opencadd.structure.core.Structure.empty

classmethod Structure.empty(n_atoms, n_residues=1, n_segments=1, atom_resindex=None, residue_segindex=None, trajectory=False, velocities=False, forces=False)

Create a blank Universe

Useful for building a Universe without requiring existing files, for example for system building.

If trajectory is set to True, a MDAnalysis.coordinates.memory.MemoryReader will be attached to the Universe.

Parameters

  • n_atoms (int) – number of Atoms in the Universe

  • n_residues (int, default 1) – number of Residues in the Universe, defaults to 1

  • n_segments (int, default 1) – number of Segments in the Universe, defaults to 1

  • atom_resindex (array like, optional) – mapping of atoms to residues, e.g. with 6 atoms, atom_resindex=[0, 0, 1, 1, 2, 2] would put 2 atoms into each of 3 residues.

  • residue_segindex (array like, optional) – mapping of residues to segments

  • trajectory (bool, optional) – if True, attaches a MDAnalysis.coordinates.memory.MemoryReader allowing coordinates to be set and written.

  • velocities (bool, optional) – include velocities in the MDAnalysis.coordinates.memory.MemoryReader

  • forces (bool, optional) – include forces in the MDAnalysis.coordinates.memory.MemoryReader

Returns

Universe instance with dummy values for atoms and undefined coordinates/velocities/forces

Return type

Universe

Examples

For example to create a new Universe with 6 atoms in 2 residues, with positions for the atoms and a mass attribute:

u = mda.Universe.empty(6, 2,
                       atom_resindex=np.array([0, 0, 0, 1, 1, 1]),
                       trajectory=True,
      )
u.add_TopologyAttr('masses')

New in version 0.17.0.

Changed in version 0.19.0: The attached Reader when trajectory=True is now a MemoryReader

Changed in version 1.0.0: Universes can now be created with 0 atoms