API Reference

biotite

This is the top-level package of Biotite.

biotite.structure

A subpackage for handling molecular structures.

biotite.structure.io

A subpackage for reading and writing structure related data.

biotite.structure.io.pdb

This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the popular PDB format.

biotite.structure.io.gro

This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the Gro format used by the gromacs software package.

biotite.structure.io.tng

This subpackage is used for reading and writing trajectories in the compressed Gromacs TNG format.

biotite.structure.io.trr

This subpackage is used for reading and writing trajectories in the uncompressed Gromacs TRR format.

biotite.structure.io.pdbx

This subpackage provides support for the the modern PDBx/mmCIF file format.

biotite.structure.io.netcdf

This subpackage is used for reading and writing trajectories in the AMBER NetCDF format.

biotite.structure.io.dcd

This subpackage is used for reading and writing trajectories in the CDC format used by software like CHARMM, OpenMM and NAMD.

biotite.structure.io.mmtf

This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the binary MMTF format.

biotite.structure.io.xtc

This subpackage is used for reading and writing trajectories in the compressed Gromacs XTC format.

biotite.structure.io.npz

This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the internal NPZ file format.

biotite.structure.info

A subpackage for obtaining all kinds of chemical information about atoms and residues, including masses, radii, bonds, etc.

biotite.sequence

A subpackage for handling sequences.

biotite.sequence.io

A subpackage for reading and writing sequence related data.

biotite.sequence.io.gff

This subpackage is used for reading and writing sequence features in the Generic Feature Format 3 (GFF3).

biotite.sequence.io.fasta

This subpackage is used for reading and writing sequence objects using the popular FASTA format.

biotite.sequence.io.genbank

This subpackage is used for reading/writing information (especially sequence features) from/to files in the GenBank and GenPept format.

biotite.sequence.io.fastq

This subpackage is used for reading and writing sequencing data using the popular FASTQ format.

biotite.sequence.align

This subpackage provides functionality for sequence alignemnts.

biotite.sequence.phylo

biotite.sequence.graphics

A subpackage for visualization of sequence related objects.

biotite.application

A subpackage that provides interfaces for external software in case Biotite’s integrated functionality is not sufficient for your tasks.

biotite.application.dssp

A subpackage for protein secondary structure annotation using DSSP.

biotite.application.clustalo

A subpackage for multiple sequence alignments using Clustal-Omega.

biotite.application.blast

A subpackage for heuristic local alignments against a large database using BLAST.

biotite.application.mafft

A subpackage for multiple sequence alignments using MAFFT.

biotite.application.muscle

A subpackage for multiple sequence alignments using MUSCLE.

biotite.database

A subpackage for fetching data from online databases.

biotite.database.entrez

A subpackage for downloading files from the NCBI Entrez database.

biotite.database.rcsb

A subpackage for downloading files from the RCSB PDB.