Biskit

Main Classes

The most important classes which can be directly imported from the Biskit namespace.

PDBModel Store and manipulate coordinates and atom infos stemming from a PDB file.
ProfileCollection Manage profiles (arrays or lists of values) for Trajectory frames or atoms/residues in PDBModel.
PDBCleaner PDBCleaner performs the following tasks:
Trajectory
EnsembleTraj
Residue
AmberResidueType Standard description of a certain class of residues.
AmberPrepParser Parse Amber Residue libraries (off or prep files) which are usually found in amber/dat/leap/prep.
LogFile Simple log file that can be passed between objects.
StdLog Print to std out.
ErrLog Print to stderr instead.

Interaction with external programs

Executor
ExeConfig
ExeConfigCache
AmberCrdEntropist
AmberCrdParser
AmberLeap
AmberParmBuilder
AmberRstParser
AmberResidueLibrary A collection of reference residue types taken from Amber topology files.
TMAlign

Supporting classes and modules

BioUnit
LocalPath Encapsulate a file name that might look differently in different environments depending on environment settings.
SettingsManager
SettingsParser

Helper Modules

Modules with utility and helper methods.

gnuplot Simple Gnuplot interface.
hist create a histogram from data
tools general purpose utility methods.
molUtils Utilities for handling structures and sequences
mathUtils general purpose math methods
match2seq Match 2 sequences against each other, deleting all positions that differ.
rmsFit superimpose 2 structures iteratively

Errors

Errors that are raised by biskit classes.

EHandler Default Error Handler for Biskit classes.
BiskitError Root for all Errors raised by Biskit scripts.
LocalPathError
PDBError
ProfileError