espressomd.MDA_ESP package¶
Module contents¶
This modules allows to expose ESPREsSo’s coordinates and particle attributes to MDAnalysis without need to save information to files.
The main class is Stream(), which is used to initialize the stream of data to MDAnalysis’ readers. These are the topology reader ESPParser(TopologyReaderBase) and the coordinates reader ESPReader(SingleFrameReaderBase).
A minimal working example is the following:
>>> # imports
>>> import espressomd
>>> from espressomd import MDA_ESP
>>> import MDAnalysis as mda
>>> # system setup
>>> system = espressomd.System()
>>> system.time_step = 1.
>>> system.cell_system.skin = 1.
>>> system.box_l = [10.,10.,10.]
>>> system.part.add(id=0,pos=[1.,2.,3.])
>>> # set up the stream
>>> eos = MDA_ESP.Stream(system)
>>> # feed Universe with a topology and with coordinates
>>> u = mda.Universe(eos.topology,eos.trajectory)
>>> print u
<Universe with 1 atoms>