espressomd.MDA_ESP package

Module contents

This modules exposes ESPResSo’s coordinates and particle attributes to MDAnalysis without the need to save any 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 and the coordinates reader ESPReader.

A minimal working example is the following:

>>> import espressomd
>>> import espressomd.MDA_ESP
>>> import MDAnalysis as mda
>>> # system setup
>>> system = espressomd.System(box_l=[10., 10., 10.])
>>> system.time_step = 1.
>>> system.cell_system.skin = 1.
>>> system.part.add(pos=[1., 2., 3.])
>>> # set up the stream
>>> eos = espressomd.MDA_ESP.Stream(system)
>>> # feed Universe with a topology and coordinates
>>> u = mda.Universe(eos.topology, eos.trajectory)
>>> print(u)
<Universe with 1 atoms>

class espressomd.MDA_ESP.ESPParser(filename, **kwargs)

Bases: MDAnalysis.topology.base.TopologyReaderBase

An MDAnalysis reader of ESPResSo’s topology.

format = 'ESP'

parse()

Access ESPResSo data and return the topology object.

Returns

top – a topology object

Return type

MDAnalysis.core.topology.Topology

class espressomd.MDA_ESP.ESPReader(filename, convert_units=True, n_atoms=None, **kwargs)

Bases: MDAnalysis.coordinates.base.SingleFrameReaderBase

An MDAnalysis single frame reader for the stream provided by Stream.

format = 'ESP'

units = {'length': 'nm', 'time': None, 'velocity': 'nm/ps'}

dict with units of of time and length (and velocity, force, … for formats that support it)

class espressomd.MDA_ESP.Stream(system)

Bases: object

Create an object that provides a MDAnalysis topology and a coordinate reader

>>> eos = espressomd.MDA_ESP.Stream(system)
>>> u = mda.Universe(eos.topology, eos.trajectory)

Parameters

system (espressomd.system.System)

property trajectory

Particles’ coordinates at the current time

Returns

stream – A stream in the format that can be parsed by ESPReader

Return type

MDAnalysis.lib.util.NamedStream

class espressomd.MDA_ESP.Timestep(n_atoms, **kwargs)

Bases: MDAnalysis.coordinates.base.Timestep

property dimensions

unitcell dimensions (A, B, C, alpha, beta, gamma)

lengths a, b, c are in the MDAnalysis length unit (Å), and angles are in degrees.

Setting dimensions will populate the underlying native format description of box dimensions