close_atoms_from_different_molecules  
manipulation rotate_molecule_around_pivot_point   
manipulation rotate_molecule_around_pivot_atom   
other_molecules get_other_molecule_aligned_to_this     
other_molecules steric_clash_with_another_molecule  
other_molecules get_distance_to_another_molecule  
other_molecules get_rmsd_heuristic Calculate RMSD between two sets of atoms  
atoms_and_bonds create_bonds_by_distance Determine which atoms are bonded based on distance between them