Examples

Oliver Beckstein edited this page Mar 9, 2018 · 14 revisions

NOTE: This page may contain outdated code. You can edit the wiki to correct it. And/or ask on the user mailinglist. (It is difficult to maintain the wiki in sync with the standard documentation https://docs.mdanalysis.org so we apologize for any inconsistencies here. Please contribute!) — @orbeckst 2018-03-09


Add your own examples either to the page itself or in the comments at the bottom of the page.

Frame-based analysis

A typical usage pattern is to iterate through a trajectory and analyze coordinates for every frame. In the following example the end-to-end distance of a protein and the radius of gyration of the backbone atoms is calculated:

import MDAnalysis
from MDAnalysis.tests.datafiles import PSF,DCD   # test trajectory
import numpy.linalg
u = MDAnalysis.Universe(PSF,DCD)                 # always start with a Universe
nterm = u.s4AKE.N[0]   # can access structure via segid (s4AKE) and atom name
cterm = u.s4AKE.C[-1]  # ... takes the last atom named 'C'
bb = u.selectAtoms('protein and backbone')  # a selection (a AtomGroup)
for ts in u.trajectory:     # iterate through all frames
  r = cterm.pos - nterm.pos # end-to-end vector from atom positions
  d = numpy.linalg.norm(r)  # end-to-end distance
  rgyr = bb.radiusOfGyration()  # method of a AtomGroup; updates with each frame
  print "frame = %d: d = %f Angstroem, Rgyr = %f Angstroem" % (ts.frame, d, rgyr)

Molecular editing

MDAnalysis also has rudimentary abilities for structure editing and extraction.

Extracting a chain from a PDB

Load a PDB, select what you want, and then write out the selection in PDB (or any other) file format:

import MDAnalysis
u = MDAnalysis.Universe('1ES7.pdb') 
A = u.selectAtoms('segid A')
A.write('1ES7_A.pdb')

Note:

  • MDAnalysis uses PDB chain identifiers to set the segment id ("segid") of Segments. Thus for chain selections (which is PDB specific) you need to select for ''segid''.

Interactive analysis of structures

Residue charges in a PQR file

PQR files contain the atomic partial charges. If you want to know the charge on each residue (e.g. in order to check the actual protonation state assigned by pdb2pqr) then you can do this quickly (e.g. in the ipython shell):

u = MDAnalysis.Universe("protein.pqr")
for resname, resid, q in zip(u.residues.resnames, u.residues.resids, u.residues.charges):
  print("%s %d     %+4.2f" % (resname, resid, q))

This will print the residue and the total charge for all residues.

You can also define a function that returns the data in a list, prints it to screen or alternatively to a file filename:

def rescharges(u, filename=None, epsilon=0.01):
    if filename is not None:
        out = open(filename, "w")
    else:
        import sys
        out = sys.stdout
    resq = []
    for resname, resid, q in zip(u.residues.resnames, u.residues.resids, u.residues.charges):
        out.write("%s %d     %+4.2f" % (resname, resid, q))
    if filename is not None:
        out.close()
    return resq

File format conversion

Converting a single frame is straightforward: read it into a universe and write out the atoms. For instance, converting from PQR to PDB:

from MDAnalysis import Universe
u = Universe("system.pqr")
u.atoms.write("system.pdb")

In order to convert trajectories you obtain a trajectory Writer for the desired output, loop through the input trajectory frame by frame, and write each frame to the output (see dcd2xtc.py for the conversion from DCD to XTC. The core of this short script is:

from MDAnalysis import Universe, Writer
u = Universe("system.psf", "system.dcd")
with Writer("system.xtc", u.trajectory.n_atoms) as w:
    for ts in u.trajectory:
        w.write(ts)

(You might also want to write a PDB file to be used together with the XTC.)

Simple scripts

Have a look at the examples subdirectory for some other examples. Note: These examples were all written using numpy version 1.0.2. Older versions of numpy may not work correctly (since the api wasn't finalized until 1.0). Some of the scripts are incomplete in that one has to enter a psf and a dcd file somewhere at the top. The main purpose is to give an idea of how to quickly code up some interesting analysis tasks with the help of MDAnalysis.

Analysis module

Since MDAnalysis 0.6.2 there exists a collection of analysis modules. One can use them by importing the appropriate module

import MDAnalysis.analysis
help(MDAnalysis.analysis)           # see what's available
import MDAnalysis.analysis.contacts # use the native-contacts analysis

The source code of the analysis sub-modules can be used to learn how to do fairly complicated things with MDAnalysis.

Note that some of the sub-modules require additional python packages. One can automatically install dependencies for the analysis optional package with (something like... see InstallRecipes)

  cd MDAnalysis-0.6.3
  easy_install-2.6 . MDAnalysis[analysis] 

(The optional package is added in brackets after the name of the package; see the easy_install docs.)

Parallel analysis on multiple cores

  • A limited number of functions have parallel versions such as the distance computations in MDAnalysis.core.parallel.distances. When they are used instead of the serial code they use all available cores.
  • As demonstrated in Multicore_MDAnalysis one can also use the Python multiprocessing module to split analysis tasks and work on them in parallel.

Project Information

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GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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