API Reference

biotite	This is the top-level package of Biotite.
biotite.application	A subpackage that provides interfaces for external software in case Biotite’s integrated functionality is not sufficient for your tasks.
biotite.application.sra	A subpackage for obtaining sequencing data from the NCBI sequence read archive (SRA).
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.autodock	A subpackage for static ligand docking with Autodock.
biotite.application.muscle	A subpackage for multiple sequence alignments using MUSCLE.
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.blast	A subpackage for heuristic local alignments against a large database using BLAST.
biotite.sequence	A subpackage for handling sequences.
biotite.sequence.phylo	This subpackage provides functions and data structures for creating (phylogenetic) trees.
biotite.sequence.io	A subpackage for reading and writing sequence related data.
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.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.align	This subpackage provides functionality for sequence alignments.
biotite.sequence.graphics	A subpackage for visualization of sequence related objects.
biotite.structure	A subpackage for handling molecular structures.
biotite.structure.info	A subpackage for obtaining all kinds of chemical information about atoms and residues, including masses, radii, bonds, etc.
biotite.structure.io	A subpackage for reading and writing structure related data.
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.mol	The MOL format is used to depict atom positions and bonds for small molecules.
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.xtc	This subpackage is used for reading and writing trajectories in the compressed Gromacs XTC format.
biotite.structure.io.trr	This subpackage is used for reading and writing trajectories in the uncompressed Gromacs TRR 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.mmtf	This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the binary MMTF format.
biotite.structure.io.pdb	This subpackage is used for reading and writing an AtomArray or AtomArrayStack using the popular PDB format.
biotite.structure.io.pdbx	This subpackage provides support for the the modern PDBx/mmCIF file format.
biotite.structure.io.tng	This subpackage is used for reading and writing trajectories in the compressed Gromacs TNG 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.netcdf	This subpackage is used for reading and writing trajectories in the AMBER NetCDF format.
biotite.structure.graphics	A subpackage for visualizing structure related objects.
biotite.database	A subpackage for fetching data from online databases.
biotite.database.rcsb	A subpackage for downloading files from the RCSB PDB.
biotite.database.entrez	A subpackage for downloading files from the NCBI Entrez database.
biotite.database.pubchem	A subpackage for searching and downloading files from the PubChem database.
biotite.database.uniprot	A subpackage for downloading files from the UniProt.