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5.14. Gromacs XTC file IO — MDAnalysis.coordinates.XTC

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5.15. XYZ trajectory reader — MDAnalysis.coordinates.XYZ

Resources: the XYZ format was taken from http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html and is therefore compatible with VMD (you need a PDB or PSF file to define the topology, just as here)

  • comments are not allowed in the XYZ file
  • the atom name (first column) is ignored
  • the coordinates are assumed to be space-delimited rather than fixed width (this may cause issues - see below)
  • all fields to the right of the z-coordinate are ignored
  • it is assumed that the coordinates are in Angstroms
  • the unitcell information is all zeros since this is not recorded in the XYZ format
  • the length of a timestep can be set by passing the delta argument, it’s assumed to be in ps (default: 1 ps)

There appears to be no rigid format definition so it is likely users will need to tweak this Class.

class MDAnalysis.coordinates.XYZ.XYZReader(xyzfilename, **kwargs)[source]

Reads from an XYZ file

Data:
ts

Timestep object containing coordinates of current frame

Methods:
len(xyz)

return number of frames in xyz

for ts in xyz:

iterate through trajectory

File format: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html

Validation: the geometric centre of 1284 atoms was calculated over 500 frames using both MDAnalysis and a VMD Tcl script. There was exact agreement (measured to 3DP). bzipped and gzipped versions of the XYZ file were also tested

close()[source]

Close xyz trajectory file if it was open.

numatoms[source]

number of atoms in a frame

rewind()[source]

reposition on first frame