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#
Visualization utilities#
Specifiy the font size of an existing Text object in coordinates of the object's reference coordiante system. |
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A FancyArrow with fixed head shape. |
Miscellaneous#
Base class for all objects, that should be copyable. |
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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. |
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Subpackages#
A subpackage for handling sequences. |
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A subpackage for visualization of sequence related objects. |
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This subpackage provides functionality for sequence alignments. |
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A subpackage for reading and writing sequence related data. |
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This subpackage is used for reading and writing sequencing data using the popular FASTQ format. |
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This subpackage is used for reading and writing sequence objects using the popular FASTA format. |
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This subpackage is used for reading and writing sequence features in the Generic Feature Format 3 (GFF3). |
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This subpackage is used for reading/writing information (especially sequence features) from/to files in the GenBank and GenPept format. |
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This subpackage provides functions and data structures for creating (phylogenetic) trees. |
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A subpackage that provides interfaces for external software in case Biotite’s integrated functionality is not sufficient for your tasks. |
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A subpackage for static ligand docking with Autodock. |
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A subpackage for multiple sequence alignments using Clustal-Omega. |
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A subpackage for obtaining sequencing data from the NCBI sequence read archive (SRA). |
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A subpackage for multiple sequence alignments using MAFFT. |
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A subpackage for protein secondary structure annotation using DSSP. |
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A subpackage for masking sequence regions using the tantan software. |
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A subpackage for multiple sequence alignments using MUSCLE. |
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A subpackage that provides interfaces to the ViennaRNA software package. |
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A subpackage for heuristic local alignments against a large database using BLAST. |
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A subpackage for fetching data from online databases. |
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A subpackage for searching and downloading files from the PubChem database. |
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A subpackage for downloading files from the RCSB PDB. |
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A subpackage for downloading files from the UniProt. |
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A subpackage for downloading files from the NCBI Entrez database. |
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A subpackage for handling molecular structures. |
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A subpackage for visualizing structure related objects. |
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A subpackage for reading and writing structure related data. |
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The MOL format is used to depict atom positions and bonds for small molecules. |
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This subpackage is used for reading and writing trajectories in the uncompressed Gromacs TRR format. |
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This subpackage is used for reading and writing an |
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This subpackage is used for reading and writing trajectories in the AMBER NetCDF format. |
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This subpackage is used for reading and writing trajectories in the CDC format used by software like CHARMM, OpenMM and NAMD. |
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This subpackage is used for reading and writing trajectories in the compressed Gromacs XTC format. |
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This subpackage is used for reading and writing an |
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This subpackage provides support for the the modern PDBx file formats. |
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This subpackage is used for reading and writing an |
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A subpackage for obtaining all kinds of chemical information about atoms and residues, including masses, radii, bonds, etc. |