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 | ✓ | ✓ | |