wepy.util.mdtraj module¶

Utilities for converting formats used in wepy to mdtraj objects.

Requires mdtraj be installed.

wepy.util.mdtraj.mdtraj_to_json_topology(mdj_top)[source]¶

Generate a JSON string topology from an mdtraj.Topology object.

This is the primary way in which JSON toplogies can be generated.

This format was created for use in the HDF5 format generated by the mdtraj library.

Parameters: mdj_top (mdtraj.Topology object) – The topology you want to serialize to a JSON string.
Returns: json_top – JSON string of the topology.
Return type: str

Warning

The topology format for wepy is subject to change in the future!

Notes

Copied in part from MDTraj.formats.hdf5.topology setter.

wepy.util.mdtraj.json_to_mdtraj_topology(json_string)[source]¶

Convert a JSON string topology to an mdtraj.Toplogy object.

This can be used to write out different topology formats from mdtraj.

Warning

The topology format for wepy is subject to change in the future!

Notes

Copied in part from MDTraj.formats.hdf5 topology property.

wepy.util.mdtraj._new_json_to_mdtraj_topology(json_string)[source]¶

Another implementation of converting JSON to mdtraj.

TODO what is the difference between this and the other one?

wepy.util.mdtraj.traj_fields_to_mdtraj(traj_fields, json_topology, rep_key='positions')[source]¶

Create an mdtraj.Trajectory object directly from a dictionary of fields values.

The time value in the trajectory will just be the frame indices for the positions.

Parameters

traj_fields (dict of str: values) – The values for the trajectory, must have a positions field specified by the rep_key kwarg, and a ‘box_vectors’ field.
json_topology (str) – JSON format topology of the positions.
rep_key (str) – The key that will be used to access the field that will be used as the positions in the trajectory, and must match the topology.

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