Data Science in Chemistry by Thorsten Gressling

Author:Thorsten Gressling [Thorsten Gressling]
Language: eng
Format: epub
Publisher: De Gruyter
Published: 2020-10-30T00:00:00+00:00

# Analyze coordinates in a trajectory (MDAnalysis) # author: MDAnalysis team # license: GPL-2 # code: github.com/MDAnalysis/…/examples/ # activity: active (2020) # index: 53-2 import MDAnalysis from MDAnalysis.tests.datafiles import PSF, DCD # test trajectory import numpy.linalg u = MDAnalysis.Universe(PSF,DCD) # always start with a Universe # can access via segid (4AKE) and atom name # we take the first atom named N and the last atom named C nterm = u.select_atoms('segid 4AKE and name N')[0] cterm = u.select_atoms('segid 4AKE and name C')[-1] bb = u.select_atoms('protein and backbone') # a selection (AtomGroup) for ts in u.trajectory: # iterate through all frames r = cterm.position - nterm.position # end-to-end vector from atom positions d = numpy.linalg.norm(r) # end-to-end distance rgyr = bb.radius_of_gyration() # method of AtomGroup print("frame = {0}: d = {1} A, Rgyr = {2} A".format( ts.frame, d, rgyr))

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