Mdtraj

Mdtraj: A modern open library for the analysis of molecular dynamics trajectories. Read, write and analyze MD trajectories with only a few lines of Python code. With MDTraj, you can Read and write from every MD format imaginable (pdb, xtc, trr, dcd, binpos, netcdf, mdcrd, prmtop, ...) Run blazingly fast RMSD calculations (4x the speed of the original Theobald QCP). Use tons of analysis functions like bonds/angles/dihedrals, hydrogen bonding identification, secondary structure assignment, NMR observables. Use a lightweight API, with a focus on speed and vectorized operations. For details, see the website at mdtraj.org. To get involved, take a look at the github issue tracker and/or the user forums discourse.mdtraj.org.