mdtraj.load_hoomdxml

mdtraj.load_hoomdxml(filename, top=None)

Load a single conformation from an HOOMD-Blue XML file.

For more information on this file format, see: http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html Notably, all node names and attributes are in all lower case. HOOMD-Blue does not contain residue and chain information explicitly. For this reason, chains will be found by looping over all the bonds and finding what is bonded to what. Each chain consisists of exactly one residue.

Parameters

filenamepath-like

The path on disk to the XML file

topNone

This argumet is ignored

Returns

trajectorymd.Trajectory

The resulting trajectory, as an md.Trajectory object, with corresponding Topology.

Notes

This function requires the NetworkX python package.