13.3.1. Low-level Gromacs XDR trajectory reading — MDAnalysis.lib.formats.libmdaxdr
libmdaxdr contains the classes XTCFile and
TRRFile. Both can be used to read and write frames from and to
Gromacs XTC and TRR files. These classes are used internally by MDAnalysis in
MDAnalysis.coordinates.XTC and MDAnalysis.coordinates.TRR. They
behave similar to normal file objects.
For example, one can use a XTCFile to directly calculate mean
coordinates (where the coordinates are stored in x attribute of the
namedtuple frame):
with XTCFile("trajectory.xtc") as xtc:
n_atoms = xtc.n_atoms
mean = np.zeros((n_atoms, 3))
# iterate over trajectory
for frame in xtc:
mean += frame.x
The XTCFile class can be useful as a compressed storage format.
Besides iteration, XTCFile and TRRFile one can also seek to
arbitrary frames using the seek() method. This is provided by
lazily generating a offset list for stored frames. The offset list is generated
the first time len() or :~XTCFile.seek is called.
(For more details on how to use XTCFile and TRRFile on their
own please see the source code in lib/formats/libmdaxdr.pyx for the time being.)
- class MDAnalysis.lib.formats.libmdaxdr.TRRFile
File-like wrapper for gromacs TRR files.
This class can be similar to the normal file objects in python. The read() function will return a frame and all information in it instead of a single line. Additionally the context-manager protocoll is supported as well.
- Parameters:
fname (str) – The filename to open.
mode (('r', 'w')) – The mode in which to open the file, either ‘r’ read or ‘w’ write
Examples
>>> from MDAnalysis.lib.formats.libmdaxdr import TRRFile >>> with TRRFile('foo.trr') as f: >>> for frame in f: >>> print(frame.x)
Notes
This class can be pickled. The pickle will store filename, mode, current frame and offsets
Changed in version 2.4.0: Added read_direct_xvf method to read into an existing positions array
- calc_offsets()
read byte offsets from TRR file directly
- offsets
get byte offsets from current xdr file
See also
- open(fname, mode)
Open a XDR file
If another XDR file is currently opened it will be closed
- read()
Read next frame in the TRR file
- Returns:
frame – namedtuple with frame information
- Return type:
libmdaxdr.TRRFrame
See also
TRRFrame,XTCFile- Raises:
IOError –
- read_direct_xvf(positions, velocities, forces)
Read next frame in the TRR file with positions read directly into a pre-existing array.
- Parameters:
positions (np.ndarray) – positions array to read positions into
- Returns:
frame – namedtuple with frame information
- Return type:
libmdaxdr.TRRFrame
See also
TRRFrame,XTCFile- Raises:
IOError –
New in version 2.4.0.
- seek(frame)
Seek to Frame.
Please note that this function will generate internal file offsets if they haven’t been set before. For large file this means the first seek can be very slow. Later seeks will be very fast.
- set_offsets(offsets)
set frame offsets
- tell()
Get current frame
- write(xyz, velocity, forces, box, step, time, _lambda, natoms)
write one frame into TRR file.
- Parameters:
xyz (array_like, shape=(n_atoms, 3), optional) – cartesion coordinates. Only written if not
None.velocity (array_like, shape=(n_atoms, 3), optional) – cartesion velocities. Only written if not
None.forces (array_like, shape=(n_atoms, 3), optional) – cartesion forces. Only written if not
None.box (array_like, shape=(3, 3)) – Box vectors for this frame
step (int) – current step number, 1 indexed
time (float) – current time
_lambda (float) – current lambda value
natoms (int) – number of atoms in frame
- Raises:
IOError –
- class MDAnalysis.lib.formats.libmdaxdr.XTCFile
File-like wrapper for gromacs XTC files.
This class can be similar to the normal file objects in python. The read() function will return a frame and all information in it instead of a single line. Additionally the context-manager protocoll is supported as well.
- Parameters:
fname (str) – The filename to open.
mode (('r', 'w')) – The mode in which to open the file, either ‘r’ read or ‘w’ write
Examples
>>> from MDAnalysis.lib.formats.libmdaxdr import XTCFile >>> with XTCFile('foo.trr') as f: >>> for frame in f: >>> print(frame.x)
Notes
This class can be pickled. The pickle will store filename, mode, current frame and offsets
Changed in version 2.4.0: Added read_direct_x method to read into an existing positions array
- calc_offsets()
Calculate offsets from XTC file directly
- offsets
get byte offsets from current xdr file
See also
- open(fname, mode)
Open a XDR file
If another XDR file is currently opened it will be closed
- read()
Read next frame in the XTC file
- Returns:
frame – namedtuple with frame information
- Return type:
libmdaxdr.XTCFrame
See also
XTCFrame,TRRFile- Raises:
IOError –
- read_direct_x(positions)
Read next frame in the XTC file with positions read directly into a pre-existing array.
- Parameters:
positions (np.ndarray) – positions array to read positions into
- Returns:
frame – namedtuple with frame information
- Return type:
libmdaxdr.XTCFrame
See also
XTCFrame,TRRFile- Raises:
IOError –
New in version 2.4.0.
- seek(frame)
Seek to Frame.
Please note that this function will generate internal file offsets if they haven’t been set before. For large file this means the first seek can be very slow. Later seeks will be very fast.
- set_offsets(offsets)
set frame offsets
- tell()
Get current frame
- write(xyz, box, step, time, precision=1000.0)
write one frame to the XTC file
- Parameters:
Notes
Gromacs specifies the precision a little bit strange. The coordinates will be multiplied by precision and then converted to an integer. This means a precision of 1000 yields an accuracy of 3 decimal places.
- Raises:
IOError –