The analysis module

This module contains some utilities that can be used to analyse oxDNA trajectory files from Python.

AnalysisBackend

An object that can be used to analyse oxDNA trajectory files.

class oxpy.core.analysis.AnalysisBackend(self: oxpy.core.analysis.AnalysisBackend, arg0: oxpy.core.InputFile)

Bases: pybind11_object

An object that can be used to analyse oxDNA trajectory files.

The constructor takes an InputFile that specifies the options needed to build the backend.

analyse(self: oxpy.core.analysis.AnalysisBackend) → None

Analyse the current configuration using the observables set through the input file.

property conf_step

The time step at which the current configuration was printed.

config_info(self: oxpy.core.analysis.AnalysisBackend) → oxpy.core.ConfigInfo

Return the simulation’s ConfigInfo.

Returns:

The object that stores all the simulation’s details (particles, interaction, etc).

Return type:

ConfigInfo

done(self: oxpy.core.analysis.AnalysisBackend) → bool

True if the backend has reached the last configuration in the trajectory file, False otherwise.

Returns:

The completion status of the analysis.

Return type:

bool

property flattened_conf

A flattened (that is, composed by arrays rather than class instances) view of the current configuration, stored in a FlattenedConfigInfo object.

property particles

The list of all the particles.

read_next_configuration(self: oxpy.core.analysis.AnalysisBackend, binary: bool = False) → bool

Load up the next configuration from the trajectory file.