Software Embedded in UCSF ChimeraX
UCSF ChimeraX is built upon other great software.
- Python version 3.7
- “The Python programming language and interpreter.”
History and License: open source
ChimeraX is distributed as Python packages,
either written in the Python language
or as a binary package written in C or C++.
- Rotamer libraries (amino acid sidechain conformations and associated information) from the following sources:
-
- FFmpeg version 3.2.4
- “A complete, cross-platform solution to record, convert and stream audio and video.”
License: GNU General Public License v3
Embedded licenses: FFmpeg embedded licences
FFmpeg is bundled as a convenience for users of ChimeraX.
It is a separate product,
and thus, its license does not affect ChimeraX's license.
FFmpeg can be freely redistributed separately from ChimeraX.
See the GPL FAQ for more details.
It can be found in the bin directory.
- OpenMM version 7.3.0
-
A high performance toolkit for molecular simulation.
License type: MIT and LGPL.
All licenses: OpenMM licences
Any work that uses OpenMM should cite the following publication:
P. Eastman, J. Swails, J. D. Chodera, R. T. McGibbon, Y. Zhao, K. A. Beauchamp, L.-P. Wang, A. C. Simmonett, M. P. Harrigan, C. D. Stern, R. P. Wiewiora, B. R. Brooks, and V. S. Pande.
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLOS Comp. Biol. 13(7): e1005659. (2017)
-
GNU FreeFont
- “GNU FreeFont is a free family of scalable outline fonts, suitable for general use on computers and for desktop publishing. It is Unicode-encoded for compatibility with all modern operating systems.”
License: GNU Public License v3 or later and the following exception:
"As a special exception, if you create a document which uses this font, and embed this font or unaltered portions of this font into the document, this font does not by itself cause the resulting document to be covered by the GNU General Public License. This exception does not however invalidate any other reasons why the document might be covered by the GNU General Public License.”
GNU FreeFont is bundled as a convenience for users of ChimeraX.
It is a separate product,
and thus, its license does not affect ChimeraX's license.
GNU FreeFont can be freely redistributed separately from ChimeraX.
See the GPL FAQ
and the GNU FreeFont FAQ for more details.
It can be found in the bin/share/fonts/freefont directory.
- xdg-utils version 1.1.1
- “xdg-utils is a set of tools that allows applications to easily integrate with the desktop environment of the user, regardless of the specific desktop environment that the user runs.”
License type: free
Linux only.
- Minicons Free Vector Icons Pack (downloaded 28 November 2016)
- The Minicons Free Vector Icon Pack is a free set of scalable icons.
License type: Creative Commons Abbtributions 3.0 Unported
Linux only.
- BasicProperty (and BasicTypes) for Python (downloaded 15 February 2018)
- The flatten function in basictypes/latebind.py is the basis for our chimerax.core.utils.flattened function. The Python packages are not included.
License type: BSD license
- AmberTools
- Certain executables from the AmberTools package are included with ChimeraX in order to compute partial charges. These executables are unmodified relative to their AmberTools versions, and are communicated with via their normal inputs and outputs.
License: Most of AmberTools is covered under the GNU Public License v3.
For convenience,
the ChimeraX distribution includes the Python packages that it depends on.
Both the direct and indirect dependencies are shown below.
The package names are links to the home page of the corresponding Python package.
The license type is shown, and if a license is bundled with the package,
a link to it is provided.
Note: this list is automatically generated.
Packages:
alabaster, appdirs, asttokens, auditwheel, autocommand, babel, backports.tarfile, beautifulsoup4, blockdiag, blosc2, build, certifi, cftime, charset-normalizer, colorama, comm, contourpy, cxservices, cycler, Cython, debugpy, decorator, distro, docutils, executing, filelock, fonttools, funcparserlib, glfw, grako, h5py, html2text, idna, ihm, imagecodecs, imagesize, importlib_metadata, importlib_resources, inflect, ipykernel, ipython, ipywidgets, jaraco.context, jaraco.functools, jaraco.text, jedi, Jinja2, jupyter_client, jupyter_core, jupyterlab_widgets, kiwisolver, line_profiler, lxml, lz4, MarkupSafe, matplotlib, matplotlib-inline, more-itertools, msgpack, ndindex, nest-asyncio, netCDF4, networkx, nibabel, nptyping, numexpr, numpy, openvr, ordered-set, packaging, packaging, ParmEd, parso, pep517, pexpect, pillow, pip, pkginfo, platformdirs, platformdirs, prompt_toolkit, psutil, ptyprocess, pure_eval, py-cpuinfo, pycollada, pydicom, pyelftools, Pygments, pynmrstar, pynrrd, PyOpenGL, PyOpenGL-accelerate, pyopenxr, pyparsing, pyproject_hooks, PyQt6-commercial, PyQt6-Qt6, PyQt6-WebEngine-commercial, PyQt6-WebEngine-Qt6, PyQt6-WebEngineSubwheel-Qt6, PyQt6_sip, python-dateutil, pytz, pyzmq, qtconsole, QtPy, qtshim, RandomWords, requests, scipy, setuptools, sfftk-rw, six, snowballstemmer, sortedcontainers, soupsieve, Sphinx, sphinx-autodoc-typehints, sphinxcontrib-applehelp, sphinxcontrib-blockdiag, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-jsmath, sphinxcontrib-qthelp, sphinxcontrib-serializinghtml, stack-data, superqt, tables, tcia_utils, tifffile, tinyarray, tomli, tornado, traitlets, typeguard, typing_extensions, typing_extensions, tzdata, urllib3, wcwidth, webcolors, wheel, wheel, wheel-filename, widgetsnbextension, zipp.
- alabaster version 1.0.0
- A light, configurable Sphinx theme
License type: BSD License
- appdirs version 1.4.4
- A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".
License type: MIT License
- asttokens version 2.4.1
- Annotate AST trees with source code positions
License type: Apache 2.0
- auditwheel version 6.1.0
- Cross-distribution Linux wheels
License type: MIT License
- autocommand version 2.2.2
- A library to create a command-line program from a function
License type: GNU Lesser General Public License v3 (LGPLv3)
- babel version 2.16.0
- Internationalization utilities
License type: BSD License
- backports.tarfile version 1.2.0
- Backport of CPython tarfile module
License type: MIT License
- beautifulsoup4 version 4.12.3
- Screen-scraping library
License type: MIT License
- blockdiag version 3.0.0
- blockdiag generates block-diagram image from text
License type: Apache Software License
- blosc2 version 2.7.1
- Python wrapper for the C-Blosc2 library
License type: BSD License
- build version 1.2.1
- A simple, correct Python build frontend
License type: MIT License
- certifi version 2024.8.30
- Python package for providing Mozilla's CA Bundle.
License type: Mozilla Public License 2.0 (MPL 2.0)
- cftime version 1.6.4.post1
- Time-handling functionality from netcdf4-python
License type: MIT License
- charset-normalizer version 3.4.0
- The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.
License type: MIT License
- colorama version 0.4.6
- Cross-platform colored terminal text.
License type: BSD License
- comm version 0.2.2
- Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc.
License type: BSD License
- contourpy version 1.3.0
- Python library for calculating contours of 2D quadrilateral grids
License type: BSD License
- cxservices version 1.2.3
- RBVI ChimeraX Web Services
- cycler version 0.12.1
- Composable style cycles
License type: BSD License
- Cython version 3.0.10
- The Cython compiler for writing C extensions in the Python language.
License type: Apache Software License
- debugpy version 1.8.7
- An implementation of the Debug Adapter Protocol for Python
License type: MIT License
- decorator version 5.1.1
- Decorators for Humans
License type: BSD License
- distro version 1.9.0
- Distro - an OS platform information API
License type: Apache Software License
- docutils version 0.21.2
- Docutils -- Python Documentation Utilities
License type: Public Domain, Python Software Foundation License, BSD License, GNU General Public License (GPL)
- executing version 2.1.0
- Get the currently executing AST node of a frame, and other information
License type: MIT License
- filelock version 3.15.4
- A platform independent file lock.
License type: The Unlicense (Unlicense)
- fonttools version 4.54.1
- Tools to manipulate font files
License type: MIT License
- funcparserlib version 2.0.0a0
- Recursive descent parsing library based on functional combinators
License type: MIT License
- glfw version 2.7.0
- A ctypes-based wrapper for GLFW3.
License type: MIT License
- grako version 3.16.5
- Grako (for "grammar compiler") takes a grammar in a variation of EBNF as input, and outputs a memoizing PEG/Packrat parser in Python.
License type: BSD License
- h5py version 3.12.1
- Read and write HDF5 files from Python
License type: BSD License
- html2text version 2024.2.26
- Turn HTML into equivalent Markdown-structured text.
License type: GNU General Public License (GPL)
- idna version 3.10
- Internationalized Domain Names in Applications (IDNA)
License type: BSD License
- ihm version 1.3
- Package for handling IHM mmCIF and BinaryCIF files
License type: MIT License
- imagecodecs version 2024.6.1
- Image transformation, compression, and decompression codecs
License type: BSD License
- imagesize version 1.4.1
- Getting image size from png/jpeg/jpeg2000/gif file
License type: MIT License
- importlib_metadata version 8.0.0
- Read metadata from Python packages
License type: Apache Software License
- importlib_resources version 6.4.0
- Read resources from Python packages
License type: Apache Software License
- inflect version 7.3.1
- Correctly generate plurals, singular nouns, ordinals, indefinite articles
License type: MIT License
- ipykernel version 6.29.5
- IPython Kernel for Jupyter
License type: BSD License
- ipython version 8.26.0
- IPython: Productive Interactive Computing
License type: BSD License
- ipywidgets version 8.1.5
- Jupyter interactive widgets
License type: BSD License
- jaraco.context version 5.3.0
- Useful decorators and context managers
License type: MIT License
- jaraco.functools version 4.0.1
- Functools like those found in stdlib
License type: MIT License
- jaraco.text version 3.12.1
- Module for text manipulation
License type: MIT License
- jedi version 0.19.1
- An autocompletion tool for Python that can be used for text editors.
License type: MIT License
- Jinja2 version 3.1.4
- A very fast and expressive template engine.
License type: BSD License
- jupyter_client version 8.6.2
- Jupyter protocol implementation and client libraries
License type: BSD License
- jupyter_core version 5.7.2
- Jupyter core package. A base package on which Jupyter projects rely.
License type: BSD License
- jupyterlab_widgets version 3.0.13
- Jupyter interactive widgets for JupyterLab
License type: BSD License
- kiwisolver version 1.4.7
- A fast implementation of the Cassowary constraint solver
License type: BSD License
- line_profiler version 4.1.3
- Line-by-line profiler
License type: BSD License
- lxml version 5.2.2
- Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API.
License type: BSD License
- lz4 version 4.3.3
- LZ4 Bindings for Python
License type: BSD License
- MarkupSafe version 3.0.2
- Safely add untrusted strings to HTML/XML markup.
License type: BSD License
- matplotlib version 3.9.2
- Python plotting package
License type: Python Software Foundation License
- matplotlib-inline version 0.1.7
- Inline Matplotlib backend for Jupyter
License type: BSD License
- more-itertools version 10.3.0
- More routines for operating on iterables, beyond itertools
License type: MIT License
- msgpack version 1.0.8
- MessagePack serializer
License type: Apache Software License
- ndindex version 1.9.2
- A Python library for manipulating indices of ndarrays.
License type: MIT License
- nest-asyncio version 1.6.0
- Patch asyncio to allow nested event loops
License type: BSD License
- netCDF4 version 1.6.5
- Provides an object-oriented python interface to the netCDF version 4 library
License type: MIT License
- networkx version 3.3
- Python package for creating and manipulating graphs and networks
License type: BSD License
- nibabel version 5.2.0
- Access a multitude of neuroimaging data formats
License type: MIT License
- nptyping version 2.5.0
- Type hints for NumPy.
License type: MIT License
- numexpr version 2.10.1
- Fast numerical expression evaluator for NumPy
License type: MIT License
- numpy version 1.26.4
- Fundamental package for array computing in Python
License type: BSD License
- openvr version 1.26.701
- Unofficial python bindings for Valve OpenVR SDK
License type: BSD License
- ordered-set version 4.1.0
- An OrderedSet is a custom MutableSet that remembers its order, so that every
License type: MIT License
- packaging version 23.2
- Core utilities for Python packages
License type: Apache Software License, BSD License
- packaging version 24.1
- Core utilities for Python packages
License type: Apache Software License, BSD License
- ParmEd version 4.2.2
- Inter-package toolkit for molecular mechanical simulations
License type: LGPL
- parso version 0.8.4
- A Python Parser
License type: MIT License
- pep517 version 0.13.1
- Wrappers to build Python packages using PEP 517 hooks
License type: MIT License
- pexpect version 4.9.0
- Pexpect allows easy control of interactive console applications.
License type: ISC License (ISCL)
- pillow version 10.4.0
- Python Imaging Library (Fork)
License type: Historical Permission Notice and Disclaimer (HPND)
- pip version 24.2
- The PyPA recommended tool for installing Python packages.
License type: MIT License
- pkginfo version 1.11.1
- Query metadata from sdists / bdists / installed packages.
License type: MIT License
- platformdirs version 4.3.6
- A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`.
License type: MIT License
- platformdirs version 4.2.2
- A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`.
License type: MIT License
- prompt_toolkit version 3.0.48
- Library for building powerful interactive command lines in Python
License type: BSD License
- psutil version 6.0.0
- Cross-platform lib for process and system monitoring in Python.
License type: BSD License
- ptyprocess version 0.7.0
- Run a subprocess in a pseudo terminal
License type: ISC License (ISCL)
- pure_eval version 0.2.3
- Safely evaluate AST nodes without side effects
License type: MIT License
- py-cpuinfo version 9.0.0
- Get CPU info with pure Python
License type: MIT License
- pycollada version 0.8
- python library for reading and writing collada documents
License type: BSD
- pydicom version 2.4.4
- A pure Python package for reading and writing DICOM data
License type: MIT License
- pyelftools version 0.31
- Library for analyzing ELF files and DWARF debugging information
License type: Public domain
- Pygments version 2.18.0
- Pygments is a syntax highlighting package written in Python.
License type: BSD License
- pynmrstar version 3.3.4
- PyNMR-STAR provides tools for reading, writing, modifying, and interacting with NMR-STAR files. Maintained by the BMRB.
License type: MIT License
- pynrrd version 1.0.0
- Pure python module for reading and writing NRRD files.
License type: MIT License
- PyOpenGL version 3.1.7
- Standard OpenGL bindings for Python
License type: BSD License
- PyOpenGL-accelerate version 3.1.7
- Acceleration code for PyOpenGL
License type: BSD License
- pyopenxr version 1.0.3401
- Unofficial python bindings for OpenXR VR/AP device access
License type: Apache Software License
- pyparsing version 3.2.0
- pyparsing module - Classes and methods to define and execute parsing grammars
License type: MIT License
- pyproject_hooks version 1.2.0
- Wrappers to call pyproject.toml-based build backend hooks.
License type: MIT License
- PyQt6-commercial version 6.7.1
- Python bindings for the Qt cross platform application toolkit
License type: Riverbank Commercial License
- PyQt6-Qt6 version 6.7.3
- The subset of a Qt installation needed by PyQt6.
License type: LGPL v3
- PyQt6-WebEngine-commercial version 6.7.0
- Python bindings for the Qt WebEngine framework
License type: Riverbank Commercial License
- PyQt6-WebEngine-Qt6 version 6.7.3
- The subset of a Qt installation needed by PyQt6-WebEngine.
License type: LGPL v3
- PyQt6-WebEngineSubwheel-Qt6 version 6.7.3
- The subset of a Qt installation needed by PyQt6-WebEngine.
License type: LGPL v3
- PyQt6_sip version 13.8.0
- The sip module support for PyQt6
License type: SIP
- python-dateutil version 2.9.0.post0
- Extensions to the standard Python datetime module
License type: BSD License, Apache Software License
- pytz version 2024.2
- World timezone definitions, modern and historical
License type: MIT License
- pyzmq version 26.2.0
- Python bindings for 0MQ
License type: BSD License
- qtconsole version 5.5.2
- Jupyter Qt console
License type: BSD License
- QtPy version 2.4.2
- Provides an abstraction layer on top of the various Qt bindings (PyQt5/6 and PySide2/6).
License type: MIT License
- qtshim version 1.0
- Qt shim that handles PyQt5/6 and PySide2/6
License type: Free for non-commercial use
- RandomWords version 0.4.0
- A useful module for a random text, e-mails and lorem ipsum.
License type: MIT License
- requests version 2.32.3
- Python HTTP for Humans.
License type: Apache Software License
- scipy version 1.14.0
- Fundamental algorithms for scientific computing in Python
License type: BSD License
- setuptools version 72.1.0
- Easily download, build, install, upgrade, and uninstall Python packages
License type: MIT License
- sfftk-rw version 0.8.1
- Toolkit for reading and writing EMDB-SFF files
License type: Apache Software License
- six version 1.16.0
- Python 2 and 3 compatibility utilities
License type: MIT License
- snowballstemmer version 2.2.0
- This package provides 29 stemmers for 28 languages generated from Snowball algorithms.
License type: BSD License
- sortedcontainers version 2.4.0
- Sorted Containers -- Sorted List, Sorted Dict, Sorted Set
License type: Apache Software License
- soupsieve version 2.6
- A modern CSS selector implementation for Beautiful Soup.
License type: MIT License
- Sphinx version 8.0.2
- Python documentation generator
License type: BSD License
- sphinx-autodoc-typehints version 2.2.3
- Type hints (PEP 484) support for the Sphinx autodoc extension
License type: MIT License
- sphinxcontrib-applehelp version 2.0.0
- sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books
License type: BSD License
- sphinxcontrib-blockdiag version 3.0.0
- Sphinx "blockdiag" extension
License type: BSD License
- sphinxcontrib-devhelp version 2.0.0
- sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents
License type: BSD License
- sphinxcontrib-htmlhelp version 2.1.0
- sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files
License type: BSD License
- sphinxcontrib-jsmath version 1.0.1
- A sphinx extension which renders display math in HTML via JavaScript
License type: BSD License
- sphinxcontrib-qthelp version 2.0.0
- sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents
License type: BSD License
- sphinxcontrib-serializinghtml version 2.0.0
- sphinxcontrib-serializinghtml is a sphinx extension which outputs "serialized" HTML files (json and pickle)
License type: BSD License
- stack-data version 0.6.3
- Extract data from python stack frames and tracebacks for informative displays
License type: MIT License
- superqt version 0.6.3
- Missing widgets and components for PyQt/PySide
License type: BSD License
- tables version 3.10.1
- Hierarchical datasets for Python
License type: BSD License
- tcia_utils version 1.5.1
- A package to simplify common tasks one might perform when interacting with The Cancer Imaging Archive (TCIA) via Jupyter/Python.
License type: Apache Software License
- tifffile version 2024.7.24
- Read and write TIFF files
License type: BSD License
- tinyarray version 1.2.4
- Arrays of numbers for Python, optimized for small sizes
License type: BSD License
- tomli version 2.0.1
- A lil' TOML parser
License type: MIT License
- tornado version 6.4.1
- Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed.
License type: Apache Software License
- traitlets version 5.14.3
- Traitlets Python configuration system
License type: BSD License
- typeguard version 4.3.0
- Run-time type checker for Python
License type: MIT License
- typing_extensions version 4.12.2
- Backported and Experimental Type Hints for Python 3.8+
License type: Python Software Foundation License
- typing_extensions version 4.12.2
- Backported and Experimental Type Hints for Python 3.8+
License type: Python Software Foundation License
- tzdata version 2024.2
- Provider of IANA time zone data
License type: Apache Software License
- urllib3 version 2.2.3
- HTTP library with thread-safe connection pooling, file post, and more.
License type: MIT License
- wcwidth version 0.2.13
- Measures the displayed width of unicode strings in a terminal
License type: MIT License
- webcolors version 24.6.0
- A library for working with the color formats defined by HTML and CSS.
License type: BSD License
- wheel version 0.43.0
- A built-package format for Python
License type: MIT License
- wheel version 0.43.0
- A built-package format for Python
License type: MIT License
- wheel-filename version 1.4.1
- Parse wheel filenames
License type: MIT License
- widgetsnbextension version 4.0.13
- Jupyter interactive widgets for Jupyter Notebook
License type: BSD License
- zipp version 3.19.2
- Backport of pathlib-compatible object wrapper for zip files
License type: MIT License