`biotite`#

This is the top-level package of Biotite. Although it does not provide useful functionality for most users, it does provide utilities and base classes used by a lot of Biotite’s modules.

File classes#

`File`	Base class for all file classes.
`TextFile`	Base class for all line based text files.

Visualization utilities#

`plot_scaled_text`	Create a `matplotlib.textpath.TextPath`, whose text size is given in coordinates instead of font size.
`AdaptiveFancyArrow`	A FancyArrow with fixed head shape.

Miscellaneous#

`Copyable`	Base class for all objects, that should be copyable.
`DeserializationError`
`InvalidFileError`	Indicates that the file is not suitable for the requested action, either because the file does not contain the required data or because the file is malformed.
`SerializationError`
`set_font_size_in_coord`	Specifiy the font size of an existing Text object in coordinates of the object's reference coordiante system.

Subpackages#

`biotite.interface`	This subpackage provides interfaces to other Python packages in the bioinformatics ecosystem.
`biotite.interface.rdkit`	This subpackage provides an interface to the RDKit cheminformatics package.
`biotite.interface.pymol`	This package enables the transfer of structures from Biotite to PyMOL for visualization and vice versa, via PyMOL's Python API:
`biotite.interface.openmm`	This subpackage provides an interface to the OpenMM molecular simulation toolkit.
`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.alphabet`	A subpackage for converting structures to structural alphabet sequences.
`biotite.structure.io`	A subpackage for reading and writing structure related data.
`biotite.structure.io.xtc`	This subpackage is used for reading and writing trajectories in the compressed Gromacs XTC 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.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.netcdf`	This subpackage is used for reading and writing trajectories in the AMBER NetCDF 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 file formats.
`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.graphics`	A subpackage for visualizing structure related objects.
`biotite.database`	A subpackage for fetching data from online databases.
`biotite.database.uniprot`	A subpackage for downloading files from the UniProt.
`biotite.database.pubchem`	A subpackage for searching and downloading files from the PubChem database.
`biotite.database.rcsb`	A subpackage for downloading files from the RCSB PDB.
`biotite.database.afdb`	A subpackage for downloading predicted protein structures from the AlphaFold DB.
`biotite.database.entrez`	A subpackage for downloading files from the NCBI Entrez database.
`biotite.sequence`	A subpackage for handling sequences.
`biotite.sequence.align`	This subpackage provides functionality for sequence alignments.
`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.fastq`	This subpackage is used for reading and writing sequencing data using the popular FASTQ format.
`biotite.sequence.io.fasta`	This subpackage is used for reading and writing sequence objects using the popular FASTA format.
`biotite.sequence.io.clustal`	This subpackage is used for reading and writing sequence alignment objects using the ClustalW format (`.aln`).
`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.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.viennarna`	A subpackage that provides interfaces to the ViennaRNA software package.
`biotite.application.clustalo`	A subpackage for multiple sequence alignments using Clustal-Omega.
`biotite.application.dssp`	A subpackage for protein secondary structure annotation using DSSP.
`biotite.application.mafft`	A subpackage for multiple sequence alignments using MAFFT.
`biotite.application.autodock`	A subpackage for static ligand docking with Autodock.
`biotite.application.tantan`	A subpackage for masking sequence regions using the tantan software.
`biotite.application.muscle`	A subpackage for multiple sequence alignments using MUSCLE.
`biotite.application.blast`	A subpackage for heuristic local alignments against a large database using BLAST.
`biotite.application.sra`	A subpackage for obtaining sequencing data from the NCBI sequence read archive (SRA).