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
and the coordinates reader ESPReader
.
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>
-
class
espressomd.MDA_ESP.
ESPParser
(filename, **kwargs)[source]¶ Bases:
MDAnalysis.topology.base.TopologyReaderBase
An MDAnalysis reader of espresso’s topology
-
format
= 'ESP'¶
-
-
class
espressomd.MDA_ESP.
ESPReader
(filename, convert_units=None, n_atoms=None, **kwargs)[source]¶ 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'}¶
-
-
class
espressomd.MDA_ESP.
Stream
(system)[source]¶ Bases:
object
Create an object that provides a MDAnalysis topology and a coordinate reader
>>> eos = MDA_ESP.Stream(system) >>> u = mda.Universe(eos.topology,eos.trajectory)
- Parameters
system (
espressomd.system.System
)
-
class
espressomd.MDA_ESP.
Timestep
(n_atoms, **kwargs)[source]¶ 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
-
property