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%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np
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import MDAnalysis as mda
mda.__version__
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TOPOLOGY = 'data/adk.psf'
u = mda.Universe(TOPOLOGY)
Universe extract all the information in the topology and make them available to you. For example you can see how many atoms are in the topology
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u.atoms.n_atoms
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Or the number of individual residues
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u.residues.n_residues
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We can also leverage numpy to see how many unique residue types there are. Residue names are stored in resnames.
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np.unique(u.residues.resnames)
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bb = u.atoms.select_atoms('backbone')
To check that only backbone atoms are selected we can look if we only have C, CA, N and O atoms
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print('number of backbone atoms : {}'.format(bb.n_atoms))
print('unique atoms types : {}'.format(np.unique(bb.names)))
Or we want to only select the C$_{\alpha}$-atoms.
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ca = u.atoms.select_atoms('protein and name CA')
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print('number of Ca atoms : {}'.format(ca.n_atoms))
print('unique atoms types : {}'.format(np.unique(ca.names)))
The complete syntax and possible selection can be look up here
NOTE
It is very important to select C$_{\alpha}$-atoms with the string protein and name CA because Calcium ions also have the name CA.
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TRAJECTORY = 'data/adk_dims.dcd'
u = mda.Universe(TOPOLOGY, TRAJECTORY)
now we can look how many frames the trajectory has
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u.trajectory.n_frames
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Iterating over a trajectory work pythonically.
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for time_step in u.trajectory:
print(time_step.time)