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pytraj: rmsd_two_parms.py
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| """calculate RMSD for two proteins with different topologies""" | |
| from pytraj import io as mdio | |
| # create trajectory objects (having frames) | |
| traj_0 = mdio.load("../tests/data/Tc5b.crd", "../tests/data/Tc5b.top") | |
| traj_1 = mdio.load("../tests/data/ala3.dcd", "../tests/data/ala3.psf") | |
| # get new traj objects with given mask | |
| traj_0_new = traj_0[":8-10@CA :frame"] | |
| traj_1_new = traj_1[":1-3@CA :frame"] | |
| # note: | |
| # traj_0[":8-10@CA"] (without `:frame`) will return 3D-array with shape (n_frames, n_atoms, 3) | |
| # calculate rmsd between 1st frame of traj_1_new and 1st frame of traj_0_new | |
| # best fit, no mass | |
| print (traj_1_new[0].rmsd(traj_0_new[0])) |
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