{"library":"mdanalysis","title":"MDAnalysis","description":"MDAnalysis is an open-source, object-oriented toolkit for the analysis of molecular dynamics trajectories and other atomistic simulation data. It provides Python classes to represent and manipulate atomistic data, enabling users to perform various analyses from simple selections to complex calculations. The current version is 2.10.0, and new minor releases are frequent, typically on a monthly or bi-monthly cadence.","language":"python","status":"active","last_verified":"Sun May 17","install":{"commands":["pip install MDAnalysis"],"cli":null},"imports":["import MDAnalysis as mda\nu = mda.Universe(...)","from MDAnalysis.analysis import ...","from MDAnalysis.transformations import ..."],"auth":{"required":false,"env_vars":[]},"quickstart":{"code":"import MDAnalysis as mda\nimport numpy as np\n\n# Create an empty Universe to demonstrate basic operations without requiring files\n# In real applications, you would load structure and trajectory files (e.g., PDB, XTC).\n# u = mda.Universe(\"path/to/structure.pdb\", \"path/to/trajectory.xtc\")\n\nu = mda.Universe.empty(n_atoms=4, trajectory=True)\n\n# Add dummy atom data to the empty Universe\nu.add_atomgroup(mda.AtomGroup([u.select_atoms(\"all\")[0]], universe=u, name='C'))\nu.add_atomgroup(mda.AtomGroup([u.select_atoms(\"all\")[1]], universe=u, name='H'))\nu.add_atomgroup(mda.AtomGroup([u.select_atoms(\"all\")[2]], universe=u, name='O'))\nu.add_atomgroup(mda.AtomGroup([u.select_atoms(\"all\")[3]], universe=u, name='N'))\nu.atoms.types = ['C', 'H', 'O', 'N']\nu.atoms.masses = [12.01, 1.008, 15.999, 14.007]\n\n# Set dummy positions for a single frame\nu.atoms.positions = np.array([\n    [0.0, 0.0, 0.0],\n    [1.0, 0.0, 0.0],\n    [0.0, 1.0, 0.0],\n    [1.0, 1.0, 0.0]\n])\n\nprint(f\"Universe created with {u.atoms.n_atoms} atoms.\")\nprint(f\"First atom: {u.atoms[0].type} at {u.atoms[0].position}\")\n\n# Select atoms based on properties\ncarbon_atoms = u.select_atoms(\"type C\")\nprint(f\"\\nSelected {carbon_atoms.n_atoms} carbon atom(s).\")\nprint(f\"Carbon atom position: {carbon_atoms.positions}\")\n\n# Calculate a simple property, e.g., center of mass\ncenter_of_mass = u.atoms.center_of_mass()\nprint(f\"\\nCenter of mass of all atoms: {center_of_mass}\")","lang":"python","description":"This quickstart demonstrates how to create a simple MDAnalysis Universe object in memory, populate it with dummy atom data, select atoms, and perform a basic calculation. In a typical workflow, you would load data from actual structure (e.g., PDB) and trajectory (e.g., XTC, DCD) files using `mda.Universe('structure.pdb', 'trajectory.xtc')`.","tag":null,"tag_description":null,"last_tested":null,"results":[]},"compatibility":{"tag":null,"tag_description":null,"last_tested":"2026-05-17","installed_version":"2.7.0","pypi_latest":"2.10.0","is_stale":true,"summary":{"python_range":"3.10–3.9","success_rate":50,"avg_install_s":13.1,"avg_import_s":1.65,"wheel_type":"wheel"},"results":[{"runtime":"python:3.10-alpine","python_version":"3.10","os_libc":"alpine (musl)","variant":"MDAnalysis","exit_code":1,"wheel_type":null,"failure_reason":"build_error","import_side_effects":null,"install_time_s":null,"import_time_s":null,"mem_mb":null,"disk_size":null},{"runtime":"python:3.10-slim","python_version":"3.10","os_libc":"slim (glibc)","variant":"MDAnalysis","exit_code":0,"wheel_type":"wheel","failure_reason":null,"import_side_effects":"clean","install_time_s":13.1,"import_time_s":1.04,"mem_mb":32.6,"disk_size":"362M"},{"runtime":"python:3.11-alpine","python_version":"3.11","os_libc":"alpine (musl)","variant":"MDAnalysis","exit_code":1,"wheel_type":null,"failure_reason":"build_error","import_side_effects":null,"install_time_s":null,"import_time_s":null,"mem_mb":null,"disk_size":null},{"runtime":"python:3.11-slim","python_version":"3.11","os_libc":"slim (glibc)","variant":"MDAnalysis","exit_code":0,"wheel_type":"wheel","failure_reason":null,"import_side_effects":"clean","install_time_s":12.7,"import_time_s":1.98,"mem_mb":37.2,"disk_size":"391M"},{"runtime":"python:3.12-alpine","python_version":"3.12","os_libc":"alpine (musl)","variant":"MDAnalysis","exit_code":1,"wheel_type":null,"failure_reason":"build_error","import_side_effects":null,"install_time_s":null,"import_time_s":null,"mem_mb":null,"disk_size":null},{"runtime":"python:3.12-slim","python_version":"3.12","os_libc":"slim (glibc)","variant":"MDAnalysis","exit_code":0,"wheel_type":"wheel","failure_reason":null,"import_side_effects":"clean","install_time_s":12.5,"import_time_s":2.16,"mem_mb":36.7,"disk_size":"375M"},{"runtime":"python:3.13-alpine","python_version":"3.13","os_libc":"alpine (musl)","variant":"MDAnalysis","exit_code":1,"wheel_type":null,"failure_reason":"build_error","import_side_effects":null,"install_time_s":null,"import_time_s":null,"mem_mb":null,"disk_size":null},{"runtime":"python:3.13-slim","python_version":"3.13","os_libc":"slim (glibc)","variant":"MDAnalysis","exit_code":0,"wheel_type":"wheel","failure_reason":null,"import_side_effects":"clean","install_time_s":12.6,"import_time_s":2.04,"mem_mb":37.1,"disk_size":"373M"},{"runtime":"python:3.9-alpine","python_version":"3.9","os_libc":"alpine (musl)","variant":"MDAnalysis","exit_code":1,"wheel_type":null,"failure_reason":"build_error","import_side_effects":null,"install_time_s":null,"import_time_s":null,"mem_mb":null,"disk_size":null},{"runtime":"python:3.9-slim","python_version":"3.9","os_libc":"slim (glibc)","variant":"MDAnalysis","exit_code":0,"wheel_type":"wheel","failure_reason":null,"import_side_effects":"clean","install_time_s":14.6,"import_time_s":1.02,"mem_mb":29.4,"disk_size":"357M"}]}}