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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.
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add_element
(e)¶ Appends a pipeline stage.
Appends the given element to the end of the current chain.
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dtrajs
¶ get discrete trajectories
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logger
¶ The logger for this class instance
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name
¶ The name of this instance
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parametrize
()¶ Reads all data and discretizes it into discrete trajectories.
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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’)
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set_element
(index, e)¶ Replaces a pipeline stage.
Replace an element in chain and return replaced element.
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class
pyemma.coordinates.pipelines.
Pipeline
(chain, chunksize=None, param_stride=1)¶ Data processing pipeline.
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add_element
(e)¶ Appends a pipeline stage.
Appends the given element to the end of the current chain.
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logger
¶ The logger for this class instance
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name
¶ The name of this instance
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parametrize
()¶ Reads all data and discretizes it into discrete trajectories.
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set_element
(index, e)¶ Replaces a pipeline stage.
Replace an element in chain and return replaced element.
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