jonekoo / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

MDAnalysis Repository README

[*]

MDAnalysis is a Python toolkit to analyze molecular dynamics trajectories generated by a wide range of popular simulation packages including DL_Poly, CHARMM, Amber, NAMD, LAMMPS, and Gromacs. (See the lists of supported trajectory formats and topology formats.)

import MDAnalysis as mda

# Load simulation results with a single line
u = mda.Universe('topol.tpr','traj.trr')

# Select atoms
ag = u.select_atoms('name OH')

# Atom data made available as Numpy arrays
ag.positions
ag.velocities
ag.forces

# Iterate through trajectories
for ts in u.trajectory:
    print(ag.center_of_mass())

Source code

Source code is hosted in a git repository at

https://github.com/MDAnalysis/mdanalysis

and is available under the GNU General Public License, version 2 (see the file LICENSE).

This is the top level of the master repository. It contains

1. the MDAnalysis toolkit source files in the directory

   package/
   

2. the unit tests together with any input files required for running those tests in the directory

   testsuite/
   

The directory maintainer contains scripts only needed for maintaining releases and are not generally useful for the user or the typical developer. The vm directory contains configurations for virtual machines.

(For more details on the directory layout see Issue 87 on the MDAnalysis issue tracker.)

[*]	build: Unit testing is for the whole package; coverage is shown for the core library modules and the analysis modules (which excludes MDAnalysis.visualization at the moment).

mdanalysis's Issues

Selection may not contain residues as a whole

Expected behaviour

In waterdynamics.WaterOrientationalRelaxation.run_bulk(...) The selection of atoms should contain water residues as a whole.

Actual behaviour

Currently it is not checked if the whole residue is contained in the analyzed selection.

Tests for bulk=True in WOR

The current test values for WaterOrientationalRelaxation are not valid when bulk=True.

Create separate class for bulk water WaterOrientationalRelaxation

The bulk=True and bulk=False cases share very little code. Separating them to two different classes would clarify the usage as well as help in merging changes from upstream.