mdtraj.formats.XTCTrajectoryFile¶
-
class
mdtraj.formats.
XTCTrajectoryFile
(filenamee, mode='r', force_overwrite=True, **kwargs)¶ Interface for reading and writing to a GROMACS XTC file. This is a file-like objec that supports both reading and writing. It also supports the context manager ptorocol, so you can use it with the python ‘with’ statement.
The conventional units in the XTC file are nanometers and picoseconds. The format only supports saving coordinates, the time, the md step, and the unit cell parametrs (box vectors)
Parameters: filename : str
The filename to open. A path to a file on disk.
mode : {‘r’, ‘w’}
The mode in which to open the file, either ‘r’ for read or ‘w’ for write.
force_overwrite : bool
If opened in write mode, and a file by the name of filename already exists on disk, should we overwrite it?
Other Parameters: min_chunk_size : int, default=100
In read mode, we need to allocate a buffer in which to store the data without knowing how many frames are in the file. This parameter is the minimum size of the buffer to allocate.
chunk_size_multiplier : int, default=1.5
In read mode, we need to allocate a buffer in which to store the data without knowing how many frames are in the file. We can guess this information based on the size of the file on disk, but it’s not perfect. This parameter inflates the guess by a multiplicative factor.
See also
mdtraj.load_xtc
- High-level wrapper that returns a
md.Trajectory
Examples
>>> # read the data from from an XTC file >>> with XTCTrajectoryFile('traj.xtc') as f: >>> xyz, time, step, box = f.read()
>>> # write some random coordinates to an XTC file >>> with XTCTrajectoryFile('output.xtc', 'w') as f: >>> f.write(np.random.randn(10,1,3))
Attributes
distance_unit
offsets
get byte offsets from current xtc file Methods
close
Close the XTC file handle read
([n_frames, stride, atom_indices])Read data from an XTC file read_as_traj
(topology[, n_frames, stride, …])Read a trajectory from an XTC file seek
(offset[, whence])Move to a new file position tell
Current file position write
(xyz[, time, step, box])Write data to an XTC file -
__init__
($self, /, *args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
Methods
close
Close the XTC file handle read
([n_frames, stride, atom_indices])Read data from an XTC file read_as_traj
(topology[, n_frames, stride, …])Read a trajectory from an XTC file seek
(offset[, whence])Move to a new file position tell
Current file position write
(xyz[, time, step, box])Write data to an XTC file -
close
()¶ Close the XTC file handle
-
offsets
¶ get byte offsets from current xtc file
-
read
(n_frames=None, stride=None, atom_indices=None)¶ Read data from an XTC file
Parameters: n_frames : int, None
The number of frames you would like to read from the file. If None, all of the remaining frames will be loaded.
stride : int, optional
Read only every stride-th frame.
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it required an extra copy, but will save memory.
Returns: xyz : np.ndarray, shape=(n_frames, n_atoms, 3), dtype=np.float32
The cartesian coordinates, in nanometers
time : np.ndarray, shape=(n_frames), dtype=np.float32
The simulation time, in picoseconds, corresponding to each frame
step : np.ndarray, shape=(n_frames), dtype=np.int32
The step in the simulation corresponding to each frame
box : np.ndarray, shape=(n_frames, 3, 3), dtype=np.float32
The box vectors in each frame.
See also
read_as_traj
- Returns a Trajectory object
-
read_as_traj
(topology, n_frames=None, stride=None, atom_indices=None)¶ Read a trajectory from an XTC file
Parameters: topology : Topology
The system topology
n_frames : int, None
The number of frames you would like to read from the file. If None, all of the remaining frames will be loaded.
stride : int, optional
Read only every stride-th frame.
atom_indices : array_like, optional
If not none, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it required an extra copy, but will save memory.
Returns: trajectory : Trajectory
A trajectory object containing the loaded portion of the file.
See also
read
- Returns the raw data from the file
-
seek
(offset, whence=0)¶ Move to a new file position
Parameters: offset : int
A number of frames.
whence : {0, 1, 2}
0: offset from start of file, offset should be >=0. 1: move relative to the current position, positive or negative 2: move relative to the end of file, offset should be <= 0. Seeking beyond the end of a file is not supported
-
tell
()¶ Current file position
Returns: offset : int
The current frame in the file.
-
write
(xyz, time=None, step=None, box=None)¶ Write data to an XTC file
Parameters: xyz : np.ndarray, dtype=np.float32, shape=(n_frames, n_atoms, 3)
The cartesian coordinates of the atoms, in nanometers
time : np.ndarray, dtype=float32, shape=(n_frames), optional
The simulation time corresponding to each frame, in picoseconds. If not supplied, the numbers 0..n_frames will be written.
step : np.ndarray, dtype=int32, shape=(n_frames), optional
The simulation timestep corresponding to each frame, in steps. If not supplied, the numbers 0..n_frames will be written
box : np.ndarray, dtype=float32, shape=(n_frames, 3, 3), optional
The periodic box vectors of the simulation in each frame, in nanometers. If not supplied, the vectors (1,0,0), (0,1,0) and (0,0,1) will be written for each frame.