Documentation

`synd.models.base`	Abstract base SynD model class.
`synd.models.discrete.discrete.DiscreteGenerator`	Abstract base class for discrete SynD models.
`synd.models.discrete.markov.MarkovGenerator`	Generator using discrete Markov dynamics.
`synd.core`	Functions for interacting with SynD models.
`synd.hosted`	Store/retrieve SynD models from an S3 host.

SynD Models (synd.models)

class synd.models.discrete.markov.MarkovGenerator(transition_matrix, backmapper, seed=None)[source]

Generator using discrete Markov dynamics.

__init__(transition_matrix, backmapper, seed=None)[source]

Parameters

transition_matrix – A valid discrete transition matrix
backmapper – Callable mapping a discrete state index to a full-coordinate representation
seed – The seed for random number generator

add_backmapper(backmapper, name)[source]

Define a new backmapper.

Parameters

backmapper – A callable defining a new backmapper.
name – The name to associate with the new backmapper.

backmap(discrete_index, mapper='default')[source]

Return the full-coordinate representation of a discrete state.

Parameters

discrete_index – Discrete state index
mapper – Optional string to specify a backmapper for this model.

Return type

Array of coordinates

generate_trajectory(initial_states, n_steps)[source]

Parameters

initial_states – Array of initial discrete states to propagate trajectories from
n_steps – Number of steps forward to propagate from each initial state. Total trajectory length will be n_steps

Return type

Union[_SupportsArray[dtype[Any]], _NestedSequence[_SupportsArray[dtype[Any]]], bool, int, float, complex, str, bytes, _NestedSequence[Union[bool, int, float, complex, str, bytes]]]

static validate_transition_matrix(transition_matrix)[source]

Validate that a transition matrix is valid. Raises an AssertionError if it is not.

Parameters: transition_matrix – A transition matrix

save(outfile)

Saves a SynD model to a file on disk.

Parameters: outfile – Name of the file to save the model to.

serialize()

Get the serialized representation of the SynD model.

Return type: Serialized representation of the model.

class synd.models.discrete.discrete.DiscreteGenerator[source]

Abstract base class for discrete SynD models.

abstract backmap(discrete_index)[source]

abstract generate_trajectory(initial_distribution, n_steps)[source]

save(outfile)

Saves a SynD model to a file on disk.

Parameters: outfile – Name of the file to save the model to.

serialize()

Get the serialized representation of the SynD model.

Return type: Serialized representation of the model.

Abstract base SynD model class.

class synd.models.base.BaseSynDModel[source]

Abstract base SynD model.

serialize()[source]

Get the serialized representation of the SynD model.

Return type: Serialized representation of the model.

save(outfile)[source]

Saves a SynD model to a file on disk.

Parameters: outfile – Name of the file to save the model to.

WESTPA Propagator

SynD Core (synd.core)

Functions for interacting with SynD models.

synd.core.load_model(filename)[source]

Load a SynD model from a file.

Parameters: filename – Path to SynD model file
Returns: SynD model

Model Hosting

Store/retrieve SynD models from an S3 host.

synd.hosted.make_minio_client(access_key, secret_key, model_host='minios.jdrusso.dev', **client_kwargs)[source]

Return type: Minio

synd.hosted.download_model(identifier, client, bucket='models')[source]

Return type: BaseSynDModel

synd.hosted.upload_model(model, identifier, client, bucket='models')[source]