class pyemma.coordinates.pipelines.Discretizer(reader, transform=None, cluster=None, chunksize=None, param_stride=1)

A Discretizer gets a FeatureReader, which extracts features (distances, angles etc.) of given trajectory data and passes this data in a memory efficient way through the given pipeline of a StreamingTransformer and Clustering. The clustering object is responsible for assigning the data to the cluster centers.

Parameters

• reader (a FeatureReader object) – reads trajectory data and selects features.

• transform (a StreamingTransformer object (optional)) – the StreamingTransformer will be used to e.g reduce dimensionality of inputs.

• cluster (a clustering object) – used to assign input data to discrete states/ discrete trajectories.

• chunksize (int, optional) – how many frames shall be processed at once.

add_element(e)

Appends a pipeline stage.

Appends the given element to the end of the current chain.

dtrajs

get discrete trajectories

logger

The logger for this class instance

name

The name of this instance

parametrize()

Reads all data and discretizes it into discrete trajectories.

save_dtrajs(prefix='', output_dir='.', output_format='ascii', extension='.dtraj')

Saves calculated discrete trajectories. Filenames are taken from given reader. If data comes from memory dtrajs are written to a default filename.

Parameters

• prefix (str) – prepend prefix to filenames.

• output_dir (str (optional)) – save files to this directory. Defaults to current working directory.

• output_format (str) – if format is ‘ascii’ dtrajs will be written as csv files, otherwise they will be written as NumPy .npy files.

• extension (str) – file extension to append (eg. ‘.itraj’)

set_element(index, e)

Replaces a pipeline stage.

Replace an element in chain and return replaced element.

class pyemma.coordinates.pipelines.Pipeline(chain, chunksize=None, param_stride=1)

Data processing pipeline.

add_element(e)

Appends a pipeline stage.

Appends the given element to the end of the current chain.

logger

The logger for this class instance

name

The name of this instance

parametrize()

Reads all data and discretizes it into discrete trajectories.

set_element(index, e)

Replaces a pipeline stage.

Replace an element in chain and return replaced element.