- 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: Parse Amber restart files.
- 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.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.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.ProfileCollection: Manage profiles.
- Biskit.ProfileMirror: Work in progress
- 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.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.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: Interface to Xplor
- 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.test: Module tests are extremely important to keep the Biskit package
manageable and functional.
- Biskit.tools: simply - everyday tools
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