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++.

PyQt version 5
“PyQt is a set of Python v2 and v3 bindings for The Qt Company's Qt application framework and runs on all platforms supported by Qt including Windows, OS X, Linux, iOS and Android.” “PyQt is dual licensed on all supported platforms under the GNU GPL v3 and the Riverbank Commercial License.”
License: ChimeraX is develped with a commercial license for PyQt. See the Riverbank License FAQ for more details.

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/ is the basis for our chimerax.core.utils.flattened function. The Python packages are not included.
License type: BSD license

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, appdirs, appnope, attrs, Babel, backcall, blockdiag, certifi, chardet, colorama, comtypes, cycler, Cython, decorator, distlib, docutils, filelock, funcparserlib, grako, html2text, idna, ihm, imagecodecs-lite, imagesize, ipykernel, ipython, ipython-genutils, jedi, Jinja2, jupyter-client, jupyter-core, kiwisolver, line-profiler, lxml, MarkupSafe, matplotlib, msgpack, networkx, numexpr, numpy, numpydoc, openvr, packaging, parso, pexpect, pickleshare, Pillow, pip, pkginfo, prompt-toolkit, psutil, ptyprocess, pycollada, pydicom, Pygments, PyOpenGL, PyOpenGL-accelerate, pyparsing, PyQt5, PyQt5_sip, PyQtWebEngine, python-dateutil, pytz, pyzmq, qtconsole, requests, scipy, setuptools, six, snowballstemmer, sortedcontainers, Sphinx, sphinxcontrib-applehelp, sphinxcontrib-blockdiag, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-jsmath, sphinxcontrib-qthelp, sphinxcontrib-serializinghtml, suds-jurko, tables, tifffile, tinyarray, tornado, traitlets, urllib3, wcwidth, webcolors, wheel.

alabaster version 0.7.12
A configurable sidebar-enabled Sphinx theme
License type: BSD License
appdirs version 1.4.3
A small Python module for determining appropriate platform-specific dirs, e.g. a "user data dir".
License type: MIT License
appnope version 0.1.0
Disable App Nap on OS X 10.9
License type: BSD License
attrs version 19.1.0
Classes Without Boilerplate
License type: MIT License
Babel version 2.7.0
Internationalization utilities
License type: BSD License
backcall version 0.1.0
Specifications for callback functions passed in to an API
License type: BSD License
blockdiag version 1.5.4
blockdiag generates block-diagram image from text
License type: Apache Software License
certifi version 2019.6.16
Python package for providing Mozilla's CA Bundle.
License type: Mozilla Public License 2.0 (MPL 2.0)
chardet version 3.0.4
Universal encoding detector for Python 2 and 3
License type: GNU Library or Lesser General Public License (LGPL)
colorama version 0.4.1
Cross-platform colored terminal text.
License type: BSD License
comtypes version 1.1.7
Pure Python COM package
License type: MIT License
cycler version 0.10.0
Composable style cycles
License type: BSD
Cython version 0.29.13
The Cython compiler for writing C extensions for the Python language.
License type: Apache Software License
decorator version 4.4.0
Better living through Python with decorators
License type: BSD License
distlib version 0.2.9.post0
Distribution utilities
License type: Python Software Foundation License
docutils version 0.15.2
Docutils -- Python Documentation Utilities
License type: Public Domain, Python Software Foundation License, BSD License, GNU General Public License (GPL)
filelock version 3.0.12
A platform independent file lock.
License type: Public Domain
funcparserlib version 0.3.6
Recursive descent parsing library based on functional combinators
License type: MIT
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
html2text version 2018.1.9
Turn HTML into equivalent Markdown-structured text.
License type: GNU General Public License (GPL)
idna version 2.8
Internationalized Domain Names in Applications (IDNA)
License type: BSD License
ihm version 0.10
Package for handling IHM mmCIF and BinaryCIF files
License type: MIT License
imagecodecs-lite version 2019.4.20
Subset of image transformation, compression, and decompression codecs
License type: BSD License
imagesize version 1.1.0
Getting image size from png/jpeg/jpeg2000/gif file
License type: MIT License
ipykernel version 5.1.1
IPython Kernel for Jupyter
License type: BSD License
ipython version 7.7.0
IPython: Productive Interactive Computing
License type: BSD License
ipython-genutils version 0.2.0
Vestigial utilities from IPython
License type: BSD License
jedi version 0.15.1
An autocompletion tool for Python that can be used for text editors.
License type: MIT License
Jinja2 version 2.10.1
A small but fast and easy to use stand-alone template engine written in pure python.
License type: BSD License
jupyter-client version 5.3.1
Jupyter protocol implementation and client libraries
License type: BSD License
jupyter-core version 4.5.0
Jupyter core package. A base package on which Jupyter projects rely.
License type: BSD License
kiwisolver version 1.1.0
A fast implementation of the Cassowary constraint solver
License type: BSD
line-profiler version 2.1.2
Line-by-line profiler.
License type: BSD License
lxml version 4.4.0
Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API.
License type: BSD License
MarkupSafe version 1.1.1
Safely add untrusted strings to HTML/XML markup.
License type: BSD License
matplotlib version 3.1.1
Python plotting package
License type: Python Software Foundation License
msgpack version 0.6.1
MessagePack (de)serializer.
License type: Apache Software License
networkx version 2.3
Python package for creating and manipulating graphs and networks
License type: BSD License
numexpr version 2.7.0
Fast numerical expression evaluator for NumPy
License type: MIT
numpy version 1.17.0
NumPy is the fundamental package for array computing with Python.
License type: OSI Approved
numpydoc version 0.9.1
Sphinx extension to support docstrings in Numpy format
License type: BSD License
openvr version 1.5.1701
Unofficial python bindings for Valve OpenVR SDK
License type: BSD License
packaging version 19.1
Core utilities for Python packages
License type: Apache Software License, BSD License
parso version 0.5.1
A Python Parser
License type: MIT License
pexpect version 4.7.0
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 6.1.0
Python Imaging Library (Fork)
License type: Historical Permission Notice and Disclaimer (HPND)
pip version 19.2.1
The PyPA recommended tool for installing Python packages.
License type: MIT License
pkginfo version
Query metadatdata from sdists / bdists / installed packages.
License type: MIT License
prompt-toolkit version 2.0.9
Library for building powerful interactive command lines in Python
License type: BSD License
psutil version 5.6.3
Cross-platform lib for process and system monitoring in Python.
License type: BSD License
ptyprocess version 0.6.0
Run a subprocess in a pseudo terminal
License type: ISC License (ISCL)
pycollada version 0.6
python library for reading and writing collada documents
License type: BSD
pydicom version 1.3.0
Pure python package for DICOM medical file reading and writing
License type: MIT License
Pygments version 2.4.2
Pygments is a syntax highlighting package written in Python.
License type: BSD License
PyOpenGL version 3.1.3b2
Standard OpenGL bindings for Python
License type: BSD License
PyOpenGL-accelerate version 3.1.3b1
Acceleration code for PyOpenGL
License type: BSD License
pyparsing version 2.4.2
Python parsing module
License type: MIT License
PyQt5 version 5.12.2
Python bindings for the Qt cross platform UI and application toolkit
License type: Riverbank Commercial License
PyQt5_sip version 4.19.17
Python extension module support for PyQt5
PyQtWebEngine version 5.12.1
Python bindings for the Qt WebEngine framework
License type: Riverbank Commercial License
python-dateutil version 2.8.0
Extensions to the standard Python datetime module
License type: BSD License, Apache Software License
pytz version 2019.2
World timezone definitions, modern and historical
License type: MIT License
pyzmq version 18.1.0
Python bindings for 0MQ
License type: GNU Library or Lesser General Public License (LGPL), BSD License
qtconsole version 4.5.2
Jupyter Qt console
License type: BSD License
requests version 2.22.0
Python HTTP for Humans.
License type: Apache Software License
scipy version 1.3.0
SciPy: Scientific Library for Python
License type: BSD License
setuptools version 41.0.1
Easily download, build, install, upgrade, and uninstall Python packages
License type: MIT License
six version 1.12.0
Python 2 and 3 compatibility utilities
License type: MIT License
snowballstemmer version 1.9.0
This package provides 23 stemmers for 22 languages generated from Snowball algorithms.
License type: BSD License
sortedcontainers version 2.1.0
Sorted Containers -- Sorted List, Sorted Dict, Sorted Set
License type: Apache Software License
Sphinx version 2.1.2
Python documentation generator
License type: BSD License
sphinxcontrib-applehelp version 1.0.1

License type: BSD License
sphinxcontrib-blockdiag version 1.5.5
Sphinx "blockdiag" extension
License type: BSD License
sphinxcontrib-devhelp version 1.0.1

License type: BSD License
sphinxcontrib-htmlhelp version 1.0.2

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 1.0.2

License type: BSD License
sphinxcontrib-serializinghtml version 1.1.3

License type: BSD License
suds-jurko version 0.6
Lightweight SOAP client (Jurko's fork)
License type: GNU Library or Lesser General Public License (LGPL)
tables version 3.4.4
Hierarchical datasets for Python
License type: BSD License
tifffile version 2019.7.26
Read and write TIFF(r) files
License type: BSD License
tinyarray version 1.2.1
Arrays of numbers for Python, optimized for small sizes
License type: BSD License
tornado version 6.0.3
Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed.
License type: Apache Software License
traitlets version 4.3.2
Traitlets Python config system
License type: BSD License
urllib3 version 1.25.3
HTTP library with thread-safe connection pooling, file post, and more.
License type: MIT License
wcwidth version 0.1.7
Measures number of Terminal column cells of wide-character codes
License type: MIT License
webcolors version 1.9.1
A library for working with color names and color values formats defined by HTML and CSS.
License type: BSD License
wheel version 0.33.4
A built-package format for Python.
License type: MIT License