API Reference

biotite

This is the top-level package of Biotite.

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.

biotite.database.uniprot

A subpackage for downloading files from the UniProt.

biotite.structure

A subpackage for handling molecular structures.

biotite.structure.io

A subpackage for reading and writing structure related data.

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.mmtf

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

This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the PDBQT format used by the AutoDock software series.

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.pdb

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

biotite.structure.io.mol

The MOL format is used to depict atom positions and bonds for small molecules.

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.npz

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

biotite.structure.io.xtc

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

biotite.structure.graphics

A subpackage for visualizing structure related objects.

biotite.structure.info

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

biotite.application

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

biotite.application.tantan

A subpackage for masking sequence regions using the tantan software.

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.muscle

A subpackage for multiple sequence alignments using MUSCLE.

biotite.application.sra

A subpackage for obtaining sequencing data from the NCBI sequence read archive (SRA).

biotite.application.viennarna

A subpackage that provides interfaces to the ViennaRNA software package.

biotite.application.mafft

A subpackage for multiple sequence alignments using MAFFT.

biotite.application.dssp

A subpackage for protein secondary structure annotation using DSSP.

biotite.application.autodock

A subpackage for static ligand docking with Autodock.

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.genbank

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

biotite.sequence.io.fasta

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

biotite.sequence.io.fastq

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

biotite.sequence.graphics

A subpackage for visualization of sequence related objects.

biotite.sequence.align

This subpackage provides functionality for sequence alignments.

biotite.sequence.phylo

This subpackage provides functions and data structures for creating (phylogenetic) trees.