5.12. AMBER trajectories — MDAnalysis.coordinates.TRJ
¶
AMBER can write ASCII trajectories (“traj”) and binary trajectories (“netcdf”). MDAnalysis supports reading of both formats and writing for the binary trajectories.
Note
Support for AMBER is experimental and feedback and contributions are highly appreciated. Use the Issue Tracker or get in touch on the MDAnalysis mailinglist.
Units
- lengths in Angstrom (Å)
- time in ps (but see below)
AMBER trajectory coordinate frames are based on a Timestep
object.
-
class
MDAnalysis.coordinates.TRJ.
Timestep
(arg, **kwargs)[source]¶ AMBER trajectory Timestep.
The Timestep can be initialized with arg being
- an integer (the number of atoms) and an optional keyword argument velocities to allocate space for both coordinates and velocities;
- another
Timestep
instance, in which case a copy is made (If the copied Timestep does not contain velocities but velocities =True
is provided, then space for velocities is allocated); - a
numpy.ndarray
of shape(numatoms, 3)
(for positions only) or(numatoms, 6)
(for positions and velocities):positions = arg[:,:3]
,velocities = arg[:,3:6]
.
-
_pos
¶ coordinates of the atoms as a
numpy.ndarray
of shape (numatoms, 3)
-
_velocities
¶ velocities of the atoms as a
numpy.ndarray
of shape (numatoms, 3); only available if the trajectory contains velocities or if the velocities =True
keyword has been supplied.
-
dimensions
¶ unitcell dimensions (A, B, C, alpha, beta, gamma)
- A, B, C are the lengths of the primitive cell vectors e1, e2, e3
- alpha = angle(e1, e2)
- beta = angle(e1, e3)
- gamma = angle(e2, e3)
Note
A ASCII AMBER trajectory only contains box lengths A,B,C; we assume an orthorhombic box and set all angles to 90º.
5.12.1. ASCII TRAJ trajectories¶
ASCII AMBER TRJ coordinate files (as defined in AMBER TRJ format)
are handled by the TRJReader
. It is also possible to directly
read bzip2 or gzip compressed files.
AMBER ASCII trajectories are recognised by the suffix ‘.trj’ or ‘.mdcrd’ (possibly with an additional ‘.gz’ or ‘.bz2’).
Limitations
- Periodic boxes are only stored as box lengths A, B, C in an AMBER trajectory; the reader always assumes that these are orthorhombic boxes.
- The trajectory does not contain time information so we simply set the time step to 1 ps (or the user could provide it as kwarg delta)
- No direct access of frames is implemented, only iteration through the trajectory.
- Trajectories with fewer than 4 atoms probably fail to be read (BUG).
- If the trajectory contains exactly one atom then it is always assumed to be non-periodic (for technical reasons).
-
class
MDAnalysis.coordinates.TRJ.
TRJReader
(filename, numatoms=None, **kwargs)[source]¶ AMBER trajectory reader.
Reads the ASCII formatted AMBER TRJ format. Periodic box information is auto-detected.
The number of atoms in a timestep must be provided in the numatoms keyword because it is not stored in the trajectory header and cannot be reliably autodetected. The constructor raises a
ValueError
if numatoms is left at its default value ofNone
.The length of a timestep is not stored in the trajectory itself but can be set by passing the delta keyword argument to the constructor; it is assumed to be in ps. The default value is 1 ps.
Functionality is currently limited to simple iteration over the trajectory.
-
numframes
¶ Number of frames (obtained from reading the whole trajectory).
-
5.12.2. Binary NetCDF trajectories¶
The AMBER netcdf format make use of NetCDF (Network Common Data
Form) format. Such binary trajectories are recognized in MDAnalysis by
the ‘.ncdf’ suffix and read by the NCDFReader
.
Binary trajectories can also contain velocities and can record the exact time
step. In principle, the trajectories can be in different units than the AMBER
defaults of ångström and picoseconds but at the moment MDAnalysis only supports
those and will raise a NotImplementedError
if anything else is detected.
-
class
MDAnalysis.coordinates.TRJ.
NCDFReader
(filename, numatoms=None, **kwargs)[source]¶ Reader for AMBER NETCDF format (version 1.0).
AMBER binary trajectories are automatically recognised by the file extension ”.ncdf”.
The number of atoms (numatoms) does not have to be provided as it can be read from the trajectory. The trajectory reader can randomly access frames and therefore supports direct indexing (with 0-based frame indices) and full-feature trajectory iteration, including slicing.
Velocities are autodetected and read into the
Timestep._velocities
attribute.Periodic unit cell information is detected and used to populate the
Timestep.dimensions
attribute. (If no unit cell is available in the trajectory, thenTimestep.dimensions
will return[0,0,0,0,0,0]
.)Current limitations:
- only trajectories with time in ps and lengths in Angstroem are processed
- scale_factors are not supported (and not checked)
See also
-
__getitem__
(frame)[source]¶ Return the Timestep corresponding to frame.
If frame is a integer then the corresponding frame is returned. Negative numbers are counted from the end.
If frame is a
slice
then an iterator is returned that allows iteration over that part of the trajectory.Note
frame is a 0-based frame index.
-
Writer
(filename, **kwargs)[source]¶ Returns a NCDFWriter for filename with the same parameters as this NCDF.
All values can be changed through keyword arguments.
Arguments: - filename
filename of the output NCDF trajectory
Keywords: - numatoms
number of atoms
- delta
length of one timestep in picoseconds
- remarks
string that is stored in the title field
Returns:
-
class
MDAnalysis.coordinates.TRJ.
NCDFWriter
(filename, numatoms, start=0, step=1, delta=1.0, remarks=None, convert_units=None, zlib=False, cmplevel=1)[source]¶ Writer for AMBER NETCDF format (version 1.0).
AMBER binary trajectories are automatically recognised by the file extension ”.ncdf”.
Velocities are written out if they are detected in the input
Timestep
. The trajectories are always written with ångström for the lengths and picoseconds for the time (and hence Å/ps for velocities).Unit cell information is written if available.
See also
Create a new NCDFWriter
Arguments: - filename
name of output file
- numatoms
number of atoms in trajectory file
Keywords: - start
starting timestep
- step
skip between subsequent timesteps
- delta
timestep
- convert_units
True
: units are converted to the AMBER base format;None
selects the value ofMDAnalysis.core.flags
[‘convert_lengths’]. (see Flags)- zlib
compress data [
False
]- cmplevel
compression level (1-9) [1]