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.

Temporary files

temp_dir

Get the temporary directory path.

temp_file

Get a file path to a temporary file.

Visualization utilities

set_font_size_in_coord

Specifiy the font size of an existing Text object in coordinates of the object's reference coordiante system.

AdaptiveFancyArrow

A FancyArrow with fixed head shape.

Miscellaneous

Copyable

Base class for all objects, that should be copyable.

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.

Subpackages

biotite.structure

A subpackage for handling molecular structures.

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.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.pdb

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

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

biotite.structure.io.trr

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

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.tng

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

biotite.structure.io.pdbx

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

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

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.uniprot

A subpackage for downloading files from the UniProt.

biotite.database.rcsb

A subpackage for downloading files from the RCSB PDB.

biotite.database.pubchem

A subpackage for searching and downloading files from the PubChem database.

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.muscle

A subpackage for multiple sequence alignments using MUSCLE.

biotite.application.tantan

A subpackage for masking sequence regions using the tantan software.

biotite.application.viennarna

A subpackage that provides interfaces to the ViennaRNA software package.

biotite.application.autodock

A subpackage for static ligand docking with Autodock.

biotite.application.clustalo

A subpackage for multiple sequence alignments using Clustal-Omega.

biotite.application.sra

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

biotite.application.mafft

A subpackage for multiple sequence alignments using MAFFT.

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.align

This subpackage provides functionality for sequence alignments.

biotite.sequence.graphics

A subpackage for visualization of sequence related objects.

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.genbank

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

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