API ReferenceΒΆ

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.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 information (especially sequence features) from 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
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.