Package csb :: Package bio

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# Package bio

source code

Core bioinformatics abstractions and I/O.

Submodules

- csb.bio.fragments: APIs for working with protein structure fragments and libraries.
  - csb.bio.fragments.rosetta: Rosetta fragment libraries.
- csb.bio.hmm: HHpred and Hidden Markov Model APIs.
  - csb.bio.hmm.pseudocounts
- csb.bio.io: I/O for various biological file formats.
  - csb.bio.io.clans: Classes for parsing/manipulating/writing CLANS (by Tancred Frickey) files
  - csb.bio.io.cs: Simple NMR STAR chemical shift readers.
  - csb.bio.io.dssp: DSSP Parser
  - csb.bio.io.fasta: FASTA format sequence I/O.
  - csb.bio.io.hhpred: HHpred-related format parsers.
  - csb.bio.io.mrc: Cryo-EM density map I/O
  - csb.bio.io.noe: Simple XEASY and Sparky peak list parsers.
  - csb.bio.io.procheck: Procheck parser
  - csb.bio.io.psipred: PSIPRED Parser
  - csb.bio.io.svg: Build SVG diagrams from various csb objects.
  - csb.bio.io.vasco: VASCO Chemical Shift format parser.
  - csb.bio.io.whatif: Simple WhatIf/WhatCheck Summary parser
  - csb.bio.io.wwpdb: PDB structure parsers, format builders and database providers.
- csb.bio.nmr: NMR related objects.
- csb.bio.sequence: Sequence and sequence alignment APIs.
  - csb.bio.sequence.alignment: Collection of sequence alignment algorithms.
- csb.bio.structure: 3D and secondary structure APIs.
- csb.bio.utils: Computational utility functions.

Variables
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