PBxplore
1.1
  • Protein Blocks
  • Installation
  • Utilization
  • PBassign
  • PBcount
  • PBstat
  • PBclust
  • API Cookbook
  • API Reference
    • Protein Blocks related data — pbxplore.PB
      • Protein blocks definition
      • Substitution matrix
      • Exceptions
    • Protein structure manipulation — pbxplore.structure
    • Protrein Block assignation — pbxplore.assignment
    • Input/Output in files — pbxplore.io
    • Analyses – pbxplore.analysis
    • Demonstration files — pbxplore.demo
    • Functions directly accessible at the module level
PBxplore
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  • Protein Blocks related data — pbxplore.PB
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Protein Blocks related data — pbxplore.PB¶

Protein blocks definition¶

  • REFERENCES The definition of each block as a dictionary; each key is a block name (as a lower case letter), and each value is a list of the dihedral angle values that define the block.
  • NAMES The names of all the protein blocks.

Substitution matrix¶

  • SUBSTITUTION_MATRIX_NAME The absolute path to the file that contains the subtitution matrix
pbxplore.PB.load_substitution_matrix(name)[source]¶

Load PB substitution matrix.

The matrix must be 16x16.

Parameters:name (str) – Name of the file containing the PBs susbtitution matrix.
Returns:mat – Array of floats.
Return type:numpy array
Raises:InvalidBlockError – encountered an unexpected PB

Exceptions¶

exception pbxplore.PB.SizeError[source]¶

Exception raised when a sequence does not have the expected length.

exception pbxplore.PB.InvalidBlockError(block=None)[source]¶

Exception raised when encounter an invalid protein block.

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© Copyright 2015, Pierre Poulain, and Alexandre G. deBrevern.

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