Module Hierarchy

Biskit

Biskit.AmberCrdEntropist: Run ptraj entropy analysis on existing amber trajectory (.crd) and topology (.parm7) file.
Biskit.AmberCrdParser: Convert single amber crd into Trajectory object
Biskit.AmberEntropist: Run ptraj entropy analysis on Trajectory instance.
Biskit.AmberEntropyMaster: Parallellized AmberEntropist calculation.
Biskit.AmberEntropySlave: Parallellized AmberEntropist calculation.
Biskit.AmberParmBuilder: Create Amber topology and coordinate file from PDB.
Biskit.AmberRstParser: Convert Amber restart file to array, PDBModel or Amber crd file.
Biskit.BisList: organise, sort, and filter collection of dictionaries or similar objects → abstract base class (aka interface)
Biskit.Blast2Seq: Blast 2 sequences against each other, Return sequence identity
Biskit.ChainCleaner: Fill in missing atoms, and report low occupancies
Biskit.ChainSeparator: Seperate PDB into continuous peptide chains for XPlor.
Biskit.ChainWriter: Write cleaned peptide_chains as PDB for import into XPlor
Biskit.ColorSpectrum: Create color scales.
Biskit.DSSP: Calculates the secondary structure using DSSP.
Biskit.DictList: organise, sort, and filter list of dictionaries or similar objects
Biskit.Dock: Protein-protein docking related modules

Biskit.Dock.Analyzer: Analyze HEX docking result.
Biskit.Dock.Complex: collect and manage information about a docking result
Biskit.Dock.ComplexEvolving: Complex that keeps track of its previous versions (conformations).
Biskit.Dock.ComplexEvolvingList: List of ComplexEvolving instances.
Biskit.Dock.ComplexList: List of Complex objects.
Biskit.Dock.ComplexModelRegistry: This is a helper class for ComplexList.
Biskit.Dock.ComplexRandomizer: Create Complexes with random orientation
Biskit.Dock.ComplexTraj: Trajectory of two proteins.
Biskit.Dock.ContactMaster: Distribute calculation of contact matrices for many complexes over many nodes.
Biskit.Dock.ContactSlave: Calculate contact matrix and some scores for complexes.
Biskit.Dock.Docker: Prepare and run a HEX docking.
Biskit.Dock.FixedList: List that blocks any modifications
Biskit.Dock.HexParser: Parse output file from hex docking run.
Biskit.Dock.hexTools: Various common functions used by the docking modeles.
Biskit.Dock.settings: This module provides Dock-global settings as fields.

Biskit.EnsembleTraj: Multi copy trajectory
Biskit.ErrorHandler: Default Error Handler for Biskit classes.
Biskit.Errors: Errors raised by Biskit scripts.
Biskit.ExeConfig: Collect settings for an external program from a configuration file.
Biskit.ExeConfigCache: Singleton Cache of ExeConfig instances
Biskit.Executor: Class for calls to external programs.
Biskit.Fold_X: Get binding energy from fold_X
Biskit.FuzzyCluster: Implementation of the fuzzy c-means algorithm
Biskit.Hmmer: Search Hmmer Pfam database and retrieve conservation data.
Biskit.IcmCad: Calculate Contact Area Difference (CAD) with ICMBrowser.
Biskit.LocalPath: Path handling.
Biskit.LogFile: Simple log file.
Biskit.MatrixPlot: Plot a 2D matrix (up to 100 x 100)
Biskit.Mod

Biskit.Mod.Aligner: Sequence Alignment
Biskit.Mod.AlignerMaster: Parallelise Sequence Alignment
Biskit.Mod.AlignerSlave: Parallelise Sequence Alignment
Biskit.Mod.Analyse: Analyze model quality
Biskit.Mod.Benchmark: Modeling benchmark
Biskit.Mod.CheckIdentities: Check sequence identity between templates.
Biskit.Mod.ModelMaster: Parallelize Modeller runs
Biskit.Mod.ModelSlave: Parallelize Modeller runs
Biskit.Mod.Modeller: Interface to Modeller
Biskit.Mod.NCBIStandalone: This module provides code to work with the standalone version of BLAST, either blastall or blastpgp, provided by the NCBI.
Biskit.Mod.SequenceSearcher: Search one or more sequence databases (SwissProt, Tremble) with a sequence using the method of choice (Blast , FastA)
Biskit.Mod.TemplateCleaner: Prepare template coordinates for modelling.
Biskit.Mod.TemplateSearcher: Search for templates.
Biskit.Mod.ValidationSetup: Setup directory structure for the validation.
Biskit.Mod.modUtils: utility funtions for Mod package
Biskit.Mod.settings: This module provides Mod-global settings as fields.

Biskit.ModelList: organise, sort, and filter list of PDBModels
Biskit.PCRModel: PDBModel with attached Xplor topology (PSF).
Biskit.PDBCleaner: Clean PDB-files so that they can be used for MD.
Biskit.PDBDope: Calculate and add various properties to PDBModel
Biskit.PDBModel: Store and manipulate coordinates and atom information.
Biskit.PDBParseFile: Parse a PDB file into a PDBModel.
Biskit.PDBParseModel: Parse a in-memory PDBModel instance into a new PDBModel
Biskit.PDBParsePickle: Parse a pickled PDBModel from disc into a new PDBModel instance
Biskit.PDBParser: Parse a certain file / memory object into a PDBModel.
Biskit.PDBParserFactory: @see Biskit.PDBParser @see Biskit.PDBParseFile @see Biskit.PDBParseModel @see Biskit.PDBParsePickle
Biskit.PVM: High-level parallelisation with PVM.

Biskit.PVM.ExampleMaster: An example of a Master/Slave setup
Biskit.PVM.ExampleSlave: An example of a Slave/Master setup.
Biskit.PVM.PVMThread: Binding incoming pvm-messages to methods.
Biskit.PVM.Status: Thread - save job handling for JobMaster (see dispatcher).
Biskit.PVM.TrackingJobMaster: Add some extra functionality to JobMaster
Biskit.PVM.dispatcher: Manage Master/Slave tasks.
Biskit.PVM.pvm: PVM interface.
Biskit.PVM.pvmTools: low-level tools for PVM

Biskit.ProfileCollection: Manage profiles.
Biskit.Prosa: Run a ProsaII job.
Biskit.Prosa2003: Analyze a structure using Prosa2003.
Biskit.Pymoler: Display Structures with Pymol
Biskit.QualMaster: Parallizes calculation and plotting of ensemble trajectory RMSDs
Biskit.QualSlave: Plot RMSD, Energy of ensemble trajectory.
Biskit.Ramachandran: Display a Ramachandran plot for a list of PDBModels with the same atom contents.
Biskit.ReduceCoordinates: Create structures with reduced number of atoms.
Biskit.SettingsManager: Manage Biskit settings.
Biskit.SettingsParser: Parse a Biskit settings file.
Biskit.SparseArray: Memory saving representation of a sparse array.
Biskit.Statistics

Biskit.Statistics.Density: Analyze a density distribution of values.
Biskit.Statistics.lognormal: lognormal distribution
Biskit.Statistics.pstat: pstat.py module
Biskit.Statistics.stats: stats.py module

Biskit.StructureMaster: Parallizes the convertion of PDB files into pickled PDBModel objects.
Biskit.StructureSlave: Convert a PDB file to a pickled PDBModel object.
Biskit.SurfaceRacer: Calculates accessible, molecular surface areas and average curvature.
Biskit.Table
Biskit.Test
Biskit.TrajCluster: Cluster the members of a trajectory.
Biskit.TrajFlexMaster: Parallize calculation of pairwise rmsd between the frames of a trajectory
Biskit.TrajFlexSlave: Parallize calculation of pairwise rmsd between the frames of a trajectory.
Biskit.Trajectory: Trajectory - Collection of coordinate frames of a molecule
Biskit.WhatIf: Run WhatIf, calculate and collect accessibility data
Biskit.XplorInput: Create Xplor input files.
Biskit.Xplorer: Prepare and run a xplor job.
Biskit.decorators: Defines method decorators.
Biskit.default_hosts: List of cluster computers.
Biskit.difflib_old: Older version of difflib.
Biskit.gnuplot: Simple Gnuplot interface.
Biskit.hist: create a histogram from data
Biskit.hosts: List of cluster computers.
Biskit.match2seq: Match 2 sequences against each other, deleting all positions that differ.
Biskit.mathUtils: general purpose math methods
Biskit.molTools: Various structure related calculations.
Biskit.molUtils: Utilities for handling structures and sequences
Biskit.msms: Use MSMS to calculate surface info.
Biskit.plotUtils: bar-plotting for Biggles
Biskit.rmsFit: superimpose 2 structures iteratively
Biskit.settings: This module provides global settings as fields.
Biskit.surfaceRacerTools: Reference data for SurfaceRacer.
Biskit.tools: simply - everyday tools