The XYZ format is a loosely defined, simple coordinate trajectory format. The implemented format definition was taken from the VMD xyzplugin and is therefore compatible with VMD.
Note the following: * comments are not allowed in the XYZ file (we neither read nor write
them to remain compatible with VMD)
Units * Coordinates are in Angstroms. * 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.
Definiton used by the XYZReader and XYZWriter (and the VMD xyzplugin from whence the definition was taken):
[ comment line ] !! NOT IMPLEMENTED !! DO NOT INCLUDE
[ N ] # of atoms, required by this xyz reader plugin line 1
[ molecule name ] name of molecule (can be blank) line 2
atom1 x y z [optional data] atom name followed by xyz coords line 3
atom2 x y z [ ... ] and (optionally) other data.
...
atomN x y z [ ... ] line N+2
Reads from an XYZ file
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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
Returns a XYZWriter for filename with the same parameters as this XYZ.
All values can be changed through keyword arguments.
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Returns : | XYZWriter (see there for more details) |
Writes an XYZ file
The XYZ file format is not formally defined. This writer follows the implement http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html .
Initialize the XYZ trajectory writer
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