6.20. XYZ trajectory reader — MDAnalysis.coordinates.XYZ¶
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).
The atom name (first column) is ignored during reading.
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.
The unitcell information is all zeros since this is not recorded in the XYZ format.
Units
Coordinates are in Angstroms.
The length of a timestep can be set by passing the dt 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.
6.20.1. XYZ File format¶
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
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
6.20.2. Classes¶
-
class
MDAnalysis.coordinates.XYZ.XYZReader(filename, **kwargs)[source]¶ Reads from an XYZ file
- Data
tsTimestep object containing coordinates of current frame
- Methods
len(xyz)return number of frames in xyz
for ts in xyz:iterate through trajectory
The XYZ file format follows VMD’s xyzplugin and is also described under XYZ format.
Changed in version 0.11.0: Frames now 0-based instead of 1-based. Added dt and time_offset keywords (passed to
Timestep)-
Writer(filename, n_atoms=None, **kwargs)[source]¶ Returns a XYZWriter for filename with the same parameters as this XYZ.
- Parameters
- Returns
- Return type
XYZWriter(see there for more details)
See also
-
property
n_atoms¶ number of atoms in a frame
-
class
MDAnalysis.coordinates.XYZ.XYZWriter(filename, n_atoms=None, atoms=None, convert_units=None, remark=None, **kwargs)[source]¶ Writes an XYZ file
The XYZ file format is not formally defined. This writer follows the VMD implementation for the molfile xyzplugin.
Initialize the XYZ trajectory writer
- Parameters
filename (str) – filename of trajectory file. If it ends with “gz” then the file will be gzip-compressed; if it ends with “bz2” it will be bzip2 compressed.
n_atoms (int (optional)) – Number of atoms in trajectory. By default assume that this is None and that this file is used to store several different models instead of a single trajectory. If a number is provided each written TimeStep has to contain the same number of atoms.
atoms (str | list (optional)) – Provide atom names: This can be a list of names or an
AtomGroup. If none is provided, atoms will be called ‘X’ in the output. These atom names will be used when a trajectory is written from rawTimestepobjects which do not contain atom information. If you write aAtomGroupwithXYZWriter.write()then atom information is taken at each step and atoms is ignored.remark (str (optional)) – single line of text (“molecule name”). By default writes MDAnalysis version
