`DCDFile`#

class biotite.structure.io.dcd.DCDFile[source]#

Bases: TrajectoryFile

This file class represents a DCD trajectory file.

copy()#

This operation is not implemented for trajectory files.

Raises:

NotImplementedError

get_box()#

Get the box vectors for each frame.

Returns:

boxndarray, dtype=float, shape=(m,3,3): An array containing the box dimensions for the frames, that were read from the file.

get_coord()#

Extract only the atom coordinates from the trajectory file.

Returns:

coordndarray, dtype=float, shape=(m,n,3): The coordinates stored in the trajectory file.

get_structure(template)#

Convert the trajectory file content into an AtomArrayStack.

Since trajectory files usually only contain atom coordinate information and no topology information, this method requires a template atom array or stack. This template can be acquired for example from a PDB file, which is associated with the trajectory file.

Parameters:

templateAtomArray or AtomArrayStack: The template array or stack, where the atom annotation data is taken from.

Returns:

array_stackAtomArrayStack: A stack containing the annontation arrays from template but the coordinates and the simulation boxes from the trajectory file.

get_time()#

Get the simlation time in ps values for each frame.

Returns:

timendarray, dtype=float, shape=(m,): A one dimensional array containing the time values for the frames, that were read from the file.

classmethod prepare_write_values(coord, box, time)#

Convert the coord, box and time attribute into a dictionary that is given as kwargs to the respective biotraj.TrajectoryFile.write() method.

PROTECTED: Override when inheriting.

Parameters:

coordndarray, dtype=float, shape=(m,n,3): The atom coordinates in Å for each frame.
boxndarray, dtype=float, shape=(m,3,3): The box vectors in Å for each frame.
timendarray, dtype=float, shape=(m,): The simulation time in ps for each frame.

Returns:

parametersdict: This dictionary is given as kwargs parameter to the respective biotraj.TrajectoryFile.write() method.

classmethod process_read_values(read_values)#

Convert the return value of the read() method of the respective biotraj.TrajectoryFile into coordinates, simulation box and simulation time.

PROTECTED: Override when inheriting.

Parameters:

read_valuestuple: The return value of the respective biotraj.TrajectoryFile.read() method.

Returns:

coordndarray, dtype=float, shape=(m,n,3): The atom coordinates in Å for each frame.
boxndarray, dtype=float, shape=(m,3,3) or None: The box vectors in Å for each frame.
timendarray, dtype=float, shape=(m,) or None: The simulation time in ps for each frame.

classmethod read(file_name, start=None, stop=None, step=None, atom_i=None, chunk_size=None)#

Read a trajectory file.

A trajectory file can be seen as a file representation of an AtomArrayStack. Therefore, start, stop and step represent slice parameters of the index of the first dimension and atom_i represents an index array for the second dimension.

Parameters:

file_namestr: The path of the file to be read. A file-like-object cannot be used.
startint, optional: The frame index, where file parsing is started. If no value is given, parsing starts at the first frame. The index starts at 0.
stopint, optional: The exclusive frame index, where file parsing ends. If no value is given, parsing stops after the last frame. The index starts at 0.
stepint, optional: If this value is set, the function reads only every n-th frame from the file.
atom_indarray, dtype=int, optional: If this parameter is set, only the atoms at the given indices are read from each frame.
chunk_sizeint, optional: If this parameter is set, the trajectory is read in chunks: Only the number of frames specified by this parameter are read at once. The resulting chunks of frames are automatically concatenated, after all chunks are collected. Use this parameter, if a MemoryError is raised when a trajectory file is read. Although lower values can decrease the memory consumption of reading trajectories, they also increase the computation time.

Returns:

file_objectTrajectoryFile: The parsed trajectory file.

classmethod read_iter(file_name, start=None, stop=None, step=None, atom_i=None, stack_size=None)#

Create an iterator over each frame of the given trajectory file in the selected range.

Parameters:

file_namestr: The path of the file to be read. A file-like-object cannot be used.
startint, optional: The frame index, where file parsing is started. If no value is given, parsing starts at the first frame. The index starts at 0.
stopint, optional: The exclusive frame index, where file parsing ends. If no value is given, parsing stops at the end of file. The index starts at 0.
stepint, optional: If this value is set, the function reads only every n-th frame from the file.
atom_indarray, dtype=int, optional: If this parameter is set, only the atoms at the given indices are read from each frame.
stack_sizeint, optional: If this parameter is set, the given number of frames m are read at once. As result an additional dimension is added to the return values. If the number of frames is not a multiple of stack_size, the final stack is smaller than stack_size.

Yields:

coordndarray, dtype=float32, shape=(n,3) or shape=(m,n,3): The atom coordinates in the current frame or stack.
boxndarray, dtype=float32, shape=(3,3) or shape=(m,3,3) or None: The box vectors of the current frame or stack.
timefloat or ndarray, dtype=float32, shape=(n,) or None: The simulation time of the current frame or stack in ps.

DCDFile#

`DCDFile`#