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

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5.14. 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)

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()

Close xyz trajectory file if it was open.

numatoms

number of atoms in a frame

rewind()

reposition on first frame