API for the TNGFileIterator Class

class pytng.TNGFileIterator

File handle object for TNG files

Supports use as a context manager (“with” blocks).

block_ids

Dictionary of block names and block ids (long longs) in the TNG file

Returns:: block_ids – dictionary of block names (keys) and block ids (values)
Return type:: dict

block_strides

Dictionary of block names and the strides (in integrator steps) at which they are written in the TNG file

Returns:: block_strides – dictionary of block names (keys) and strides of each block (values)
Return type:: dict

current_integrator_step

Class that retrieves data from the file at the current integrator: step

Returns:: current_integrator_step – The data accessor at the current integrator step
Return type:: TNGCurrentIntegratorStep

make_ndarray_for_block_from_id(self, int64_t block_id) → ndarray

Make a NumPy array that can hold a specified block from the block id

Parameters:: block_id (int64_t) – a block id
Returns:: target – A NumPy array that can hold the data values for a specified block
Return type:: np.ndarray

See also

block_ids: dict dictionary of block names (keys) and block ids (values) available in this TNG file

n_atoms

The number of atoms in the TNG file

Returns:: n_atoms – number of atoms
Return type:: int

n_data_frames

Dictionary of block names and the number of actual steps with data for that block in the TNG file

Returns:: n_data_frames – dictionary of block names (keys) and number of steps with data (values)
Return type:: dict

n_steps

The number of integrator steps in the TNG file

Returns:: n_steps – number of integrator steps
Return type:: int

particle_dependencies

Dictionary of block names and whether the block is particle dependent

Returns:: particle_dependencies – dictionary of block names (keys) and particle dependencies (values)
Return type:: dict

read_step(self, step) → TNGCurrentIntegratorStep

Read a step (integrator step) from the file

Parameters:: step (int) – step to read from the file
Returns:: current_integrator_step – The data accessor at the current integrator step
Return type:: TNGCurrentIntegratorStep
Raises:: ValueError – attempt to read a negative step or step number greater than that in the input file

step

The current integrator step being read

Returns:: step – the current step in the TNG file
Return type:: int

values_per_frame

Dictionary of block names and the number of values per frame for the block

Returns:: values_per_frame – dictionary of block names (keys) and number of values per frame (values)
Return type:: dict

class pytng.TNGCurrentIntegratorStep

Retrieves data at the curent trajectory step

frame_strides_blockid

frame_stride

Returns:: frame_strides_blockid – Dictionary of frame strides
Return type:: dict
Type:: Dictionary of blockid

get_blockid(self, int64_t block_id, ndarray data)

Get a block ID present at the current step and read it into a NumPy array

Parameters:

block_id (int64_t) – TNG block id to read from the current step
data (np.ndarray) – NumPy array to read the data into, the required shape is determined by the block dependency and the number of values per frame.

Raises:

TypeError – The dtype of the numpy array provided is not supported by TNG datatypes or does not match the underlying datatype.
IOError – The block data type cannot be understood.
IndexError – The shape of the numpy array provided does not match the shape of the data to be read from disk.

get_box(self, ndarray data) → ndarray

Get the box vectors present at the current step and read them into a NumPy array. The box vectors are a (3,3) matrix comprised of 3 three-dimensional basis vectors for the coordinate system of the simulation. The vectors can be accessed in their proper shape by reshaping the resulting (1,9) matrix to be (3,3) with ndarray.reshape(3,3).

Parameters:: data (np.ndarray) – NumPy array to read the data into. As this is NOT a particle dependent block, the shape should be (1, n_values_per_frame) ie (1,9)

get_forces(self, ndarray data) → ndarray

Get the forces present at the current step and read them into a NumPy array

Parameters:: data (np.ndarray) – NumPy array to read the data into. As this is a particle dependent block, the shape should be (n_atoms, n_values_per_frame) ie (n_atoms, 3).

get_positions(self, ndarray data) → ndarray

Get the positions present at the current step and read them into a NumPy array

Parameters:: data (np.ndarray) – NumPy array to read the data into. As this is a particle dependent block, the shape should be (n_atoms, n_values_per_frame) ie (n_atoms, 3).

get_time(self)

Get the time of the current integrator step being read from the file

Returns:: time – the time of the current step
Return type:: int

get_velocities(self, ndarray data) → ndarray

Get the velocities present at the current step and read them into a NumPy array

Parameters:: data (np.ndarray) – NumPy array to read the data into. As this is a particle dependent block, the shape should be (n_atoms, n_values_per_frame) ie (n_atoms, 3).

read_success

Indicates whether the last attempt to read data was successful

Returns:: read_success – Whether the last attempt to read data was successful
Return type:: bool

step

The current integrator step being read

Returns:: step – the current step in the TNG file
Return type:: int