biotite 1.5.0__cp314-cp314-macosx_10_13_x86_64.whl

biotite-1.5.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: biotite
+Version: 1.5.0
+Summary: A comprehensive library for computational molecular biology
+Project-URL: homepage, https://www.biotite-python.org
+Project-URL: repository, https://github.com/biotite-dev/biotite
+Project-URL: documentation, https://www.biotite-python.org
+Author: The Biotite contributors
+License-Expression: BSD-3-Clause
+License-File: LICENSE.rst
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: biotraj<2.0,>=1.0
+Requires-Dist: msgpack>=0.5.6
+Requires-Dist: networkx>=2.0
+Requires-Dist: numpy>=1.25
+Requires-Dist: packaging>=24.0
+Requires-Dist: requests>=2.12
+Provides-Extra: lint
+Requires-Dist: numpydoc==1.8.0; extra == 'lint'
+Requires-Dist: ruff==0.9.7; extra == 'lint'
+Provides-Extra: test
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-codspeed; extra == 'test'
+Description-Content-Type: text/x-rst
+
+.. image:: https://img.shields.io/pypi/v/biotite.svg
+   :target: https://pypi.python.org/pypi/biotite
+   :alt: Biotite at PyPI
+.. image:: https://img.shields.io/pypi/pyversions/biotite.svg
+   :alt: Python version
+.. image:: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml/badge.svg
+   :target: https://github.com/biotite-dev/biotite/actions/workflows/test_and_deploy.yml
+   :alt: Test status
+
+.. image:: https://www.biotite-python.org/_static/assets/general/biotite_logo_m.png
+   :alt: The Biotite Project
+
+Biotite project
+===============
+
+*Biotite* is your Swiss army knife for bioinformatics.
+Whether you want to identify homologous sequence regions in a protein family
+or you would like to find disulfide bonds in a protein structure: *Biotite*
+has the right tool for you.
+This package bundles popular tasks in computational molecular biology
+into a uniform *Python* library.
+It can handle a major part of the typical workflow
+for sequence and biomolecular structure data:
+
+   - Searching and fetching data from biological databases
+   - Reading and writing popular sequence/structure file formats
+   - Analyzing and editing sequence/structure data
+   - Visualizing sequence/structure data
+   - Interfacing external applications for further analysis
+
+*Biotite* internally stores most of the data as *NumPy* `ndarray` objects,
+enabling
+
+   - fast C-accelerated analysis,
+   - intuitive usability through *NumPy*-like indexing syntax,
+   - extensibility through direct access of the internal *NumPy* arrays.
+
+As a result the user can skip writing code for basic functionality (like
+file parsers) and can focus on what their code makes unique - from
+small analysis scripts to entire bioinformatics software packages.
+
+If you use *Biotite* in a scientific publication, please cite:
+
+| Kunzmann, P. & Hamacher, K. BMC Bioinformatics (2018) 19:346.
+| `<https://doi.org/10.1186/s12859-018-2367-z>`_
+
+
+Installation
+------------
+
+*Biotite* requires the following packages:
+
+   - **numpy**
+   - **requests**
+   - **msgpack**
+   - **networkx**
+
+Some functions require some extra packages:
+
+   - **matplotlib** - Required for plotting purposes.
+
+*Biotite* can be installed via *Conda*...
+
+.. code-block:: console
+
+   $ conda install -c conda-forge biotite
+
+... or *pip*
+
+.. code-block:: console
+
+   $ pip install biotite
+
+
+Usage
+-----
+
+Here is a small example that downloads two protein sequences from the
+*NCBI Entrez* database and aligns them:
+
+.. code-block:: python
+
+   import biotite.sequence.align as align
+   import biotite.sequence.io.fasta as fasta
+   import biotite.database.entrez as entrez
+
+   # Download FASTA file for the sequences of avidin and streptavidin
+   file_name = entrez.fetch_single_file(
+       uids=["CAC34569", "ACL82594"], file_name="sequences.fasta",
+       db_name="protein", ret_type="fasta"
+   )
+
+   # Parse the downloaded FASTA file
+   # and create 'ProteinSequence' objects from it
+   fasta_file = fasta.FastaFile.read(file_name)
+   avidin_seq, streptavidin_seq = fasta.get_sequences(fasta_file).values()
+
+   # Align sequences using the BLOSUM62 matrix with affine gap penalty
+   matrix = align.SubstitutionMatrix.std_protein_matrix()
+   alignments = align.align_optimal(
+       avidin_seq, streptavidin_seq, matrix,
+       gap_penalty=(-10, -1), terminal_penalty=False
+   )
+   print(alignments[0])
+
+.. code-block::
+
+   MVHATSPLLLLLLLSLALVAPGLSAR------KCSLTGKWDNDLGSNMTIGAVNSKGEFTGTYTTAV-TA
+   -------------------DPSKESKAQAAVAEAGITGTWYNQLGSTFIVTA-NPDGSLTGTYESAVGNA
+
+   TSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFS----ESTTVFTGQCFIDRNGKEV-LKTMWLLRSSVN
+   ESRYVLTGRYDSTPATDGSGT--ALGWTVAWKNNYRNAHSATTWSGQYV---GGAEARINTQWLLTSGTT
+
+   DIGDDWKATRVGINIFTRLRTQKE---------------------
+   -AANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ
+
+More documentation, including a tutorial, an example gallery and the API
+reference is available at `<https://www.biotite-python.org/>`_.
+
+
+Contribution
+------------
+
+Interested in improving *Biotite*?
+Have a look at the
+`contribution guidelines <https://www.biotite-python.org/latest/contribution/index.html>`_.
+Feel free to join our community chat on `Discord <https://discord.gg/cUjDguF>`_.

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biotite-1.5.0.dist-info/licenses/LICENSE.rst

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+BSD 3-Clause License
+--------------------
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+Copyright 2017, The Biotite contributors
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+Redistribution and use in source and binary forms, with or without modification,
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+1. Redistributions of source code must retain the above copyright notice, this
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