mdanalysis

import MDAnalysis as mda import numpy as np # Create an empty Universe to demonstrate basic operations without requiring files # In real applications, you would load structure and trajectory files (e.g., PDB, XTC). # u = mda.Universe("path/to/structure.pdb", "path/to/trajectory.xtc") u = mda.Universe.empty(n_atoms=4, trajectory=True) # Add dummy atom data to the empty Universe u.add_atomgroup(mda.AtomGroup([u.select_atoms("all")[0]], universe=u, name='C')) u.add_atomgroup(mda.AtomGroup([u.select_atoms("all")[1]], universe=u, name='H')) u.add_atomgroup(mda.AtomGroup([u.select_atoms("all")[2]], universe=u, name='O')) u.add_atomgroup(mda.AtomGroup([u.select_atoms("all")[3]], universe=u, name='N')) u.atoms.types = ['C', 'H', 'O', 'N'] u.atoms.masses = [12.01, 1.008, 15.999, 14.007] # Set dummy positions for a single frame u.atoms.positions = np.array([ [0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [1.0, 1.0, 0.0] ]) print(f"Universe created with {u.atoms.n_atoms} atoms.") print(f"First atom: {u.atoms[0].type} at {u.atoms[0].position}") # Select atoms based on properties carbon_atoms = u.select_atoms("type C") print(f"\nSelected {carbon_atoms.n_atoms} carbon atom(s).") print(f"Carbon atom position: {carbon_atoms.positions}") # Calculate a simple property, e.g., center of mass center_of_mass = u.atoms.center_of_mass() print(f"\nCenter of mass of all atoms: {center_of_mass}")