Software Embedded in UCSF ChimeraX

UCSF ChimeraX is built upon other great software.

Included 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.

Included Python Packages

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, Antergos Linux, appdirs, Babel, backcall, blockdiag, certifi, cftime, charset-normalizer, colorama, cxservices, cycler, Cython, debugpy, decorator, docutils, entrypoints, filelock, fonttools, funcparserlib, grako, h5py, html2text, idna, ihm, imagecodecs, imagesize, ipykernel, ipython, ipython-genutils, jedi, Jinja2, jupyter-client, jupyter-core, kiwisolver, line-profiler, lxml, lz4, MarkupSafe, matplotlib, matplotlib-inline, msgpack, nest-asyncio, netCDF4, networkx, numexpr, numpy, openvr, packaging, ParmEd, parso, pexpect, pickleshare, Pillow, pip, pkginfo, prompt-toolkit, psutil, ptyprocess, pycollada, pydicom, Pygments, PyOpenGL, PyOpenGL-accelerate, pyparsing, PyQt5-commercial, PyQt5-sip, PyQtWebEngine-commercial, python-dateutil, pytz, pyzmq, qtconsole, QtPy, RandomWords, requests, scipy, setuptools, sfftk-rw, six, snowballstemmer, sortedcontainers, Sphinx, sphinx-autodoc-typehints, sphinxcontrib-applehelp, sphinxcontrib-blockdiag, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-jsmath, sphinxcontrib-qthelp, sphinxcontrib-serializinghtml, suds-community, tables, tifffile, tinyarray, tornado, traitlets, urllib3, wcwidth, webcolors, wheel, wheel-filename.

alabaster version 0.7.12
A configurable sidebar-enabled Sphinx theme
License type: BSD License
Antergos Linux version 2015.10 (ISO-Rolling)
Distro - an OS platform information API
License type: Apache Software 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
Babel version 2.9.1
Internationalization utilities
License type: BSD License
backcall version 0.2.0
Specifications for callback functions passed in to an API
License type: BSD License
blockdiag version 3.0.0
blockdiag generates block-diagram image from text
License type: Apache Software License
certifi version 2021.10.8
Python package for providing Mozilla's CA Bundle.
License type: Mozilla Public License 2.0 (MPL 2.0)
cftime version 1.5.2
Time-handling functionality from netcdf4-python
License type: MIT License
charset-normalizer version 2.0.10
The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.
License type: MIT License
colorama version 0.4.4
Cross-platform colored terminal text.
License type: BSD License
cxservices version 1.1
RBVI ChimeraX Web Services
License type: UNKNOWN
cycler version 0.11.0
Composable style cycles
License type: BSD License
Cython version 0.29.26
The Cython compiler for writing C extensions for the Python language.
License type: Apache Software License
debugpy version 1.5.1
An implementation of the Debug Adapter Protocol for Python
License type: Eclipse Public License 2.0 (EPL-2.0), MIT License
decorator version 5.1.1
Decorators for Humans
License type: BSD License
docutils version 0.17.1
Docutils -- Python Documentation Utilities
License type: Public Domain, Python Software Foundation License, BSD License, GNU General Public License (GPL)
entrypoints version 0.3
Discover and load entry points from installed packages.
License type: MIT License
filelock version 3.4.2
A platform independent file lock.
License type: Public Domain
fonttools version 4.28.5
Tools to manipulate font files
License type: MIT License
funcparserlib version 1.0.0a0
Recursive descent parsing library based on functional combinators
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 3.6.0
Read and write HDF5 files from Python
License type: BSD License
html2text version 2020.1.16
Turn HTML into equivalent Markdown-structured text.
License type: GNU General Public License (GPL)
idna version 3.3
Internationalized Domain Names in Applications (IDNA)
License type: BSD License
ihm version 0.26
Package for handling IHM mmCIF and BinaryCIF files
License type: MIT License
imagecodecs version 2021.11.20
Image transformation, compression, and decompression codecs
License type: BSD License
imagesize version 1.3.0
Getting image size from png/jpeg/jpeg2000/gif file
License type: MIT License
ipykernel version 6.6.1
IPython Kernel for Jupyter
License type: BSD License
ipython version 7.31.0
IPython: Productive Interactive Computing
License type: BSD License
ipython-genutils version 0.2.0
Vestigial utilities from IPython
License type: BSD License
jedi version 0.18.1
An autocompletion tool for Python that can be used for text editors.
License type: MIT License
Jinja2 version 3.0.3
A very fast and expressive template engine.
License type: BSD License
jupyter-client version 7.1.0
Jupyter protocol implementation and client libraries
License type: BSD License
jupyter-core version 4.9.1
Jupyter core package. A base package on which Jupyter projects rely.
License type: BSD License
kiwisolver version 1.3.2
A fast implementation of the Cassowary constraint solver
License type: BSD License
line-profiler version 3.4.0
Line-by-line profiler.
License type: BSD License
lxml version 4.7.1
Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API.
License type: BSD License
lz4 version 3.1.10
LZ4 Bindings for Python
License type: BSD License
MarkupSafe version 2.0.1
Safely add untrusted strings to HTML/XML markup.
License type: BSD License
matplotlib version 3.5.1
Python plotting package
License type: Python Software Foundation License
matplotlib-inline version 0.1.3
Inline Matplotlib backend for Jupyter
License type: BSD 3-Clause
msgpack version 1.0.3
MessagePack (de)serializer.
License type: Apache Software License
nest-asyncio version 1.5.4
Patch asyncio to allow nested event loops
License type: BSD License
netCDF4 version 1.5.8
Provides an object-oriented python interface to the netCDF version 4 library.
License type: MIT License
networkx version 2.6.3
Python package for creating and manipulating graphs and networks
License type: BSD License
numexpr version 2.8.1
Fast numerical expression evaluator for NumPy
License type: MIT License
numpy version 1.22.1
NumPy is the fundamental package for array computing with Python.
License type: BSD License
openvr version 1.16.802
Unofficial python bindings for Valve OpenVR SDK
License type: BSD License
packaging version 21.3
Core utilities for Python packages
License type: Apache Software License, BSD License
ParmEd version 3.4.3
Amber parameter file editor
License type: LGPL
parso version 0.8.3
A Python Parser
License type: MIT License
pexpect version 4.8.0
Pexpect allows easy control of interactive console applications.
License type: ISC License (ISCL)
pickleshare version 0.7.5
Tiny 'shelve'-like database with concurrency support
License type: MIT License
Pillow version 9.0.0
Python Imaging Library (Fork)
License type: Historical Permission Notice and Disclaimer (HPND)
pip version 21.3.1
The PyPA recommended tool for installing Python packages.
License type: MIT License
pkginfo version 1.8.2
Query metadatdata from sdists / bdists / installed packages.
License type: MIT License
prompt-toolkit version 3.0.24
Library for building powerful interactive command lines in Python
License type: BSD License
psutil version 5.9.0
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)
pycollada version 0.7.2
python library for reading and writing collada documents
License type: BSD
pydicom version 2.2.2
Pure python package for DICOM medical file reading and writing
License type: MIT License
Pygments version 2.11.2
Pygments is a syntax highlighting package written in Python.
License type: BSD License
PyOpenGL version 3.1.5
Standard OpenGL bindings for Python
License type: BSD License
PyOpenGL-accelerate version 3.1.5
Acceleration code for PyOpenGL
License type: BSD License
pyparsing version 3.0.7
Python parsing module
License type: MIT License
PyQt5-commercial version 5.15.2
Python bindings for the Qt cross platform application toolkit
License type: Riverbank Commercial License
PyQt5-sip version 12.8.1
The sip module support for PyQt5
License type: SIP
PyQtWebEngine-commercial version 5.15.2
Python bindings for the Qt WebEngine framework
License type: Riverbank Commercial License
python-dateutil version 2.8.2
Extensions to the standard Python datetime module
License type: BSD License, Apache Software License
pytz version 2021.3
World timezone definitions, modern and historical
License type: MIT License
pyzmq version 22.3.0
Python bindings for 0MQ
License type: GNU Library or Lesser General Public License (LGPL), BSD License
qtconsole version 5.2.2
Jupyter Qt console
License type: BSD License
QtPy version 2.0.0
Provides an abstraction layer on top of the various Qt bindings (PyQt5/6 and PySide2/6).
License type: MIT License
RandomWords version 0.3.0
A useful module for a random text, e-mails and lorem ipsum.
License type: MIT License
requests version 2.27.1
Python HTTP for Humans.
License type: Apache Software License
scipy version 1.7.3
SciPy: Scientific Library for Python
License type: BSD License
setuptools version 59.8.0
Easily download, build, install, upgrade, and uninstall Python packages
License type: MIT License
sfftk-rw version 0.7.1
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
Sphinx version 4.3.2
Python documentation generator
License type: BSD License
sphinx-autodoc-typehints version 1.15.2
Type hints (PEP 484) support for the Sphinx autodoc extension
License type: MIT License
sphinxcontrib-applehelp version 1.0.2
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 1.0.2
sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document.
License type: BSD License
sphinxcontrib-htmlhelp version 2.0.0
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 1.0.3
sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document.
License type: BSD License
sphinxcontrib-serializinghtml version 1.1.5
sphinxcontrib-serializinghtml is a sphinx extension which outputs "serialized" HTML files (json and pickle).
License type: BSD License
suds-community version 1.0.0
Lightweight SOAP client (community fork)
License type: GNU Library or Lesser General Public License (LGPL)
tables version 3.7.0
Hierarchical datasets for Python
License type: BSD License
tifffile version 2021.11.2
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
tornado version 6.1
Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed.
License type: Apache Software License
traitlets version 5.1.1
Traitlets Python configuration system
License type: BSD License
urllib3 version 1.26.8
HTTP library with thread-safe connection pooling, file post, and more.
License type: MIT License
wcwidth version 0.2.5
Measures the displayed width of unicode strings in a terminal
License type: MIT License
webcolors version 1.11.1
A library for working with color names and color values formats defined by HTML and CSS.
License type: BSD License
wheel version 0.37.1
A built-package format for Python
License type: MIT License
wheel-filename version 1.3.0
Parse wheel filenames
License type: MIT License