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 |
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EnsembleTraj |
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Residue |
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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 |
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ExeConfig |
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ExeConfigCache |
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AmberCrdEntropist |
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AmberCrdParser |
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AmberLeap |
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AmberParmBuilder |
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AmberRstParser |
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AmberResidueLibrary |
A collection of reference residue types taken from Amber topology files. |
TMAlign |
Supporting classes and modules¶
BioUnit |
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LocalPath |
Encapsulate a file name that might look differently in different environments depending on environment settings. |
SettingsManager |
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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 |
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PDBError |
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ProfileError |