API reference

Generated from the docstrings of the molclusters package. Most users need only a few names, all importable from the package itself:

from molclusters import (
    MolClusters,        # run the analyses over a trajectory
    ClusterTracker,     # follow the clusters, without analyses
    Transition,         # how a frame's clusters came from the previous frame's
    FrameAnalysis,      # base class of an analysis
    Run, Frame,         # what an analysis sees of the run and of a frame
    OutputFile,         # declaration of a file an analysis writes
    Cluster, MolGroup,  # a tracked cluster, and any group of molecules
    start_logging,      # log like the command line does
)
from molclusters.config import MolClsConfig, read_config
from molclusters.report import read_report

Module	Contents
molclusters	MolClusters, the runner
molclusters.config	MolClsConfig, read_config, the rule classes
molclusters.tracker	ClusterTracker, Transition
molclusters.cluster	MolGroup, Cluster and their properties
molclusters.analysis	FrameAnalysis, Run, Frame, the built-in analyses and their registry
molclusters.output	OutputFile, RunOutput
molclusters.report	the JSON report's format and reader
molclusters.conntable	ConnectionTable, the connections of a frame
molclusters.log	start_logging