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. Default is Falsevelocities (bool, optional) – include velocities in the
MDAnalysis.coordinates.memory.MemoryReader
forces (bool, optional) – include forces in the
MDAnalysis.coordinates.memory.MemoryReader
- Returns
- Return type
MDAnalysis.Universe object
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