Dask Trajectory Build Helper

GitHub Link to Code.

DaskMDTrajectory Builder - Complex initialization logic extraction.

Handles the complex initialization process for DaskMDTrajectory instances, including cache management, Zarr store setup, and Dask array initialization.

class mdxplain.trajectory.helper.dask_trajectory_helper.dask_trajectory_build_helper.DaskMDTrajectoryBuildHelper

Builder class for creating and initializing DaskMDTrajectory instances.

Handles the complex initialization process by breaking it down into manageable steps while maintaining full compatibility with the original API.

__init__() → None

Initialize DaskMDTrajectoryBuildHelper.

Parameters

None

Returns

None: Initializes builder instance

initialize_instance(instance: DaskMDTrajectory, trajectory_file: str, topology_file: str | None = None, zarr_cache_path: str | None = None, chunk_size: int = 1000, n_workers: int | None = None) → None

Initialize a DaskMDTrajectory instance with all required components.

Parameters

instanceDaskMDTrajectory: Instance to initialize
trajectory_filestr: Path to trajectory file (.xtc, .dcd, etc.)
topology_filestr, optional: Path to topology file (.pdb, .gro, etc.)
zarr_cache_pathstr, optional: Custom path for Zarr cache file
chunk_sizeint, default=1000: Number of frames per chunk (optimized for performance)
n_workersint, optional: Number of parallel workers (defaults to CPU count)

Returns

None: Initializes instance in-place

Examples

>>> builder = DaskMDTrajectoryBuildHelper()
>>> instance = DaskMDTrajectory.__new__(DaskMDTrajectory)
>>> builder.initialize_instance(instance, 'traj.xtc', 'topology.pdb')

initialize_from_mdtraj(instance: DaskMDTrajectory, mdtraj: md.Trajectory, zarr_cache_path: str | None = None, chunk_size: int = 1000, n_workers: int | None = None) → None

Initialize DaskMDTrajectory instance from MDTraj trajectory object.

Parameters

instanceDaskMDTrajectory: Instance to initialize
mdtrajmd.Trajectory: MDTraj trajectory object
zarr_cache_pathstr, optional: Path for zarr cache. If None, creates temporary cache.
chunk_sizeint, default=1000: Number of frames per chunk
n_workersint, optional: Number of parallel workers

Returns

None: Initializes instance in-place

create_from_zarr_store(zarr_store: Group, chunk_size: int = 1000, n_workers: int | None = None) → dict

Prepare configuration data from existing Zarr store.

Parameters

zarr_storezarr.Group: Zarr group containing trajectory data
chunk_sizeint, default=1000: Chunk size for new instance
n_workersint, optional: Number of workers for parallel operations

Returns

dict: Configuration dictionary for DaskMDTrajectory creation

Examples

>>> builder = DaskMDTrajectoryBuildHelper()
>>> config = builder.create_from_zarr_store(zarr_store)
>>> # Use config to create instance in DaskMDTrajectory