mdanalysis_universe_atom_selection_trajectory_iteration_quickstart.py

1import MDAnalysis as mda
2from MDAnalysis.tests.datafiles import PSF, DCD
3
4# Load a Universe (topology and trajectory)
5# In practice, you would use: u = mda.Universe("topology.psf", "trajectory.dcd")
6u = mda.Universe(PSF, DCD)
7
8# Select specific atoms
9ca = u.select_atoms("name CA")
10
11# Access information about the selection
12print(f"Number of CA atoms: {len(ca)}")
13print(f"Positions of first 5 CA atoms:\n{ca.positions[:5]}")
14
15# Iterate through the trajectory and calculate the center of mass
16for ts in u.trajectory:
17    com = ca.center_of_mass()
18    print(f"Frame: {ts.frame}, CA Center of Mass: {com}")
19
20# Write a selection to a file
21ca.write("ca_atoms.pdb")