Created
January 9, 2025 00:20
-
-
Save orbeckst/2b3cbe554a38f5e79df39e82a8395d2d to your computer and use it in GitHub Desktop.
Create a MDAnalysis Universe for a "trajectory" in a numpy array.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import MDAnalysis as mda | |
| import numpy as np | |
| n_atoms = 6 | |
| n_steps = 4 | |
| # create empty Universe with one atom per residue | |
| u = mda.Universe.empty(n_atoms, n_residues=n_atoms, atom_resindex=np.arange(n_atoms), trajectory=True) | |
| # optional: name each atom CA | |
| u.add_TopologyAttr("name") | |
| u.atoms.names = "CA" | |
| # fake trajectory as np array | |
| coordinates = 100*np.random.random(size=(n_steps, n_atoms, 3)) - 50 | |
| # add trajectory to Universe | |
| u.load_new(coordinates) | |
| # You can now use u in the same way as a "normal" Universe that was created from | |
| # files, such as u = mda.Universe(PRMTOP, NCDF). | |
| # | |
| # Note that you have to manually add resids and other data if you want to access it. | |
| # See https://userguide.mdanalysis.org/stable/examples/constructing_universe.html#Creating-a-blank-Universe |
Author
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
If you want to add masses (such as carbon), add the appropriate topology attribute and set it with an array of mass values