.. -*- coding: utf-8 -*- .. _XYZ-format: ============== XYZ trajectory ============== .. include:: classes/XYZ.txt The :ref:`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. Reading in ========== As XYZ files only have atom name information, the atoms are all assigned to the same residue and segment. The default timestep in MDAnalysis is 1 ps. A different timestep can be defined :ref:`by passing in the dt argument to Universe `. XYZ specification ================= Definiton used by the :class:`XYZReader` and :class:`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 Note ---- * comment lines not implemented (do not include them) * molecule name: the line is required but the content is ignored at the moment * optional data (after the coordinates) are presently ignored .. Links .. _`VMD xyzplugin`: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html