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