API reference

Simulation

box.Box([name, label])	This class creates a hypothetical simulation box, to which molecules are added.
simulate.Simulate([link, box])	This class generates the simulation folder for a series of simulations.
benchmark.Benchmark(box, np, nodes[, link, …])	This class extends the simulate class poresim.simulate.Simulate for benchmarking.

Simulation-Helper

actuate.Actuate(sim_link, box_link, cluster, …)	This class creates needed shell files for running the simulation using GROMACS.
construct.Construct(sim_link, box_link, …)	This class creates shell-files for generating the and filling the simulation box using GROMACS.
parameter.Parameter(link, param)	This class generates parameter files by replacing the given parameter in prepared files.
topology.Topology(link, topol)	This class reads and extract all information from topology files of the molecules specified in the simulation box.
analyze.Analyze(sim_link, box_link)	This class creates shell-files for generating shell file for analysing a simulation.

Utilities

utils

Here popular basic methods are noted.