├── .gitignore ├── CHANGES ├── LICENSE ├── MANIFEST.in ├── README.md ├── doc ├── Makefile ├── _build │ ├── doctrees │ │ ├── documentation.doctree │ │ ├── environment.pickle │ │ ├── host.doctree │ │ ├── index.doctree │ │ ├── source │ │ │ ├── faerun.doctree │ │ │ └── modules.doctree │ │ └── tutorial.doctree │ ├── html │ │ ├── .buildinfo │ │ ├── _images │ │ │ ├── drugbank_2d_dark.png │ │ │ ├── drugbank_2d_light.png │ │ │ ├── tutorial.png │ │ │ ├── tutorial_host_label.png │ │ │ ├── tutorial_host_search.png │ │ │ └── tutorial_host_search_2.png │ │ ├── _sources │ │ │ ├── documentation.rst.txt │ │ │ ├── host.rst.txt │ │ │ ├── index.rst.txt │ │ │ ├── source │ │ │ │ ├── faerun.rst.txt │ │ │ │ └── modules.rst.txt │ │ │ └── tutorial.rst.txt │ │ ├── _static │ │ │ ├── ajax-loader.gif │ │ │ ├── basic.css │ │ │ ├── comment-bright.png │ │ │ ├── comment-close.png │ │ │ ├── comment.png │ │ │ ├── css │ │ │ │ ├── badge_only.css │ │ │ │ └── theme.css │ │ │ ├── doctools.js │ │ │ ├── documentation_options.js │ │ │ ├── down-pressed.png │ │ │ ├── down.png │ │ │ ├── drugbank_2d_dark.png │ │ │ ├── drugbank_2d_light.png │ │ │ ├── file.png │ │ │ ├── fonts │ │ │ │ ├── Inconsolata-Bold.ttf │ │ │ │ ├── Inconsolata-Regular.ttf │ │ │ │ ├── Inconsolata.ttf │ │ │ │ ├── Lato-Bold.ttf │ │ │ │ ├── Lato-Regular.ttf │ │ │ │ ├── Lato │ │ │ │ │ ├── lato-bold.eot │ │ │ │ │ ├── lato-bold.ttf │ │ │ │ │ ├── lato-bold.woff │ │ │ │ │ ├── lato-bold.woff2 │ │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ │ ├── lato-italic.eot │ │ │ │ │ ├── lato-italic.ttf │ │ │ │ │ ├── lato-italic.woff │ │ │ │ │ ├── lato-italic.woff2 │ │ │ │ │ ├── lato-regular.eot │ │ │ │ │ ├── lato-regular.ttf │ │ │ │ │ ├── lato-regular.woff │ │ │ │ │ └── lato-regular.woff2 │ │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ │ ├── RobotoSlab │ │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ └── fontawesome-webfont.woff2 │ │ │ ├── jquery-3.2.1.js │ │ │ ├── jquery.js │ │ │ ├── js │ │ │ │ ├── modernizr.min.js │ │ │ │ └── theme.js │ │ │ ├── language_data.js │ │ │ ├── minus.png │ │ │ ├── plus.png │ │ │ ├── pygments.css │ │ │ ├── searchtools.js │ │ │ ├── tutorial.png │ │ │ ├── tutorial_host_label.png │ │ │ ├── tutorial_host_search.png │ │ │ ├── tutorial_host_search_2.png │ │ │ ├── underscore-1.3.1.js │ │ │ ├── underscore.js │ │ │ ├── up-pressed.png │ │ │ ├── up.png │ │ │ └── websupport.js │ │ ├── documentation.html │ │ ├── genindex.html │ │ ├── host.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ ├── source │ │ │ ├── faerun.html │ │ │ └── modules.html │ │ └── tutorial.html │ ├── latex │ │ ├── Faerun.aux │ │ ├── Faerun.fdb_latexmk │ │ ├── Faerun.fls │ │ ├── Faerun.idx │ │ ├── Faerun.ilg │ │ ├── Faerun.ind │ │ ├── Faerun.out │ │ ├── Faerun.pdf │ │ ├── Faerun.tex │ │ ├── Faerun.toc │ │ ├── LICRcyr2utf8.xdy │ │ ├── LICRlatin2utf8.xdy │ │ ├── LatinRules.xdy │ │ ├── Makefile │ │ ├── drugbank_2d_dark.png │ │ ├── drugbank_2d_light.png │ │ ├── footnotehyper-sphinx.sty │ │ ├── latexmkjarc │ │ ├── latexmkrc │ │ ├── make.bat │ │ ├── python.ist │ │ ├── sphinx.sty │ │ ├── sphinx.xdy │ │ ├── sphinxhighlight.sty │ │ ├── sphinxhowto.cls │ │ ├── sphinxmanual.cls │ │ ├── sphinxmulticell.sty │ │ ├── tutorial.png │ │ ├── tutorial_host_label.png │ │ ├── tutorial_host_search.png │ │ └── tutorial_host_search_2.png │ └── markdown │ │ ├── documentation.md │ │ ├── host.md │ │ ├── index.md │ │ └── tutorial.md ├── _static │ ├── drugbank_2d_dark.png │ ├── drugbank_2d_light.png │ ├── tutorial.png │ ├── tutorial_host_label.png │ ├── tutorial_host_search.png │ └── tutorial_host_search_2.png ├── conf.py ├── documentation.rst ├── host.rst ├── index.rst ├── make.bat └── tutorial.rst ├── examples ├── drugbank.smi ├── example.py ├── example_sin.py ├── example_web.py ├── example_web_3d.py ├── helix.html ├── helix.js ├── index.html ├── index.js ├── index.pickle ├── test.html ├── test.js ├── tutorial.py └── tutorial_host.py ├── faerun ├── __init__.py ├── assets │ └── index_static.html ├── faerun.py ├── plot.py ├── template_default.j2 ├── template_reaction_smiles.j2 ├── template_smiles.j2 ├── template_url_image.j2 └── web.py ├── notebook ├── faerun.ipynb ├── helix.html ├── requirements.txt ├── runtime.txt ├── sin.html └── sine.html ├── requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | 6 | # C extensions 7 | *.so 8 | 9 | # Distribution / packaging 10 | .Python 11 | build/ 12 | develop-eggs/ 13 | dist/ 14 | downloads/ 15 | eggs/ 16 | .eggs/ 17 | lib/ 18 | lib64/ 19 | parts/ 20 | sdist/ 21 | var/ 22 | wheels/ 23 | *.egg-info/ 24 | .installed.cfg 25 | *.egg 26 | MANIFEST 27 | 28 | # PyInstaller 29 | # Usually these files are written by a python script from a template 30 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 31 | *.manifest 32 | *.spec 33 | 34 | # Installer logs 35 | pip-log.txt 36 | pip-delete-this-directory.txt 37 | 38 | # Unit test / coverage reports 39 | htmlcov/ 40 | .tox/ 41 | .coverage 42 | .coverage.* 43 | .cache 44 | nosetests.xml 45 | coverage.xml 46 | *.cover 47 | .hypothesis/ 48 | .pytest_cache/ 49 | 50 | # Translations 51 | *.mo 52 | *.pot 53 | 54 | # Django stuff: 55 | *.log 56 | local_settings.py 57 | db.sqlite3 58 | 59 | # Flask stuff: 60 | instance/ 61 | .webassets-cache 62 | 63 | # Scrapy stuff: 64 | .scrapy 65 | 66 | # Sphinx documentation 67 | # docs/_build 68 | 69 | # PyBuilder 70 | target/ 71 | 72 | # Jupyter Notebook 73 | .ipynb_checkpoints 74 | 75 | # pyenv 76 | .python-version 77 | 78 | # celery beat schedule file 79 | celerybeat-schedule 80 | 81 | # SageMath parsed files 82 | *.sage.py 83 | 84 | # Environments 85 | .env 86 | .venv 87 | env/ 88 | venv/ 89 | ENV/ 90 | env.bak/ 91 | venv.bak/ 92 | 93 | # Spyder project settings 94 | .spyderproject 95 | .spyproject 96 | 97 | # Rope project settings 98 | .ropeproject 99 | 100 | # mkdocs documentation 101 | /site 102 | 103 | # mypy 104 | .mypy_cache/ 105 | 106 | # Data 107 | data.js 108 | *.faerun -------------------------------------------------------------------------------- /CHANGES: -------------------------------------------------------------------------------- 1 | # Changelog 2 | ## [0.3.2] - 2019-09-20 3 | ### Added 4 | - Possibility to load custom jinja2 templates by supplying their path to the template argument (if the value for template is "default", "smiles", or "url_image", the internal templates will be loaded). 5 | ## [0.3.3] - 2019-10-09 6 | ### Added 7 | - The possibility to export screenshots at 2x the on-screen resolution 8 | ### Changed 9 | - The preserveDrawingBuffer option of Lore is set to true now in order to allow for screenshots 10 | ## [0.3.4] - 2019-11-09 11 | ### Bugfix 12 | - Fixed bug where a list of legend_labels was not recognized as such 13 | ## [0.3.5] - 2019-11-11 14 | ### Bugfix 15 | - Fixed bug where a list of legend_labels was not recognized as such, again 16 | ## [0.3.6] - 2019-12-01 17 | ### Changed 18 | - Updated lore to version 1.1.10 19 | ## [0.3.7] - 2019-12-01 20 | ### Changed 21 | - Fixed bug where hidden geometires (scatters) were not moved 22 | ## [0.3.8] - 2020-04-22 23 | ### Bugfix 24 | - Defining sizes for series is now possible just as it is with colours 25 | ## [0.3.9] - 2020-04-22 26 | ### Changes 27 | - Rounding sizes to reduce file size 28 | ## [0.3.10] - 2020-04-27 29 | ### Changes 30 | - Updated SmilesDrawer version -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 Reymond Group, University of Bern 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include faerun/template_default.j2 2 | include faerun/template_smiles.j2 3 | include faerun/template_reaction_smiles.j2 4 | include faerun/template_url_image.j2 5 | include faerun/assets/index_static.html 6 | -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /doc/_build/doctrees/documentation.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/doctrees/documentation.doctree -------------------------------------------------------------------------------- /doc/_build/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/doctrees/environment.pickle -------------------------------------------------------------------------------- /doc/_build/doctrees/host.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/doctrees/host.doctree -------------------------------------------------------------------------------- /doc/_build/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/doctrees/index.doctree -------------------------------------------------------------------------------- /doc/_build/doctrees/source/faerun.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/doctrees/source/faerun.doctree -------------------------------------------------------------------------------- /doc/_build/doctrees/source/modules.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/doctrees/source/modules.doctree -------------------------------------------------------------------------------- /doc/_build/doctrees/tutorial.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/doctrees/tutorial.doctree -------------------------------------------------------------------------------- /doc/_build/html/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: 22232186176eb38a1f262fb47044552f 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /doc/_build/html/_images/drugbank_2d_dark.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/html/_images/drugbank_2d_dark.png -------------------------------------------------------------------------------- /doc/_build/html/_images/drugbank_2d_light.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/html/_images/drugbank_2d_light.png -------------------------------------------------------------------------------- /doc/_build/html/_images/tutorial.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/html/_images/tutorial.png -------------------------------------------------------------------------------- /doc/_build/html/_images/tutorial_host_label.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/html/_images/tutorial_host_label.png -------------------------------------------------------------------------------- /doc/_build/html/_images/tutorial_host_search.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/html/_images/tutorial_host_search.png -------------------------------------------------------------------------------- /doc/_build/html/_images/tutorial_host_search_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/html/_images/tutorial_host_search_2.png -------------------------------------------------------------------------------- /doc/_build/html/_sources/documentation.rst.txt: -------------------------------------------------------------------------------- 1 | Documentation 2 | ------------- 3 | 4 | Faerun 5 | ^^^^^^ 6 | .. autoclass:: faerun.Faerun 7 | :members: 8 | 9 | Web 10 | ^^^ 11 | .. autofunction:: faerun.host 12 | -------------------------------------------------------------------------------- /doc/_build/html/_sources/host.rst.txt: -------------------------------------------------------------------------------- 1 | Web 2 | --- 3 | 4 | Introduction 5 | ^^^^^^^^^^^^ 6 | While small plots can easily be created and stored in a single HTML and JavaScript file, which are then loaded completely in the browsers memory, this is not possible for larger data sets due to browser limitations. 7 | In order to solve this problem, Faerun includes a small HTTP server (based on cherrypy) to serve the data to the browser. 8 | 9 | Creating Faerun Data Files 10 | ^^^^^^^^^^^^^^^^^^^^^^^^^^ 11 | As shown in :doc:`tutorial`, Faerun can save data as ``.faerun`` data files using ``pickle``. 12 | 13 | .. code-block:: python 14 | 15 | with open('helix.faerun', 'wb+') as handle: 16 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 17 | 18 | Starting a Faerun Web Server 19 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 20 | .. code-block:: python 21 | 22 | from faerun import host 23 | 24 | host('helix.faerun', label_type='default', 25 | theme='dark') 26 | 27 | Formatting Labels 28 | ^^^^^^^^^^^^^^^^^ 29 | Labels can be formatted by defining a custom ``label_formatter``. If no ``label_formatter`` is provided to the ``host`` function, the default is used: 30 | 31 | .. code-block:: python 32 | 33 | label_formatter = lambda label, index, name: label.split('__')[0] 34 | 35 | This default splits the label value on ``'__'`` to store different labels and enable search on different values the the displayed labels. See "Searching" for details. Defining a custom label formatter is straight forward. As an example, let's prefix each label with a string and add their index and layer name: 36 | 37 | .. code-block:: python 38 | 39 | def custom_label_formatter(label, index, name): 40 | return f'Example: {label} ({index}, {name})' 41 | 42 | host('helix.faerun', label_type='default', 43 | theme='dark', label_formatter=custom_label_formatter) 44 | 45 | This function is then called whenever a label is requested from the server. In addition to the argument ``label``, the arguments ``index`` and ``name`` can be used to further customize the displayed label and represent the integer index of the data point and the data layer they belong to (e.g. the name defined with ``add_scatter``). 46 | 47 | .. image:: _static/tutorial_host_label.png 48 | :alt: Example of a custom label formatter. 49 | 50 | Adding Hyperlinks 51 | ^^^^^^^^^^^^^^^^^ 52 | Faerun allows to link the data to an arbitrary URL which can be visited upon double-clicking a data point. In order to do this, a ``link_formatter`` has to be provided. This works similar to customizing the label. 53 | 54 | .. code-block:: python 55 | 56 | def custom_link_formatter(label, index, name): 57 | return f'https://www.google.com/search?q={label}' 58 | 59 | host('helix.faerun', label_type='default', 60 | theme='dark', link_formatter=custom_link_formatter) 61 | 62 | 63 | Searching 64 | ^^^^^^^^^ 65 | The hosted version of a Faerun visualization also allows for searching. As a default, the search searches for exact matches in labels (substring or regex searches are not possible at this time). 66 | 67 | .. image:: _static/tutorial_host_search.png 68 | :alt: The result of a search. 69 | 70 | However, the search can be customized. As described in "Formatting Labels", additional label values can be added by separating them using ``'__'``. 71 | 72 | .. code-block:: python 73 | 74 | c = np.random.randint(0, 2, len(x)) 75 | labels = [''] * len(c) 76 | 77 | for i, e in enumerate(c): 78 | labels[i] = str(e) + '__' + str(i % 20) 79 | 80 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': labels} 81 | 82 | The above examples adds an additional label value and as default, the second label value is then used by the search. 83 | 84 | .. image:: _static/tutorial_host_search_2.png 85 | :alt: The result of a custom search. 86 | 87 | If there are additional label values, the search index can be set using the ``search_index`` argument. 88 | 89 | Add Info / Documentation 90 | ^^^^^^^^^^^^^^^^^^^^^^^^ 91 | As the visualization is ready to be deployed to a publicly accessible web server, it might be of interest to add a documentation. The ``host`` method supports the argument ``info`` that accepts a (markdown formatted) string. This information is the desplayed on the generated web page. 92 | 93 | .. code-block:: python 94 | 95 | info = ('#Welcome to Fearun', 96 | 'This is a small Faerun example.' 97 | '', 98 | 'Yay markdown! This means that you can easily:', 99 | '- Add lists', 100 | '- Build tables', 101 | '- Insert images and links', 102 | '- Add code examples', 103 | '- ...' 104 | ) 105 | 106 | host('helix.faerun', label_type='default', theme='dark', 107 | label_formatter=custom_label_formatter, link_formatter=custom_link_formatter, 108 | info='\n'.join(info)) 109 | 110 | An info button is then shown next to the screenshot button, which upon click opens a window containing the info. 111 | 112 | Complete Example 113 | ^^^^^^^^^^^^^^^^ 114 | 115 | .. code-block:: python 116 | 117 | import pickle 118 | import numpy as np 119 | from faerun import Faerun, host 120 | 121 | 122 | def main(): 123 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 124 | 125 | x = np.linspace(0, 12.0, 326) 126 | y = np.sin(np.pi * x) 127 | z = np.cos(np.pi * x) 128 | c = np.random.randint(0, 2, len(x)) 129 | 130 | labels = [''] * len(c) 131 | 132 | for i, e in enumerate(c): 133 | labels[i] = str(e) + '__' + str(i % 20) 134 | 135 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': labels} 136 | 137 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 138 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 139 | 140 | f.plot('helix') 141 | 142 | with open('helix.faerun', 'wb+') as handle: 143 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 144 | 145 | def custom_label_formatter(label, index, name): 146 | return f'Example: {label} ({index}, {name})' 147 | 148 | def custom_link_formatter(label, index, name): 149 | return f'https://www.google.com/search?q={label}' 150 | 151 | info = ('#Welcome to Fearun', 152 | 'This is a small Faerun example.' 153 | '', 154 | 'Yay markdown! This means that you can easily:', 155 | '- Add lists', 156 | '- Build tables', 157 | '- Insert images and links', 158 | '- Add code examples', 159 | '- ...' 160 | ) 161 | 162 | host('helix.faerun', label_type='default', theme='dark', 163 | label_formatter=custom_label_formatter, link_formatter=custom_link_formatter, 164 | info='\n'.join(info)) 165 | 166 | 167 | if __name__ == '__main__': 168 | main() 169 | 170 | -------------------------------------------------------------------------------- /doc/_build/html/_sources/index.rst.txt: -------------------------------------------------------------------------------- 1 | Welcome to Faerun's documentation! 2 | ================================== 3 | Here are some teasers. 4 | 5 | .. image:: _static/drugbank_2d_light.png 6 | :alt: Example of Drugbank compounds in 2d with the light theme. 7 | 8 | .. image:: _static/drugbank_2d_dark.png 9 | :alt: Example of Drugbank compounds in 2d with the dark theme. 10 | 11 | Table of Contents 12 | ----------------- 13 | 14 | .. toctree:: 15 | 16 | tutorial 17 | host 18 | documentation 19 | -------------------------------------------------------------------------------- /doc/_build/html/_sources/source/faerun.rst.txt: -------------------------------------------------------------------------------- 1 | faerun package 2 | ============== 3 | 4 | Submodules 5 | ---------- 6 | 7 | faerun.faerun module 8 | -------------------- 9 | 10 | .. automodule:: faerun.faerun 11 | :members: 12 | :undoc-members: 13 | :show-inheritance: 14 | 15 | faerun.web module 16 | ----------------- 17 | 18 | .. automodule:: faerun.web 19 | :members: 20 | :undoc-members: 21 | :show-inheritance: 22 | 23 | 24 | Module contents 25 | --------------- 26 | 27 | .. automodule:: faerun 28 | :members: 29 | :undoc-members: 30 | :show-inheritance: 31 | -------------------------------------------------------------------------------- /doc/_build/html/_sources/source/modules.rst.txt: -------------------------------------------------------------------------------- 1 | faerun 2 | ====== 3 | 4 | .. toctree:: 5 | :maxdepth: 4 6 | 7 | faerun 8 | -------------------------------------------------------------------------------- /doc/_build/html/_sources/tutorial.rst.txt: -------------------------------------------------------------------------------- 1 | Getting Started 2 | --------------- 3 | 4 | Installation 5 | ^^^^^^^^^^^^ 6 | Faerun can be installed using pip. 7 | 8 | .. code-block:: bash 9 | 10 | pip install faerun 11 | 12 | In order to use it in a script, the class ``Faerun`` has to be imported from the package. 13 | 14 | .. code-block:: python 15 | 16 | from faerun import Faerun 17 | 18 | That's it for the installation. 19 | 20 | Create a Plot Document 21 | ^^^^^^^^^^^^^^^^^^^^^^ 22 | In order to plot, a plot document has to be created. To do so, create an instance of the class ``Faerun`` 23 | 24 | .. code-block:: python 25 | 26 | from faerun import Faerun 27 | 28 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 29 | 30 | Here, we set the ``title`` of the plot document. This will be used as the title of the HTML document. The clear color of the canvas, which is the background color of the plot, is set to ``'#222222'`` (which is the hex-code for a dark gray). 31 | The drawing of coordinate axes is disabled by setting ``coords=False`` and since we want to draw 3D data, the argument ``view`` is set to ``'free'`` to enable the user to pan and rotate the plot. 32 | 33 | Preparing Data for Plotting 34 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 35 | The next step is to prepare the data which is to be plotted. In the tutorial, we will just generate some nice looking data using ``numpy``. 36 | 37 | .. code-block:: python 38 | 39 | import numpy as np 40 | 41 | x = np.linspace(0, 12.0, 326) 42 | y = np.sin(np.pi * x) 43 | z = np.cos(np.pi * x) 44 | c = np.random.randint(0, 6, len(x)) 45 | 46 | This data can then be wrapped in a ``dict``. In addition, ``DataFrame`` from the ``pandas`` package are also supported by faerun. 47 | In the example, the same values are used for the colors ``c`` and labels ``labels``. 48 | 49 | .. code-block:: python 50 | 51 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': c} 52 | 53 | Adding a Scatter Layer 54 | ^^^^^^^^^^^^^^^^^^^^^^ 55 | Given the ``Faerun`` instance and the data, a scatter plot can be created using the method ``add_scatter``. 56 | 57 | .. code-block:: python 58 | 59 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 60 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 61 | 62 | The data is added as a scatter layer named helix. The chose shader will render the data points as 63 | spheres (with diffuse and specular lighting) of size 5.0 with colors from the ``matplotlib`` colormap ``'Dark2'``. 64 | As the ``c`` is categorical, the parameter ``categorical`` is set to ``True``, otherwise ``matplotlib`` will mess up the values. 65 | 66 | Finally, ``has_legend=True`` adds the scatter layer to the legend and ``legend_labels`` is a ``list`` of ``tuple``, associating values with a label. 67 | 68 | Saving to HTML 69 | ^^^^^^^^^^^^^^ 70 | The faerun document can the be plotted to an HTML document with an accompanying JavaScript data file. 71 | 72 | .. code-block:: python 73 | 74 | f.plot('helix') 75 | 76 | This saves the plot as ``helix.html` and ``helix.js``. The files can be opened locally or hosted on any web server. 77 | 78 | .. image:: _static/tutorial.png 79 | :alt: A helix drawn using faerun. 80 | 81 | Saving to Faerun Data File 82 | ^^^^^^^^^^^^^^^^^^^^^^^^^^ 83 | The faerun document can also be exported to a faerun data file, which in turn can then be hosted using the ``web`` module. 84 | 85 | .. code-block:: python 86 | 87 | import pickle 88 | 89 | with open('helix.faerun', 'wb+') as handle: 90 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 91 | 92 | Complete Example 93 | ^^^^^^^^^^^^^^^^ 94 | .. code-block:: python 95 | 96 | import pickle 97 | import numpy as np 98 | from faerun import Faerun 99 | 100 | def main(): 101 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 102 | 103 | x = np.linspace(0, 12.0, 326) 104 | y = np.sin(np.pi * x) 105 | z = np.cos(np.pi * x) 106 | c = np.random.randint(0, 2, len(x)) 107 | 108 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': c} 109 | 110 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 111 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 112 | 113 | f.plot('helix') 114 | 115 | with open('helix.faerun', 'wb+') as handle: 116 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 117 | 118 | if __name__ == '__main__': 119 | main() 120 | 121 | -------------------------------------------------------------------------------- /doc/_build/html/_static/ajax-loader.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/html/_static/ajax-loader.gif -------------------------------------------------------------------------------- /doc/_build/html/_static/comment-bright.png: -------------------------------------------------------------------------------- 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translated : translated[0]; 171 | }, 172 | 173 | ngettext : function(singular, plural, n) { 174 | var translated = Documentation.TRANSLATIONS[singular]; 175 | if (typeof translated === 'undefined') 176 | return (n == 1) ? singular : plural; 177 | return translated[Documentation.PLURALEXPR(n)]; 178 | }, 179 | 180 | addTranslations : function(catalog) { 181 | for (var key in catalog.messages) 182 | this.TRANSLATIONS[key] = catalog.messages[key]; 183 | this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')'); 184 | this.LOCALE = catalog.locale; 185 | }, 186 | 187 | /** 188 | * add context elements like header anchor links 189 | */ 190 | addContextElements : function() { 191 | $('div[id] > :header:first').each(function() { 192 | $('\u00B6'). 193 | attr('href', '#' + this.id). 194 | attr('title', _('Permalink to this headline')). 195 | appendTo(this); 196 | }); 197 | $('dt[id]').each(function() { 198 | $('\u00B6'). 199 | attr('href', '#' + this.id). 200 | attr('title', _('Permalink to this definition')). 201 | appendTo(this); 202 | }); 203 | }, 204 | 205 | /** 206 | * workaround a firefox stupidity 207 | * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075 208 | */ 209 | fixFirefoxAnchorBug : function() { 210 | if (document.location.hash && $.browser.mozilla) 211 | window.setTimeout(function() { 212 | document.location.href += ''; 213 | }, 10); 214 | }, 215 | 216 | /** 217 | * highlight the search words provided in the url in the text 218 | */ 219 | highlightSearchWords : function() { 220 | var params = $.getQueryParameters(); 221 | var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : []; 222 | if (terms.length) { 223 | var body = $('div.body'); 224 | if (!body.length) { 225 | body = $('body'); 226 | } 227 | window.setTimeout(function() { 228 | $.each(terms, function() { 229 | body.highlightText(this.toLowerCase(), 'highlighted'); 230 | }); 231 | }, 10); 232 | $('

' + _('Hide Search Matches') + '

') 234 | .appendTo($('#searchbox')); 235 | } 236 | }, 237 | 238 | /** 239 | * init the domain index toggle buttons 240 | */ 241 | initIndexTable : function() { 242 | var togglers = $('img.toggler').click(function() { 243 | var src = $(this).attr('src'); 244 | var idnum = $(this).attr('id').substr(7); 245 | $('tr.cg-' + idnum).toggle(); 246 | if (src.substr(-9) === 'minus.png') 247 | $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); 248 | else 249 | $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); 250 | }).css('display', ''); 251 | if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { 252 | togglers.click(); 253 | } 254 | }, 255 | 256 | /** 257 | * helper function to hide the search marks again 258 | */ 259 | hideSearchWords : function() { 260 | $('#searchbox .highlight-link').fadeOut(300); 261 | $('span.highlighted').removeClass('highlighted'); 262 | }, 263 | 264 | /** 265 | * make the url absolute 266 | */ 267 | makeURL : function(relativeURL) { 268 | return 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Index

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255 | © Copyright 2019, Daniel Probst (Reymond Group, University of Bern) 256 | 257 |

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153 | Example of Drugbank compounds in 2d with the light theme. 154 | Example of Drugbank compounds in 2d with the dark theme. 155 |
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Table of Contents

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208 | © Copyright 2019, Daniel Probst (Reymond Group, University of Bern) 209 | 210 |

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Python Module Index

154 | 155 |
156 | f 157 |
158 | 159 | 160 | 161 | 163 | 164 | 166 | 169 | 170 | 171 | 174 | 175 | 176 | 179 |
 
162 | f
167 | faerun 168 |
    172 | faerun.faerun 173 |
    177 | faerun.web 178 |
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192 | © Copyright 2019, Daniel Probst (Reymond Group, University of Bern) 193 | 194 |

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172 | © Copyright 2019, Daniel Probst (Reymond Group, University of Bern) 173 | 174 |

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199 | 200 | 201 | 202 | 207 | 208 | 209 | 210 | 211 | 212 | 213 | 214 | -------------------------------------------------------------------------------- /doc/_build/latex/Faerun.aux: -------------------------------------------------------------------------------- 1 | \relax 2 | \providecommand\hyper@newdestlabel[2]{} 3 | \providecommand\HyperFirstAtBeginDocument{\AtBeginDocument} 4 | \HyperFirstAtBeginDocument{\ifx\hyper@anchor\@undefined 5 | \global\let\oldcontentsline\contentsline 6 | \gdef\contentsline#1#2#3#4{\oldcontentsline{#1}{#2}{#3}} 7 | \global\let\oldnewlabel\newlabel 8 | \gdef\newlabel#1#2{\newlabelxx{#1}#2} 9 | \gdef\newlabelxx#1#2#3#4#5#6{\oldnewlabel{#1}{{#2}{#3}}} 10 | \AtEndDocument{\ifx\hyper@anchor\@undefined 11 | \let\contentsline\oldcontentsline 12 | \let\newlabel\oldnewlabel 13 | \fi} 14 | \fi} 15 | \global\let\hyper@last\relax 16 | \gdef\HyperFirstAtBeginDocument#1{#1} 17 | \providecommand\HyField@AuxAddToFields[1]{} 18 | 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\newlabel{documentation:web}{{1.3.2}{12}{Web}{subsection.1.3.2}{}} 77 | \newlabel{documentation:faerun.host}{{1.3.2}{12}{Web}{section*.12}{}} 78 | \@writefile{toc}{\contentsline {chapter}{Index}{13}{section*.13}\protected@file@percent } 79 | -------------------------------------------------------------------------------- /doc/_build/latex/Faerun.idx: -------------------------------------------------------------------------------- 1 | \indexentry{Faerun (class in faerun)@\spxentry{Faerun}\spxextra{class in faerun}|hyperpage}{9} 2 | \indexentry{\_\_init\_\_() (faerun.Faerun method)@\spxentry{\_\_init\_\_()}\spxextra{faerun.Faerun method}|hyperpage}{9} 3 | \indexentry{add\_scatter() (faerun.Faerun method)@\spxentry{add\_scatter()}\spxextra{faerun.Faerun method}|hyperpage}{10} 4 | \indexentry{add\_tree() (faerun.Faerun method)@\spxentry{add\_tree()}\spxextra{faerun.Faerun method}|hyperpage}{10} 5 | \indexentry{create\_data() (faerun.Faerun method)@\spxentry{create\_data()}\spxextra{faerun.Faerun method}|hyperpage}{11} 6 | \indexentry{create\_python\_data() (faerun.Faerun method)@\spxentry{create\_python\_data()}\spxextra{faerun.Faerun method}|hyperpage}{11} 7 | \indexentry{discrete\_cmap() (faerun.Faerun static method)@\spxentry{discrete\_cmap()}\spxextra{faerun.Faerun static method}|hyperpage}{11} 8 | \indexentry{get\_min\_max() (faerun.Faerun method)@\spxentry{get\_min\_max()}\spxextra{faerun.Faerun method}|hyperpage}{11} 9 | \indexentry{plot() (faerun.Faerun method)@\spxentry{plot()}\spxextra{faerun.Faerun method}|hyperpage}{11} 10 | \indexentry{host() (in module faerun)@\spxentry{host()}\spxextra{in module faerun}|hyperpage}{12} 11 | -------------------------------------------------------------------------------- /doc/_build/latex/Faerun.ilg: -------------------------------------------------------------------------------- 1 | This is makeindex, version 2.15 [TeX Live 2019/dev] (kpathsea + Thai support). 2 | Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). 3 | Scanning input file Faerun.idx....done (10 entries accepted, 0 rejected). 4 | Sorting entries....done (34 comparisons). 5 | Generating output file Faerun.ind....done (40 lines written, 0 warnings). 6 | Output written in Faerun.ind. 7 | Transcript written in Faerun.ilg. 8 | -------------------------------------------------------------------------------- /doc/_build/latex/Faerun.ind: -------------------------------------------------------------------------------- 1 | \begin{sphinxtheindex} 2 | \let\bigletter\sphinxstyleindexlettergroup 3 | \let\spxpagem \sphinxstyleindexpagemain 4 | \let\spxentry \sphinxstyleindexentry 5 | \let\spxextra \sphinxstyleindexextra 6 | 7 | \bigletter {\sphinxsymbolsname} 8 | \item \spxentry{\_\_init\_\_()}\spxextra{faerun.Faerun method}, \hyperpage{9} 9 | 10 | \indexspace 11 | \bigletter A 12 | \item \spxentry{add\_scatter()}\spxextra{faerun.Faerun method}, \hyperpage{10} 13 | \item \spxentry{add\_tree()}\spxextra{faerun.Faerun method}, \hyperpage{10} 14 | 15 | \indexspace 16 | \bigletter C 17 | \item \spxentry{create\_data()}\spxextra{faerun.Faerun method}, \hyperpage{11} 18 | \item \spxentry{create\_python\_data()}\spxextra{faerun.Faerun method}, \hyperpage{11} 19 | 20 | \indexspace 21 | \bigletter D 22 | \item \spxentry{discrete\_cmap()}\spxextra{faerun.Faerun static method}, \hyperpage{11} 23 | 24 | \indexspace 25 | \bigletter F 26 | \item \spxentry{Faerun}\spxextra{class in faerun}, \hyperpage{9} 27 | 28 | \indexspace 29 | \bigletter G 30 | \item \spxentry{get\_min\_max()}\spxextra{faerun.Faerun method}, \hyperpage{11} 31 | 32 | \indexspace 33 | \bigletter H 34 | \item \spxentry{host()}\spxextra{in module faerun}, \hyperpage{12} 35 | 36 | \indexspace 37 | \bigletter P 38 | \item \spxentry{plot()}\spxextra{faerun.Faerun method}, \hyperpage{11} 39 | 40 | \end{sphinxtheindex} 41 | -------------------------------------------------------------------------------- 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"ё" :string) 99 | (merge-rule "\IeC {\cyryu }" "ю" :string) 100 | (merge-rule "\IeC {\cyrz }" "з" :string) 101 | (merge-rule "\IeC {\cyrzh }" "ж" :string) 102 | -------------------------------------------------------------------------------- /doc/_build/latex/LatinRules.xdy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/latex/LatinRules.xdy -------------------------------------------------------------------------------- /doc/_build/latex/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for Sphinx LaTeX output 2 | 3 | ALLDOCS = $(basename $(wildcard *.tex)) 4 | ALLPDF = $(addsuffix .pdf,$(ALLDOCS)) 5 | ALLDVI = $(addsuffix .dvi,$(ALLDOCS)) 6 | ALLXDV = 7 | ALLPS = $(addsuffix .ps,$(ALLDOCS)) 8 | ALLIMGS = $(wildcard *.png *.gif *.jpg *.jpeg) 9 | 10 | # Prefix for archive names 11 | ARCHIVEPREFIX = 12 | # Additional LaTeX options (passed via variables in latexmkrc/latexmkjarc file) 13 | export LATEXOPTS = 14 | # Additional latexmk options 15 | LATEXMKOPTS = 16 | # format: pdf or dvi (used only by archive targets) 17 | FMT = pdf 18 | 19 | LATEX = latexmk -dvi 20 | PDFLATEX = latexmk -pdf -dvi- -ps- 21 | 22 | 23 | %.png %.gif %.jpg %.jpeg: FORCE_MAKE 24 | extractbb '$@' 25 | 26 | %.dvi: %.tex FORCE_MAKE 27 | $(LATEX) $(LATEXMKOPTS) '$<' 28 | 29 | %.ps: %.dvi 30 | dvips '$<' 31 | 32 | %.pdf: %.tex FORCE_MAKE 33 | $(PDFLATEX) $(LATEXMKOPTS) '$<' 34 | 35 | all: $(ALLPDF) 36 | 37 | all-dvi: $(ALLDVI) 38 | 39 | all-ps: $(ALLPS) 40 | 41 | all-pdf: $(ALLPDF) 42 | 43 | zip: all-$(FMT) 44 | mkdir $(ARCHIVEPREFIX)docs-$(FMT) 45 | cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT) 46 | zip -q -r -9 $(ARCHIVEPREFIX)docs-$(FMT).zip $(ARCHIVEPREFIX)docs-$(FMT) 47 | rm -r $(ARCHIVEPREFIX)docs-$(FMT) 48 | 49 | tar: all-$(FMT) 50 | mkdir $(ARCHIVEPREFIX)docs-$(FMT) 51 | cp $(ALLPDF) $(ARCHIVEPREFIX)docs-$(FMT) 52 | tar cf $(ARCHIVEPREFIX)docs-$(FMT).tar $(ARCHIVEPREFIX)docs-$(FMT) 53 | rm -r $(ARCHIVEPREFIX)docs-$(FMT) 54 | 55 | gz: tar 56 | gzip -9 < $(ARCHIVEPREFIX)docs-$(FMT).tar > $(ARCHIVEPREFIX)docs-$(FMT).tar.gz 57 | 58 | bz2: tar 59 | bzip2 -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar 60 | 61 | xz: tar 62 | xz -9 -k $(ARCHIVEPREFIX)docs-$(FMT).tar 63 | 64 | clean: 65 | rm -f *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz $(ALLPDF) $(ALLDVI) $(ALLXDV) *.fls *.fdb_latexmk 66 | 67 | .PHONY: all all-pdf all-dvi all-ps clean zip tar gz bz2 xz 68 | .PHONY: FORCE_MAKE -------------------------------------------------------------------------------- /doc/_build/latex/drugbank_2d_dark.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/latex/drugbank_2d_dark.png -------------------------------------------------------------------------------- /doc/_build/latex/drugbank_2d_light.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/latex/drugbank_2d_light.png -------------------------------------------------------------------------------- /doc/_build/latex/footnotehyper-sphinx.sty: -------------------------------------------------------------------------------- 1 | \NeedsTeXFormat{LaTeX2e} 2 | \ProvidesPackage{footnotehyper-sphinx}% 3 | [2017/10/27 v1.7 hyperref aware footnote.sty for sphinx (JFB)] 4 | %% 5 | %% Package: footnotehyper-sphinx 6 | %% Version: based on footnotehyper.sty 2017/03/07 v1.0 7 | %% as available at https://www.ctan.org/pkg/footnotehyper 8 | %% License: the one applying to Sphinx 9 | %% 10 | %% Refer to the PDF documentation at https://www.ctan.org/pkg/footnotehyper for 11 | %% the code comments. 12 | %% 13 | %% Differences: 14 | %% 1. a partial tabulary compatibility layer added (enough for Sphinx mark-up), 15 | %% 2. use of \spx@opt@BeforeFootnote from sphinx.sty, 16 | %% 3. use of \sphinxunactivateextrasandspace from sphinx.sty, 17 | %% 4. macro definition \sphinxfootnotemark, 18 | %% 5. macro definition \sphinxlongtablepatch 19 | %% 6. replaced an \undefined by \@undefined 20 | \DeclareOption*{\PackageWarning{footnotehyper-sphinx}{Option `\CurrentOption' is unknown}}% 21 | \ProcessOptions\relax 22 | \newbox\FNH@notes 23 | \newdimen\FNH@width 24 | \let\FNH@colwidth\columnwidth 25 | \newif\ifFNH@savingnotes 26 | \AtBeginDocument {% 27 | \let\FNH@latex@footnote \footnote 28 | \let\FNH@latex@footnotetext\footnotetext 29 | \let\FNH@H@@footnotetext \@footnotetext 30 | \newenvironment{savenotes} 31 | {\FNH@savenotes\ignorespaces}{\FNH@spewnotes\ignorespacesafterend}% 32 | \let\spewnotes \FNH@spewnotes 33 | \let\footnote \FNH@footnote 34 | \let\footnotetext \FNH@footnotetext 35 | \let\endfootnote \FNH@endfntext 36 | \let\endfootnotetext\FNH@endfntext 37 | \@ifpackageloaded{hyperref} 38 | {\ifHy@hyperfootnotes 39 | \let\FNH@H@@footnotetext\H@@footnotetext 40 | \else 41 | \let\FNH@hyper@fntext\FNH@nohyp@fntext 42 | \fi}% 43 | {\let\FNH@hyper@fntext\FNH@nohyp@fntext}% 44 | }% 45 | \def\FNH@hyper@fntext{\FNH@fntext\FNH@hyper@fntext@i}% 46 | \def\FNH@nohyp@fntext{\FNH@fntext\FNH@nohyp@fntext@i}% 47 | \def\FNH@fntext #1{% 48 | \ifx\ifmeasuring@\@undefined 49 | \expandafter\@secondoftwo\else\expandafter\@firstofone\fi 50 | % these two lines modified for Sphinx (tabulary compatibility): 51 | {\ifmeasuring@\expandafter\@gobbletwo\else\expandafter\@firstofone\fi}% 52 | {\ifx\equation$\expandafter\@gobbletwo\fi #1}%$ 53 | }% 54 | \long\def\FNH@hyper@fntext@i#1{% 55 | \global\setbox\FNH@notes\vbox 56 | {\unvbox\FNH@notes 57 | \FNH@startnote 58 | \@makefntext 59 | {\rule\z@\footnotesep\ignorespaces 60 | \ifHy@nesting\expandafter\ltx@firstoftwo 61 | \else\expandafter\ltx@secondoftwo 62 | \fi 63 | {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}{#1}}% 64 | {\Hy@raisedlink 65 | {\expandafter\hyper@@anchor\expandafter{\Hy@footnote@currentHref}% 66 | {\relax}}% 67 | \let\@currentHref\Hy@footnote@currentHref 68 | \let\@currentlabelname\@empty 69 | #1}% 70 | \@finalstrut\strutbox 71 | }% 72 | \FNH@endnote 73 | }% 74 | }% 75 | \long\def\FNH@nohyp@fntext@i#1{% 76 | \global\setbox\FNH@notes\vbox 77 | {\unvbox\FNH@notes 78 | \FNH@startnote 79 | \@makefntext{\rule\z@\footnotesep\ignorespaces#1\@finalstrut\strutbox}% 80 | \FNH@endnote 81 | }% 82 | }% 83 | \def\FNH@startnote{% 84 | \hsize\FNH@colwidth 85 | \interlinepenalty\interfootnotelinepenalty 86 | \reset@font\footnotesize 87 | \floatingpenalty\@MM 88 | \@parboxrestore 89 | \protected@edef\@currentlabel{\csname p@\@mpfn\endcsname\@thefnmark}% 90 | \color@begingroup 91 | }% 92 | \def\FNH@endnote{\color@endgroup}% 93 | \def\FNH@savenotes{% 94 | \begingroup 95 | \ifFNH@savingnotes\else 96 | \FNH@savingnotestrue 97 | \let\@footnotetext \FNH@hyper@fntext 98 | \let\@mpfootnotetext \FNH@hyper@fntext 99 | \let\H@@mpfootnotetext\FNH@nohyp@fntext 100 | \FNH@width\columnwidth 101 | \let\FNH@colwidth\FNH@width 102 | \global\setbox\FNH@notes\box\voidb@x 103 | \let\FNH@thempfn\thempfn 104 | \let\FNH@mpfn\@mpfn 105 | \ifx\@minipagerestore\relax\let\@minipagerestore\@empty\fi 106 | \expandafter\def\expandafter\@minipagerestore\expandafter{% 107 | \@minipagerestore 108 | \let\thempfn\FNH@thempfn 109 | \let\@mpfn\FNH@mpfn 110 | }% 111 | \fi 112 | }% 113 | \def\FNH@spewnotes {% 114 | \endgroup 115 | \ifFNH@savingnotes\else 116 | \ifvoid\FNH@notes\else 117 | \begingroup 118 | \let\@makefntext\@empty 119 | \let\@finalstrut\@gobble 120 | \let\rule\@gobbletwo 121 | \FNH@H@@footnotetext{\unvbox\FNH@notes}% 122 | \endgroup 123 | \fi 124 | \fi 125 | }% 126 | \def\FNH@footnote@envname {footnote}% 127 | \def\FNH@footnotetext@envname{footnotetext}% 128 | \def\FNH@footnote{% 129 | % this line added for Sphinx: 130 | \spx@opt@BeforeFootnote 131 | \ifx\@currenvir\FNH@footnote@envname 132 | \expandafter\FNH@footnoteenv 133 | \else 134 | \expandafter\FNH@latex@footnote 135 | \fi 136 | }% 137 | \def\FNH@footnoteenv{% 138 | % this line added for Sphinx (footnotes in parsed literal blocks): 139 | \catcode13=5 \sphinxunactivateextrasandspace 140 | \@ifnextchar[% 141 | \FNH@footnoteenv@i %] 142 | {\stepcounter\@mpfn 143 | \protected@xdef\@thefnmark{\thempfn}% 144 | \@footnotemark 145 | \def\FNH@endfntext@fntext{\@footnotetext}% 146 | \FNH@startfntext}% 147 | }% 148 | \def\FNH@footnoteenv@i[#1]{% 149 | \begingroup 150 | \csname c@\@mpfn\endcsname #1\relax 151 | \unrestored@protected@xdef\@thefnmark{\thempfn}% 152 | \endgroup 153 | \@footnotemark 154 | \def\FNH@endfntext@fntext{\@footnotetext}% 155 | \FNH@startfntext 156 | }% 157 | \def\FNH@footnotetext{% 158 | \ifx\@currenvir\FNH@footnotetext@envname 159 | \expandafter\FNH@footnotetextenv 160 | \else 161 | \expandafter\FNH@latex@footnotetext 162 | \fi 163 | }% 164 | \def\FNH@footnotetextenv{% 165 | \@ifnextchar[% 166 | \FNH@footnotetextenv@i %] 167 | {\protected@xdef\@thefnmark{\thempfn}% 168 | \def\FNH@endfntext@fntext{\@footnotetext}% 169 | \FNH@startfntext}% 170 | }% 171 | \def\FNH@footnotetextenv@i[#1]{% 172 | \begingroup 173 | \csname c@\@mpfn\endcsname #1\relax 174 | \unrestored@protected@xdef\@thefnmark{\thempfn}% 175 | \endgroup 176 | \ifFNH@savingnotes 177 | \def\FNH@endfntext@fntext{\FNH@nohyp@fntext}% 178 | \else 179 | \def\FNH@endfntext@fntext{\FNH@H@@footnotetext}% 180 | \fi 181 | \FNH@startfntext 182 | }% 183 | \def\FNH@startfntext{% 184 | \setbox\z@\vbox\bgroup 185 | \FNH@startnote 186 | \FNH@prefntext 187 | \rule\z@\footnotesep\ignorespaces 188 | }% 189 | \def\FNH@endfntext {% 190 | \@finalstrut\strutbox 191 | \FNH@postfntext 192 | \FNH@endnote 193 | \egroup 194 | \begingroup 195 | \let\@makefntext\@empty\let\@finalstrut\@gobble\let\rule\@gobbletwo 196 | \FNH@endfntext@fntext {\unvbox\z@}% 197 | \endgroup 198 | }% 199 | \AtBeginDocument{% 200 | \let\FNH@@makefntext\@makefntext 201 | \ifx\@makefntextFB\@undefined 202 | \expandafter\@gobble\else\expandafter\@firstofone\fi 203 | {\ifFBFrenchFootnotes \let\FNH@@makefntext\@makefntextFB \else 204 | \let\FNH@@makefntext\@makefntextORI\fi}% 205 | \expandafter\FNH@check@a\FNH@@makefntext{1.2!3?4,}% 206 | \FNH@@@1.2!3?4,\FNH@@@\relax 207 | }% 208 | \long\def\FNH@check@a #11.2!3?4,#2\FNH@@@#3{% 209 | \ifx\relax#3\expandafter\@firstoftwo\else\expandafter\@secondoftwo\fi 210 | \FNH@bad@makefntext@alert 211 | {\def\FNH@prefntext{#1}\def\FNH@postfntext{#2}\FNH@check@b}% 212 | }% 213 | \def\FNH@check@b #1\relax{% 214 | \expandafter\expandafter\expandafter\FNH@check@c 215 | \expandafter\meaning\expandafter\FNH@prefntext 216 | \meaning\FNH@postfntext1.2!3?4,\FNH@check@c\relax 217 | }% 218 | \def\FNH@check@c #11.2!3?4,#2#3\relax{% 219 | \ifx\FNH@check@c#2\expandafter\@gobble\fi\FNH@bad@makefntext@alert 220 | }% 221 | % slight reformulation for Sphinx 222 | \def\FNH@bad@makefntext@alert{% 223 | \PackageWarningNoLine{footnotehyper-sphinx}% 224 | {Footnotes will be sub-optimal, sorry. This is due to the document class or^^J 225 | some package modifying macro \string\@makefntext.^^J 226 | You can try to report this incompatibility at^^J 227 | https://github.com/sphinx-doc/sphinx with this info:}% 228 | \typeout{\meaning\@makefntext}% 229 | \let\FNH@prefntext\@empty\let\FNH@postfntext\@empty 230 | }% 231 | % this macro from original footnote.sty is not used anymore by Sphinx 232 | % but for simplicity sake let's just keep it as is 233 | \def\makesavenoteenv{\@ifnextchar[\FNH@msne@ii\FNH@msne@i}%] 234 | \def\FNH@msne@i #1{% 235 | \expandafter\let\csname FNH$#1\expandafter\endcsname %$ 236 | \csname #1\endcsname 237 | \expandafter\let\csname endFNH$#1\expandafter\endcsname %$ 238 | \csname end#1\endcsname 239 | \FNH@msne@ii[#1]{FNH$#1}%$ 240 | }% 241 | \def\FNH@msne@ii[#1]#2{% 242 | \expandafter\edef\csname#1\endcsname{% 243 | \noexpand\savenotes 244 | \expandafter\noexpand\csname#2\endcsname 245 | }% 246 | \expandafter\edef\csname end#1\endcsname{% 247 | \expandafter\noexpand\csname end#2\endcsname 248 | \noexpand\expandafter 249 | \noexpand\spewnotes 250 | \noexpand\if@endpe\noexpand\@endpetrue\noexpand\fi 251 | }% 252 | }% 253 | % end of footnotehyper 2017/02/16 v0.99 254 | % some extras for Sphinx : 255 | % \sphinxfootnotemark: usable in section titles and silently removed from TOCs. 256 | \def\sphinxfootnotemark [#1]% 257 | {\ifx\thepage\relax\else\protect\spx@opt@BeforeFootnote 258 | \protect\footnotemark[#1]\fi}% 259 | \AtBeginDocument{% 260 | % let hyperref less complain 261 | \pdfstringdefDisableCommands{\def\sphinxfootnotemark [#1]{}}% 262 | % to obtain hyperlinked footnotes in longtable environment we must replace 263 | % hyperref's patch of longtable's patch of \@footnotetext by our own 264 | \let\LT@p@ftntext\FNH@hyper@fntext 265 | % this *requires* longtable to be used always wrapped in savenotes environment 266 | }% 267 | \endinput 268 | %% 269 | %% End of file `footnotehyper-sphinx.sty'. 270 | -------------------------------------------------------------------------------- /doc/_build/latex/latexmkjarc: -------------------------------------------------------------------------------- 1 | $latex = 'platex ' . $ENV{'LATEXOPTS'} . ' -kanji=utf8 %O %S'; 2 | $dvipdf = 'dvipdfmx %O -o %D %S'; 3 | $makeindex = 'internal mendex %S %B %D'; 4 | sub mendex { 5 | my ($source, $basename, $destination) = @_; 6 | my $dictfile = $basename . ".dic"; 7 | unlink($destination); 8 | system("mendex", "-U", "-f", "-d", $dictfile, "-s", "python.ist", $source); 9 | if ($? > 0) { 10 | print("mendex exited with error code $? (ignored)\n"); 11 | } 12 | if (!-e $destination) { 13 | # create an empty .ind file if nothing 14 | open(FH, ">" . $destination); 15 | close(FH); 16 | } 17 | return 0; 18 | } 19 | add_cus_dep( "glo", "gls", 0, "makeglo" ); 20 | sub makeglo { 21 | return system( "mendex -J -f -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); 22 | } 23 | -------------------------------------------------------------------------------- /doc/_build/latex/latexmkrc: -------------------------------------------------------------------------------- 1 | $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; 2 | $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; 3 | $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; 4 | $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; 5 | $makeindex = 'makeindex -s python.ist %O -o %D %S'; 6 | add_cus_dep( "glo", "gls", 0, "makeglo" ); 7 | sub makeglo { 8 | return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); 9 | } -------------------------------------------------------------------------------- /doc/_build/latex/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | REM Command file for Sphinx documentation 4 | 5 | pushd %~dp0 6 | 7 | set PDFLATEX=latexmk -pdf -dvi- -ps- 8 | 9 | set "LATEXOPTS= " 10 | 11 | if "%1" == "" goto all-pdf 12 | 13 | if "%1" == "all-pdf" ( 14 | :all-pdf 15 | for %%i in (*.tex) do ( 16 | %PDFLATEX% %LATEXMKOPTS% %%i 17 | ) 18 | goto end 19 | ) 20 | 21 | if "%1" == "all-pdf-ja" ( 22 | goto all-pdf 23 | ) 24 | 25 | if "%1" == "clean" ( 26 | del /q /s *.dvi *.log *.ind *.aux *.toc *.syn *.idx *.out *.ilg *.pla *.ps *.tar *.tar.gz *.tar.bz2 *.tar.xz *.fls *.fdb_latexmk 27 | goto end 28 | ) 29 | 30 | :end 31 | popd -------------------------------------------------------------------------------- /doc/_build/latex/python.ist: -------------------------------------------------------------------------------- 1 | line_max 100 2 | headings_flag 1 3 | heading_prefix " \\bigletter " 4 | 5 | preamble "\\begin{sphinxtheindex} 6 | \\let\\bigletter\\sphinxstyleindexlettergroup 7 | \\let\\spxpagem \\sphinxstyleindexpagemain 8 | \\let\\spxentry \\sphinxstyleindexentry 9 | \\let\\spxextra \\sphinxstyleindexextra 10 | 11 | " 12 | 13 | postamble "\n\n\\end{sphinxtheindex}\n" 14 | 15 | symhead_positive "{\\sphinxsymbolsname}" 16 | numhead_positive "{\\sphinxnumbersname}" 17 | -------------------------------------------------------------------------------- /doc/_build/latex/sphinx.xdy: -------------------------------------------------------------------------------- 1 | ;;; -*- mode: lisp; coding: utf-8; -*- 2 | 3 | ;; Unfortunately xindy is out-of-the-box hyperref-incompatible. This 4 | ;; configuration is a workaround, which requires to pass option 5 | ;; hyperindex=false to hyperref. 6 | ;; textit and emph not currently used, spxpagem replaces former textbf 7 | (define-attributes (("textbf" "textit" "emph" "spxpagem" "default"))) 8 | (markup-locref :open "\textbf{\hyperpage{" :close "}}" :attr "textbf") 9 | (markup-locref :open "\textit{\hyperpage{" :close "}}" :attr "textit") 10 | (markup-locref :open "\emph{\hyperpage{" :close "}}" :attr "emph") 11 | (markup-locref :open "\spxpagem{\hyperpage{" :close "}}" :attr "spxpagem") 12 | (markup-locref :open "\hyperpage{" :close "}" :attr "default") 13 | 14 | (require "numeric-sort.xdy") 15 | 16 | ;; xindy base module latex.xdy loads tex.xdy and the latter instructs 17 | ;; xindy to ignore **all** TeX macros in .idx entries, except those 18 | ;; explicitely described in merge rule. But when after applying all 19 | ;; merge rules an empty string results, xindy raises an error: 20 | 21 | ;; ERROR: CHAR: index 0 should be less than the length of the string 22 | 23 | ;; For example when using pdflatex with utf-8 characters the index 24 | ;; file will contain \IeC macros and they will get ignored except if 25 | ;; suitable merge rules are loaded early. The texindy script coming 26 | ;; with xindy provides this, but only for Latin scripts. The texindy 27 | ;; man page says to use rather xelatex or lualatex in case of Cyrillic 28 | ;; scripts. 29 | 30 | ;; Sphinx contributes LICRcyr2utf8.xdy to provide support for Cyrillic 31 | ;; scripts for the pdflatex engine. 32 | 33 | ;; Another issue caused by xindy ignoring all TeX macros except those 34 | ;; explicitely declared reveals itself when attempting to index ">>>", 35 | ;; as the ">" is converted to "\textgreater{}" by Sphinx's LaTeX 36 | ;; escaping. 37 | 38 | ;; To fix this, Sphinx does **not** use texindy, and does not even 39 | ;; load the xindy latex.xdy base module. 40 | 41 | ;(require "latex.xdy") 42 | 43 | ;; Rather it incorporates some suitable extracts from latex.xdy and 44 | ;; tex.xdy with additional Sphinx contributed rules. 45 | 46 | ;; But, this means for pdflatex and Latin scripts that the xindy file 47 | ;; tex/inputenc/uf8.xdy is not usable because it refers to the macro 48 | ;; \IeC only sporadically, and as tex.xdy is not loaded, a rule such as 49 | ;; (merge-rule "\'e" "é" :string) 50 | ;; does not work, it must be 51 | ;; (merge-rule "\IeC {\'e}" "é" :string) 52 | ;; So Sphinx contributes LICRlatin2utf8.xdy to mitigate that problem. 53 | 54 | ;;;;;;;; extracts from tex.xdy (discarding most original comments): 55 | 56 | ;;; 57 | ;;; TeX conventions 58 | ;;; 59 | 60 | ;; Discard leading and trailing white space. Collapse multiple white 61 | ;; space characters to blank. 62 | 63 | (merge-rule "^ +" "" :eregexp) 64 | (merge-rule " +$" "" :eregexp) 65 | (merge-rule " +" " " :eregexp) 66 | 67 | ;; Handle TeX markup 68 | 69 | (merge-rule "\\([{}$%&#])" "\1" :eregexp) 70 | 71 | ;;;;;;;; end of extracts from xindy's tex.xdy 72 | 73 | ;;;;;;;; extracts from latex.xdy: 74 | 75 | ;; Standard location classes: arabic and roman numbers, and alphabets. 76 | 77 | (define-location-class "arabic-page-numbers" ("arabic-numbers")) 78 | (define-location-class "roman-page-numbers" ("roman-numbers-lowercase")) 79 | (define-location-class "Roman-page-numbers" ("roman-numbers-uppercase")) 80 | (define-location-class "alpha-page-numbers" ("alpha")) 81 | (define-location-class "Alpha-page-numbers" ("ALPHA")) 82 | 83 | ;; Output Markup 84 | 85 | (markup-letter-group-list :sep "~n~n \indexspace~n") 86 | 87 | (markup-indexentry :open "~n \item " :depth 0) 88 | (markup-indexentry :open "~n \subitem " :depth 1) 89 | (markup-indexentry :open "~n \subsubitem " :depth 2) 90 | 91 | (markup-locclass-list :open ", " :sep ", ") 92 | (markup-locref-list :sep ", ") 93 | 94 | ;;;;;;;; end of extracts from latex.xdy 95 | 96 | ;; The LaTeX \index command turns \ into normal character so the TeX macros 97 | ;; written to .idx files are not followed by a blank. This is different 98 | ;; from non-ascii letters which end up (with pdflatex) as \IeC macros in .idx 99 | ;; file, with a blank space after \IeC 100 | 101 | ;; Details of the syntax are explained at 102 | ;; http://xindy.sourceforge.net/doc/manual-3.html 103 | ;; In absence of :string, "xindy uses an auto-detection mechanism to decide, 104 | ;; if the pattern is a regular expression or not". But it is not obvious to 105 | ;; guess, for example "\\_" is not detected as RE but "\\P\{\}" is, so for 106 | ;; being sure we apply the :string switch everywhere and do not use \\ etc... 107 | 108 | ;; Go back from sphinx.util.texescape TeX macros to UTF-8 109 | 110 | (merge-rule "\sphinxleftcurlybrace{}" "{" :string) 111 | (merge-rule "\sphinxrightcurlybrace{}" "}" :string) 112 | (merge-rule "\_" "_" :string) 113 | (merge-rule "{[}" "[" :string) 114 | (merge-rule "{]}" "]" :string) 115 | (merge-rule "{}`" "`" :string) 116 | (merge-rule "\textbackslash{}" "\" :string) ; " for Emacs syntax highlighting 117 | (merge-rule "\textasciitilde{}" "~~" :string); the ~~ escape is needed here 118 | (merge-rule "\textless{}" "<" :string) 119 | (merge-rule "\textgreater{}" ">" :string) 120 | (merge-rule "\textasciicircum{}" "^" :string) 121 | (merge-rule "\P{}" "¶" :string) 122 | (merge-rule "\S{}" "§" :string) 123 | (merge-rule "\texteuro{}" "€" :string) 124 | (merge-rule "\(\infty\)" "∞" :string) 125 | (merge-rule "\(\pm\)" "±" :string) 126 | (merge-rule "\(\rightarrow\)" "→" :string) 127 | (merge-rule "\(\checkmark\)" "✓" :string) 128 | (merge-rule "\textendash{}" "–" :string) 129 | (merge-rule "\textbar{}" "|" :string) 130 | (merge-rule "\(\sp{\text{0}}\)" "⁰" :string) 131 | (merge-rule "\(\sp{\text{1}}\)" "¹" :string) 132 | (merge-rule "\(\sp{\text{2}}\)" "²" :string) 133 | (merge-rule "\(\sp{\text{3}}\)" "³" :string) 134 | (merge-rule "\(\sp{\text{4}}\)" "⁴" :string) 135 | (merge-rule "\(\sp{\text{5}}\)" "⁵" :string) 136 | (merge-rule "\(\sp{\text{6}}\)" "⁶" :string) 137 | (merge-rule "\(\sp{\text{7}}\)" "⁷" :string) 138 | (merge-rule "\(\sp{\text{8}}\)" "⁸" :string) 139 | (merge-rule "\(\sp{\text{9}}\)" "⁹" :string) 140 | (merge-rule "\(\sb{\text{0}}\)" "₀" :string) 141 | (merge-rule "\(\sb{\text{1}}\)" "₁" :string) 142 | (merge-rule "\(\sb{\text{2}}\)" "₂" :string) 143 | (merge-rule "\(\sb{\text{3}}\)" "₃" :string) 144 | (merge-rule "\(\sb{\text{4}}\)" "₄" :string) 145 | (merge-rule "\(\sb{\text{5}}\)" "₅" :string) 146 | (merge-rule "\(\sb{\text{6}}\)" "₆" :string) 147 | (merge-rule "\(\sb{\text{7}}\)" "₇" :string) 148 | (merge-rule "\(\sb{\text{8}}\)" "₈" :string) 149 | (merge-rule "\(\sb{\text{9}}\)" "₉" :string) 150 | (merge-rule "\(\alpha\)" "α" :string) 151 | (merge-rule "\(\beta\)" "β" :string) 152 | (merge-rule "\(\gamma\)" "γ" :string) 153 | (merge-rule "\(\delta\)" "δ" :string) 154 | (merge-rule "\(\epsilon\)" "ε" :string) 155 | (merge-rule "\(\zeta\)" "ζ" :string) 156 | (merge-rule "\(\eta\)" "η" :string) 157 | (merge-rule "\(\theta\)" "θ" :string) 158 | (merge-rule "\(\iota\)" "ι" :string) 159 | (merge-rule "\(\kappa\)" "κ" :string) 160 | (merge-rule "\(\lambda\)" "λ" :string) 161 | (merge-rule "\(\mu\)" "μ" :string) 162 | (merge-rule "\(\nu\)" "ν" :string) 163 | (merge-rule "\(\xi\)" "ξ" :string) 164 | (merge-rule "\(\pi\)" "π" :string) 165 | (merge-rule "\(\rho\)" "ρ" :string) 166 | (merge-rule "\(\sigma\)" "σ" :string) 167 | (merge-rule "\(\tau\)" "τ" :string) 168 | (merge-rule "\(\upsilon\)" "υ" :string) 169 | (merge-rule "\(\phi\)" "φ" :string) 170 | (merge-rule "\(\chi\)" "χ" :string) 171 | (merge-rule "\(\psi\)" "ψ" :string) 172 | (merge-rule "\(\omega\)" "ω" :string) 173 | (merge-rule "\(\Gamma\)" "Γ" :string) 174 | (merge-rule "\(\Delta\)" "Δ" :string) 175 | (merge-rule "\(\Theta\)" "Θ" :string) 176 | (merge-rule "\(\Lambda\)" "Λ" :string) 177 | (merge-rule "\(\Xi\)" "Ξ" :string) 178 | (merge-rule "\(\Pi\)" "Π" :string) 179 | (merge-rule "\(\Sigma\)" "Σ" :string) 180 | (merge-rule "\(\Upsilon\)" "Υ" :string) 181 | (merge-rule "\(\Phi\)" "Φ" :string) 182 | (merge-rule "\(\Psi\)" "Ψ" :string) 183 | (merge-rule "\(\Omega\)" "Ω" :string) 184 | 185 | ;; This xindy module provides some basic support for "see" 186 | (require "makeindex.xdy") 187 | 188 | ;; This creates one-letter headings and works fine with utf-8 letters. 189 | ;; For Cyrillic with pdflatex works thanks to LICRcyr2utf8.xdy 190 | (require "latin-lettergroups.xdy") 191 | 192 | ;; currently we don't (know how to easily) separate "Numbers" from 193 | ;; "Symbols" with xindy as is the case with makeindex. 194 | (markup-index :open "\begin{sphinxtheindex} 195 | \let\lettergroup\sphinxstyleindexlettergroup 196 | \let\lettergroupDefault\sphinxstyleindexlettergroupDefault 197 | \let\spxpagem\sphinxstyleindexpagemain 198 | \let\spxentry\sphinxstyleindexentry 199 | \let\spxextra\sphinxstyleindexextra 200 | 201 | " 202 | :close " 203 | 204 | \end{sphinxtheindex} 205 | " 206 | :tree) 207 | 208 | -------------------------------------------------------------------------------- /doc/_build/latex/sphinxhighlight.sty: -------------------------------------------------------------------------------- 1 | \NeedsTeXFormat{LaTeX2e}[1995/12/01] 2 | \ProvidesPackage{sphinxhighlight}[2016/05/29 stylesheet for highlighting with pygments] 3 | 4 | 5 | \makeatletter 6 | \def\PYG@reset{\let\PYG@it=\relax \let\PYG@bf=\relax% 7 | \let\PYG@ul=\relax \let\PYG@tc=\relax% 8 | \let\PYG@bc=\relax \let\PYG@ff=\relax} 9 | \def\PYG@tok#1{\csname PYG@tok@#1\endcsname} 10 | \def\PYG@toks#1+{\ifx\relax#1\empty\else% 11 | \PYG@tok{#1}\expandafter\PYG@toks\fi} 12 | \def\PYG@do#1{\PYG@bc{\PYG@tc{\PYG@ul{% 13 | \PYG@it{\PYG@bf{\PYG@ff{#1}}}}}}} 14 | \def\PYG#1#2{\PYG@reset\PYG@toks#1+\relax+\PYG@do{#2}} 15 | 16 | \expandafter\def\csname PYG@tok@w\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.73,0.73}{##1}}} 17 | \expandafter\def\csname PYG@tok@c\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}} 18 | \expandafter\def\csname PYG@tok@cp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 19 | \expandafter\def\csname PYG@tok@cs\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}\def\PYG@bc##1{\setlength{\fboxsep}{0pt}\colorbox[rgb]{1.00,0.94,0.94}{\strut ##1}}} 20 | \expandafter\def\csname PYG@tok@k\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 21 | \expandafter\def\csname PYG@tok@kp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 22 | \expandafter\def\csname PYG@tok@kt\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.56,0.13,0.00}{##1}}} 23 | \expandafter\def\csname PYG@tok@o\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.40,0.40,0.40}{##1}}} 24 | \expandafter\def\csname PYG@tok@ow\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 25 | \expandafter\def\csname PYG@tok@nb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 26 | \expandafter\def\csname PYG@tok@nf\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.49}{##1}}} 27 | \expandafter\def\csname PYG@tok@nc\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.05,0.52,0.71}{##1}}} 28 | \expandafter\def\csname PYG@tok@nn\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.05,0.52,0.71}{##1}}} 29 | \expandafter\def\csname PYG@tok@ne\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 30 | \expandafter\def\csname PYG@tok@nv\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}} 31 | \expandafter\def\csname PYG@tok@no\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.38,0.68,0.84}{##1}}} 32 | \expandafter\def\csname PYG@tok@nl\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.13,0.44}{##1}}} 33 | \expandafter\def\csname PYG@tok@ni\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.84,0.33,0.22}{##1}}} 34 | \expandafter\def\csname PYG@tok@na\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 35 | \expandafter\def\csname PYG@tok@nt\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.45}{##1}}} 36 | \expandafter\def\csname PYG@tok@nd\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.33,0.33,0.33}{##1}}} 37 | \expandafter\def\csname PYG@tok@s\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 38 | \expandafter\def\csname PYG@tok@sd\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 39 | \expandafter\def\csname PYG@tok@si\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.44,0.63,0.82}{##1}}} 40 | \expandafter\def\csname PYG@tok@se\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 41 | \expandafter\def\csname PYG@tok@sr\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.14,0.33,0.53}{##1}}} 42 | \expandafter\def\csname PYG@tok@ss\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.32,0.47,0.09}{##1}}} 43 | \expandafter\def\csname PYG@tok@sx\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.78,0.36,0.04}{##1}}} 44 | \expandafter\def\csname PYG@tok@m\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}} 45 | \expandafter\def\csname PYG@tok@gh\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.00,0.50}{##1}}} 46 | \expandafter\def\csname PYG@tok@gu\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.50,0.00,0.50}{##1}}} 47 | \expandafter\def\csname PYG@tok@gd\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.63,0.00,0.00}{##1}}} 48 | \expandafter\def\csname PYG@tok@gi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.63,0.00}{##1}}} 49 | \expandafter\def\csname PYG@tok@gr\endcsname{\def\PYG@tc##1{\textcolor[rgb]{1.00,0.00,0.00}{##1}}} 50 | \expandafter\def\csname PYG@tok@ge\endcsname{\let\PYG@it=\textit} 51 | \expandafter\def\csname PYG@tok@gs\endcsname{\let\PYG@bf=\textbf} 52 | \expandafter\def\csname PYG@tok@gp\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.78,0.36,0.04}{##1}}} 53 | \expandafter\def\csname PYG@tok@go\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.20,0.20,0.20}{##1}}} 54 | \expandafter\def\csname PYG@tok@gt\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.27,0.87}{##1}}} 55 | \expandafter\def\csname PYG@tok@err\endcsname{\def\PYG@bc##1{\setlength{\fboxsep}{0pt}\fcolorbox[rgb]{1.00,0.00,0.00}{1,1,1}{\strut ##1}}} 56 | \expandafter\def\csname PYG@tok@kc\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 57 | \expandafter\def\csname PYG@tok@kd\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 58 | \expandafter\def\csname PYG@tok@kn\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 59 | \expandafter\def\csname PYG@tok@kr\endcsname{\let\PYG@bf=\textbf\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 60 | \expandafter\def\csname PYG@tok@bp\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.00,0.44,0.13}{##1}}} 61 | \expandafter\def\csname PYG@tok@fm\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.02,0.16,0.49}{##1}}} 62 | \expandafter\def\csname PYG@tok@vc\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}} 63 | \expandafter\def\csname PYG@tok@vg\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}} 64 | \expandafter\def\csname PYG@tok@vi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}} 65 | \expandafter\def\csname PYG@tok@vm\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.73,0.38,0.84}{##1}}} 66 | \expandafter\def\csname PYG@tok@sa\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 67 | \expandafter\def\csname PYG@tok@sb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 68 | \expandafter\def\csname PYG@tok@sc\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 69 | \expandafter\def\csname PYG@tok@dl\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 70 | \expandafter\def\csname PYG@tok@s2\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 71 | \expandafter\def\csname PYG@tok@sh\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 72 | \expandafter\def\csname PYG@tok@s1\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.25,0.44,0.63}{##1}}} 73 | \expandafter\def\csname PYG@tok@mb\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}} 74 | \expandafter\def\csname PYG@tok@mf\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}} 75 | \expandafter\def\csname PYG@tok@mh\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}} 76 | \expandafter\def\csname PYG@tok@mi\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}} 77 | \expandafter\def\csname PYG@tok@il\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}} 78 | \expandafter\def\csname PYG@tok@mo\endcsname{\def\PYG@tc##1{\textcolor[rgb]{0.13,0.50,0.31}{##1}}} 79 | \expandafter\def\csname PYG@tok@ch\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}} 80 | \expandafter\def\csname PYG@tok@cm\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}} 81 | \expandafter\def\csname PYG@tok@cpf\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}} 82 | \expandafter\def\csname PYG@tok@c1\endcsname{\let\PYG@it=\textit\def\PYG@tc##1{\textcolor[rgb]{0.25,0.50,0.56}{##1}}} 83 | 84 | \def\PYGZbs{\char`\\} 85 | \def\PYGZus{\char`\_} 86 | \def\PYGZob{\char`\{} 87 | \def\PYGZcb{\char`\}} 88 | \def\PYGZca{\char`\^} 89 | \def\PYGZam{\char`\&} 90 | \def\PYGZlt{\char`\<} 91 | \def\PYGZgt{\char`\>} 92 | \def\PYGZsh{\char`\#} 93 | \def\PYGZpc{\char`\%} 94 | \def\PYGZdl{\char`\$} 95 | \def\PYGZhy{\char`\-} 96 | \def\PYGZsq{\char`\'} 97 | \def\PYGZdq{\char`\"} 98 | \def\PYGZti{\char`\~} 99 | % for compatibility with earlier versions 100 | \def\PYGZat{@} 101 | \def\PYGZlb{[} 102 | \def\PYGZrb{]} 103 | \makeatother 104 | 105 | \renewcommand\PYGZsq{\textquotesingle} 106 | -------------------------------------------------------------------------------- /doc/_build/latex/sphinxhowto.cls: -------------------------------------------------------------------------------- 1 | % 2 | % sphinxhowto.cls for Sphinx (http://sphinx-doc.org/) 3 | % 4 | 5 | \NeedsTeXFormat{LaTeX2e}[1995/12/01] 6 | \ProvidesClass{sphinxhowto}[2018/12/22 v1.8.3 Document class (Sphinx howto)] 7 | 8 | % 'oneside' option overriding the 'twoside' default 9 | \newif\if@oneside 10 | \DeclareOption{oneside}{\@onesidetrue} 11 | % Pass remaining document options to the parent class. 12 | \DeclareOption*{\PassOptionsToClass{\CurrentOption}{\sphinxdocclass}} 13 | \ProcessOptions\relax 14 | 15 | % Default to two-side document 16 | \if@oneside 17 | % nothing to do (oneside is the default) 18 | \else 19 | \PassOptionsToClass{twoside}{\sphinxdocclass} 20 | \fi 21 | 22 | \LoadClass{\sphinxdocclass} 23 | 24 | % Set some sane defaults for section numbering depth and TOC depth. You can 25 | % reset these counters in your preamble. 26 | % 27 | \setcounter{secnumdepth}{2} 28 | \setcounter{tocdepth}{2}% i.e. section and subsection 29 | 30 | % Change the title page to look a bit better, and fit in with the fncychap 31 | % ``Bjarne'' style a bit better. 32 | % 33 | \newcommand{\sphinxmaketitle}{% 34 | \noindent\rule{\textwidth}{1pt}\par 35 | \begingroup % for PDF information dictionary 36 | \def\endgraf{ }\def\and{\& }% 37 | \pdfstringdefDisableCommands{\def\\{, }}% overwrite hyperref setup 38 | \hypersetup{pdfauthor={\@author}, pdftitle={\@title}}% 39 | \endgroup 40 | \begin{flushright} 41 | \sphinxlogo 42 | \py@HeaderFamily 43 | {\Huge \@title }\par 44 | {\itshape\large \py@release \releaseinfo}\par 45 | \vspace{25pt} 46 | {\Large 47 | \begin{tabular}[t]{c} 48 | \@author 49 | \end{tabular}}\par 50 | \vspace{25pt} 51 | \@date \par 52 | \py@authoraddress \par 53 | \end{flushright} 54 | \@thanks 55 | \setcounter{footnote}{0} 56 | \let\thanks\relax\let\maketitle\relax 57 | %\gdef\@thanks{}\gdef\@author{}\gdef\@title{} 58 | } 59 | 60 | \newcommand{\sphinxtableofcontents}{ 61 | \begingroup 62 | \parskip = 0mm 63 | \tableofcontents 64 | \endgroup 65 | \rule{\textwidth}{1pt} 66 | \vspace{12pt} 67 | } 68 | 69 | \pagenumbering{arabic} 70 | 71 | % Fix the bibliography environment to add an entry to the Table of 72 | % Contents. 73 | % For an article document class this environment is a section, 74 | % so no page break before it. 75 | % 76 | \newenvironment{sphinxthebibliography}[1]{% 77 | % \phantomsection % not needed here since TeXLive 2010's hyperref 78 | \begin{thebibliography}{#1}% 79 | \addcontentsline{toc}{section}{\ifdefined\refname\refname\else\ifdefined\bibname\bibname\fi\fi}}{\end{thebibliography}} 80 | 81 | 82 | % Same for the indices. 83 | % The memoir class already does this, so we don't duplicate it in that case. 84 | % 85 | \@ifclassloaded{memoir} 86 | {\newenvironment{sphinxtheindex}{\begin{theindex}}{\end{theindex}}} 87 | {\newenvironment{sphinxtheindex}{% 88 | \phantomsection % needed because no chapter, section, ... is created by theindex 89 | \begin{theindex}% 90 | \addcontentsline{toc}{section}{\indexname}}{\end{theindex}}} 91 | -------------------------------------------------------------------------------- /doc/_build/latex/sphinxmanual.cls: -------------------------------------------------------------------------------- 1 | % 2 | % sphinxmanual.cls for Sphinx (http://sphinx-doc.org/) 3 | % 4 | 5 | \NeedsTeXFormat{LaTeX2e}[1995/12/01] 6 | \ProvidesClass{sphinxmanual}[2018/12/22 v1.8.3 Document class (Sphinx manual)] 7 | 8 | % chapters starting at odd pages (overridden by 'openany' document option) 9 | \PassOptionsToClass{openright}{\sphinxdocclass} 10 | 11 | % 'oneside' option overriding the 'twoside' default 12 | \newif\if@oneside 13 | \DeclareOption{oneside}{\@onesidetrue} 14 | % Pass remaining document options to the parent class. 15 | \DeclareOption*{\PassOptionsToClass{\CurrentOption}{\sphinxdocclass}} 16 | \ProcessOptions\relax 17 | 18 | % Defaults two-side document 19 | \if@oneside 20 | % nothing to do (oneside is the default) 21 | \else 22 | \PassOptionsToClass{twoside}{\sphinxdocclass} 23 | \fi 24 | 25 | \LoadClass{\sphinxdocclass} 26 | 27 | % Set some sane defaults for section numbering depth and TOC depth. You can 28 | % reset these counters in your preamble. 29 | % 30 | \setcounter{secnumdepth}{2} 31 | \setcounter{tocdepth}{1} 32 | 33 | % Change the title page to look a bit better, and fit in with the fncychap 34 | % ``Bjarne'' style a bit better. 35 | % 36 | \newcommand{\sphinxmaketitle}{% 37 | \let\spx@tempa\relax 38 | \ifHy@pageanchor\def\spx@tempa{\Hy@pageanchortrue}\fi 39 | \hypersetup{pageanchor=false}% avoid duplicate destination warnings 40 | \begin{titlepage}% 41 | \let\footnotesize\small 42 | \let\footnoterule\relax 43 | \noindent\rule{\textwidth}{1pt}\par 44 | \begingroup % for PDF information dictionary 45 | \def\endgraf{ }\def\and{\& }% 46 | \pdfstringdefDisableCommands{\def\\{, }}% overwrite hyperref setup 47 | \hypersetup{pdfauthor={\@author}, pdftitle={\@title}}% 48 | \endgroup 49 | \begin{flushright}% 50 | \sphinxlogo 51 | \py@HeaderFamily 52 | {\Huge \@title \par} 53 | {\itshape\LARGE \py@release\releaseinfo \par} 54 | \vfill 55 | {\LARGE 56 | \begin{tabular}[t]{c} 57 | \@author 58 | \end{tabular} 59 | \par} 60 | \vfill\vfill 61 | {\large 62 | \@date \par 63 | \vfill 64 | \py@authoraddress \par 65 | }% 66 | \end{flushright}%\par 67 | \@thanks 68 | \end{titlepage}% 69 | \setcounter{footnote}{0}% 70 | \let\thanks\relax\let\maketitle\relax 71 | %\gdef\@thanks{}\gdef\@author{}\gdef\@title{} 72 | \clearpage 73 | \ifdefined\sphinxbackoftitlepage\sphinxbackoftitlepage\fi 74 | \if@openright\cleardoublepage\else\clearpage\fi 75 | \spx@tempa 76 | } 77 | 78 | \newcommand{\sphinxtableofcontents}{% 79 | \pagenumbering{roman}% 80 | \begingroup 81 | \parskip \z@skip 82 | \tableofcontents 83 | \endgroup 84 | % before resetting page counter, let's do the right thing. 85 | \if@openright\cleardoublepage\else\clearpage\fi 86 | \pagenumbering{arabic}% 87 | } 88 | 89 | % This is needed to get the width of the section # area wide enough in the 90 | % library reference. Doing it here keeps it the same for all the manuals. 91 | % 92 | \renewcommand*\l@section{\@dottedtocline{1}{1.5em}{2.6em}} 93 | \renewcommand*\l@subsection{\@dottedtocline{2}{4.1em}{3.5em}} 94 | 95 | % Fix the bibliography environment to add an entry to the Table of 96 | % Contents. 97 | % For a report document class this environment is a chapter. 98 | % 99 | \newenvironment{sphinxthebibliography}[1]{% 100 | \if@openright\cleardoublepage\else\clearpage\fi 101 | % \phantomsection % not needed here since TeXLive 2010's hyperref 102 | \begin{thebibliography}{#1}% 103 | \addcontentsline{toc}{chapter}{\bibname}}{\end{thebibliography}} 104 | 105 | % Same for the indices. 106 | % The memoir class already does this, so we don't duplicate it in that case. 107 | % 108 | \@ifclassloaded{memoir} 109 | {\newenvironment{sphinxtheindex}{\begin{theindex}}{\end{theindex}}} 110 | {\newenvironment{sphinxtheindex}{% 111 | \if@openright\cleardoublepage\else\clearpage\fi 112 | \phantomsection % needed as no chapter, section, ... created 113 | \begin{theindex}% 114 | \addcontentsline{toc}{chapter}{\indexname}}{\end{theindex}}} 115 | -------------------------------------------------------------------------------- /doc/_build/latex/tutorial.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/latex/tutorial.png -------------------------------------------------------------------------------- /doc/_build/latex/tutorial_host_label.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/latex/tutorial_host_label.png -------------------------------------------------------------------------------- /doc/_build/latex/tutorial_host_search.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/latex/tutorial_host_search.png -------------------------------------------------------------------------------- /doc/_build/latex/tutorial_host_search_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_build/latex/tutorial_host_search_2.png -------------------------------------------------------------------------------- /doc/_build/markdown/host.md: -------------------------------------------------------------------------------- 1 | # Web 2 | 3 | ## Introduction 4 | 5 | While small plots can easily be created and stored in a single HTML and JavaScript file, which are then loaded completely in the browsers memory, this is not possible for larger data sets due to browser limitations. 6 | In order to solve this problem, Faerun includes a small HTTP server (based on cherrypy) to serve the data to the browser. 7 | 8 | ## Creating Faerun Data Files 9 | 10 | As shown in Getting Started, Faerun can save data as `.faerun` data files using `pickle`. 11 | 12 | ``` 13 | with open('helix.faerun', 'wb+') as handle: 14 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 15 | ``` 16 | 17 | ## Starting a Faerun Web Server 18 | 19 | ``` 20 | from faerun import host 21 | 22 | host('helix.faerun', label_type='default', 23 | theme='dark') 24 | ``` 25 | 26 | ## Formatting Labels 27 | 28 | Labels can be formatted by defining a custom `label_formatter`. If no `label_formatter` is provided to the `host` function, the default is used: 29 | 30 | ``` 31 | label_formatter = lambda label, index, name: label.split('__')[0] 32 | ``` 33 | 34 | This default splits the label value on `'__'` to store different labels and enable search on different values the the displayed labels. See “Searching” for details. Defining a custom label formatter is straight forward. As an example, let’s prefix each label with a string and add their index and layer name: 35 | 36 | ``` 37 | def custom_label_formatter(label, index, name): 38 | return f'Example: {label} ({index}, {name})' 39 | 40 | host('helix.faerun', label_type='default', 41 | theme='dark', label_formatter=custom_label_formatter) 42 | ``` 43 | 44 | This function is then called whenever a label is requested from the server. In addition to the argument `label`, the arguments `index` and `name` can be used to further customize the displayed label and represent the integer index of the data point and the data layer they belong to (e.g. the name defined with `add_scatter`). 45 | 46 | 47 | 48 | ![image](_static/tutorial_host_label.png) 49 | 50 | ## Adding Hyperlinks 51 | 52 | Faerun allows to link the data to an arbitrary URL which can be visited upon double-clicking a data point. In order to do this, a `link_formatter` has to be provided. This works similar to customizing the label. 53 | 54 | ``` 55 | def custom_link_formatter(label, index, name): 56 | return f'https://www.google.com/search?q={label}' 57 | 58 | host('helix.faerun', label_type='default', 59 | theme='dark', link_formatter=custom_link_formatter) 60 | ``` 61 | 62 | ## Searching 63 | 64 | The hosted version of a Faerun visualization also allows for searching. As a default, the search searches for exact matches in labels (substring or regex searches are not possible at this time). 65 | 66 | 67 | 68 | ![image](_static/tutorial_host_search.png) 69 | 70 | However, the search can be customized. As described in “Formatting Labels”, additional label values can be added by separating them using `'__'`. 71 | 72 | ``` 73 | c = np.random.randint(0, 2, len(x)) 74 | labels = [''] * len(c) 75 | 76 | for i, e in enumerate(c): 77 | labels[i] = str(e) + '__' + str(i % 20) 78 | 79 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': labels} 80 | ``` 81 | 82 | The above examples adds an additional label value and as default, the second label value is then used by the search. 83 | 84 | 85 | 86 | ![image](_static/tutorial_host_search_2.png) 87 | 88 | If there are additional label values, the search index can be set using the `search_index` argument. 89 | 90 | ## Add Info / Documentation 91 | 92 | As the visualization is ready to be deployed to a publicly accessible web server, it might be of interest to add a documentation. The `host` method supports the argument `info` that accepts a (markdown formatted) string. This information is the desplayed on the generated web page. 93 | 94 | ``` 95 | info = ('#Welcome to Fearun', 96 | 'This is a small Faerun example.' 97 | '', 98 | 'Yay markdown! This means that you can easily:', 99 | '- Add lists', 100 | '- Build tables', 101 | '- Insert images and links', 102 | '- Add code examples', 103 | '- ...' 104 | ) 105 | 106 | host('helix.faerun', label_type='default', theme='dark', 107 | label_formatter=custom_label_formatter, link_formatter=custom_link_formatter, 108 | info='\n'.join(info)) 109 | ``` 110 | 111 | An info button is then shown next to the screenshot button, which upon click opens a window containing the info. 112 | 113 | ## Complete Example 114 | 115 | ``` 116 | import pickle 117 | import numpy as np 118 | from faerun import Faerun, host 119 | 120 | 121 | def main(): 122 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 123 | 124 | x = np.linspace(0, 12.0, 326) 125 | y = np.sin(np.pi * x) 126 | z = np.cos(np.pi * x) 127 | c = np.random.randint(0, 2, len(x)) 128 | 129 | labels = [''] * len(c) 130 | 131 | for i, e in enumerate(c): 132 | labels[i] = str(e) + '__' + str(i % 20) 133 | 134 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': labels} 135 | 136 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 137 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 138 | 139 | f.plot('helix') 140 | 141 | with open('helix.faerun', 'wb+') as handle: 142 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 143 | 144 | def custom_label_formatter(label, index, name): 145 | return f'Example: {label} ({index}, {name})' 146 | 147 | def custom_link_formatter(label, index, name): 148 | return f'https://www.google.com/search?q={label}' 149 | 150 | info = ('#Welcome to Fearun', 151 | 'This is a small Faerun example.' 152 | '', 153 | 'Yay markdown! This means that you can easily:', 154 | '- Add lists', 155 | '- Build tables', 156 | '- Insert images and links', 157 | '- Add code examples', 158 | '- ...' 159 | ) 160 | 161 | host('helix.faerun', label_type='default', theme='dark', 162 | label_formatter=custom_label_formatter, link_formatter=custom_link_formatter, 163 | info='\n'.join(info)) 164 | 165 | 166 | if __name__ == '__main__': 167 | main() 168 | ``` 169 | -------------------------------------------------------------------------------- /doc/_build/markdown/index.md: -------------------------------------------------------------------------------- 1 | # Welcome to Faerun’s documentation! 2 | 3 | Here are some teasers. 4 | 5 | 6 | 7 | ![image](_static/drugbank_2d_light.png) 8 | 9 | 10 | 11 | ![image](_static/drugbank_2d_dark.png) 12 | 13 | ## Table of Contents 14 | 15 | * Getting Started 16 | 17 | * Installation 18 | 19 | * Create a Plot Document 20 | 21 | * Preparing Data for Plotting 22 | 23 | * Adding a Scatter Layer 24 | 25 | * Saving to HTML 26 | 27 | * Saving to Faerun Data File 28 | 29 | * Complete Example 30 | 31 | * Web 32 | 33 | * Introduction 34 | 35 | * Creating Faerun Data Files 36 | 37 | * Starting a Faerun Web Server 38 | 39 | * Formatting Labels 40 | 41 | * Adding Hyperlinks 42 | 43 | * Searching 44 | 45 | * Add Info / Documentation 46 | 47 | * Complete Example 48 | 49 | * Documentation 50 | 51 | * Faerun 52 | 53 | * Web 54 | -------------------------------------------------------------------------------- /doc/_build/markdown/tutorial.md: -------------------------------------------------------------------------------- 1 | # Getting Started 2 | 3 | ## Installation 4 | 5 | Faerun can be installed using pip. 6 | 7 | ``` 8 | pip install faerun 9 | ``` 10 | 11 | In order to use it in a script, the class `Faerun` has to be imported from the package. 12 | 13 | ``` 14 | from faerun import Faerun 15 | ``` 16 | 17 | That’s it for the installation. 18 | 19 | ## Create a Plot Document 20 | 21 | In order to plot, a plot document has to be created. To do so, create an instance of the class `Faerun` 22 | 23 | ``` 24 | from faerun import Faerun 25 | 26 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 27 | ``` 28 | 29 | Here, we set the `title` of the plot document. This will be used as the title of the HTML document. The clear color of the canvas, which is the background color of the plot, is set to `'#222222'` (which is the hex-code for a dark gray). 30 | The drawing of coordinate axes is disabled by setting `coords=False` and since we want to draw 3D data, the argument `view` is set to `'free'` to enable the user to pan and rotate the plot. 31 | 32 | ## Preparing Data for Plotting 33 | 34 | The next step is to prepare the data which is to be plotted. In the tutorial, we will just generate some nice looking data using `numpy`. 35 | 36 | ``` 37 | import numpy as np 38 | 39 | x = np.linspace(0, 12.0, 326) 40 | y = np.sin(np.pi * x) 41 | z = np.cos(np.pi * x) 42 | c = np.random.randint(0, 6, len(x)) 43 | ``` 44 | 45 | This data can then be wrapped in a `dict`. In addition, `DataFrame` from the `pandas` package are also supported by faerun. 46 | In the example, the same values are used for the colors `c` and labels `labels`. 47 | 48 | ``` 49 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': c} 50 | ``` 51 | 52 | ## Adding a Scatter Layer 53 | 54 | Given the `Faerun` instance and the data, a scatter plot can be created using the method `add_scatter`. 55 | 56 | ``` 57 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 58 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 59 | ``` 60 | 61 | The data is added as a scatter layer named helix. The chose shader will render the data points as 62 | spheres (with diffuse and specular lighting) of size 5.0 with colors from the `matplotlib` colormap `'Dark2'`. 63 | As the `c` is categorical, the parameter `categorical` is set to `True`, otherwise `matplotlib` will mess up the values. 64 | 65 | Finally, `has_legend=True` adds the scatter layer to the legend and `legend_labels` is a `list` of `tuple`, associating values with a label. 66 | 67 | ## Saving to HTML 68 | 69 | The faerun document can the be plotted to an HTML document with an accompanying JavaScript data file. 70 | 71 | ``` 72 | f.plot('helix') 73 | ``` 74 | 75 | This saves the plot as `helix.html\` and \`\`helix.js`. The files can be opened locally or hosted on any web server. 76 | 77 | 78 | 79 | ![image](_static/tutorial.png) 80 | 81 | ## Saving to Faerun Data File 82 | 83 | The faerun document can also be exported to a faerun data file, which in turn can then be hosted using the `web` module. 84 | 85 | ``` 86 | import pickle 87 | 88 | with open('helix.faerun', 'wb+') as handle: 89 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 90 | ``` 91 | 92 | ## Complete Example 93 | 94 | ``` 95 | import pickle 96 | import numpy as np 97 | from faerun import Faerun 98 | 99 | def main(): 100 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 101 | 102 | x = np.linspace(0, 12.0, 326) 103 | y = np.sin(np.pi * x) 104 | z = np.cos(np.pi * x) 105 | c = np.random.randint(0, 2, len(x)) 106 | 107 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': c} 108 | 109 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 110 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 111 | 112 | f.plot('helix') 113 | 114 | with open('helix.faerun', 'wb+') as handle: 115 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 116 | 117 | if __name__ == '__main__': 118 | main() 119 | ``` 120 | -------------------------------------------------------------------------------- /doc/_static/drugbank_2d_dark.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_static/drugbank_2d_dark.png -------------------------------------------------------------------------------- /doc/_static/drugbank_2d_light.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_static/drugbank_2d_light.png -------------------------------------------------------------------------------- /doc/_static/tutorial.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_static/tutorial.png -------------------------------------------------------------------------------- /doc/_static/tutorial_host_label.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_static/tutorial_host_label.png -------------------------------------------------------------------------------- /doc/_static/tutorial_host_search.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_static/tutorial_host_search.png -------------------------------------------------------------------------------- /doc/_static/tutorial_host_search_2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/doc/_static/tutorial_host_search_2.png -------------------------------------------------------------------------------- /doc/conf.py: -------------------------------------------------------------------------------- 1 | # Configuration file for the Sphinx documentation builder. 2 | # 3 | # This file only contains a selection of the most common options. For a full 4 | # list see the documentation: 5 | # http://www.sphinx-doc.org/en/master/config 6 | 7 | # -- Path setup -------------------------------------------------------------- 8 | 9 | # If extensions (or modules to document with autodoc) are in another directory, 10 | # add these directories to sys.path here. If the directory is relative to the 11 | # documentation root, use os.path.abspath to make it absolute, like shown here. 12 | # 13 | import os 14 | import sys 15 | 16 | import sphinx_rtd_theme 17 | 18 | sys.path.insert(0, os.path.abspath('..')) 19 | 20 | 21 | # -- Project information ----------------------------------------------------- 22 | 23 | project = 'Faerun' 24 | copyright = '2019, Daniel Probst (Reymond Group, University of Bern)' 25 | author = 'Daniel Probst (Reymond Group, University of Bern)' 26 | 27 | # The full version, including alpha/beta/rc tags 28 | release = '1.0' 29 | 30 | 31 | # -- General configuration --------------------------------------------------- 32 | 33 | # Add any Sphinx extension module names here, as strings. They can be 34 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 35 | # ones. 36 | extensions = [ 37 | 'sphinx.ext.autodoc', 38 | 'sphinx.ext.coverage', 39 | 'sphinx.ext.napoleon', 40 | 'sphinx.ext.autosummary', 41 | 'sphinx_markdown_builder' 42 | ] 43 | 44 | autoclass_content = 'both' 45 | autosummary_generate = True 46 | 47 | # Add any paths that contain templates here, relative to this directory. 48 | templates_path = ['_templates'] 49 | 50 | # List of patterns, relative to source directory, that match files and 51 | # directories to ignore when looking for source files. 52 | # This pattern also affects html_static_path and html_extra_path. 53 | exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] 54 | 55 | master_doc = 'index' 56 | 57 | # -- Options for HTML output ------------------------------------------------- 58 | 59 | # The theme to use for HTML and HTML Help pages. See the documentation for 60 | # a list of builtin themes. 61 | # 62 | # pip install sphinx_rtd_theme 63 | html_theme = 'sphinx_rtd_theme' 64 | html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] 65 | 66 | # Add any paths that contain custom static files (such as style sheets) here, 67 | # relative to this directory. They are copied after the builtin static files, 68 | # so a file named "default.css" will overwrite the builtin "default.css". 69 | html_static_path = ['_static'] 70 | htmlhelp_basename = 'faerun-doc' 71 | 72 | 73 | # -- Extension configuration ------------------------------------------------- 74 | def skip(app, what, name, obj, would_skip, options): 75 | if name == "__init__": 76 | return False 77 | return would_skip 78 | 79 | def setup(app): 80 | app.connect("autodoc-skip-member", skip) 81 | -------------------------------------------------------------------------------- /doc/documentation.rst: -------------------------------------------------------------------------------- 1 | Documentation 2 | ------------- 3 | 4 | Faerun 5 | ^^^^^^ 6 | .. autoclass:: faerun.Faerun 7 | :members: 8 | 9 | Web 10 | ^^^ 11 | .. autofunction:: faerun.host 12 | -------------------------------------------------------------------------------- /doc/host.rst: -------------------------------------------------------------------------------- 1 | Web 2 | --- 3 | 4 | Introduction 5 | ^^^^^^^^^^^^ 6 | While small plots can easily be created and stored in a single HTML and JavaScript file, which are then loaded completely in the browsers memory, this is not possible for larger data sets due to browser limitations. 7 | In order to solve this problem, Faerun includes a small HTTP server (based on cherrypy) to serve the data to the browser. 8 | 9 | Creating Faerun Data Files 10 | ^^^^^^^^^^^^^^^^^^^^^^^^^^ 11 | As shown in :doc:`tutorial`, Faerun can save data as ``.faerun`` data files using ``pickle``. 12 | 13 | .. code-block:: python 14 | 15 | with open('helix.faerun', 'wb+') as handle: 16 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 17 | 18 | Starting a Faerun Web Server 19 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 20 | .. code-block:: python 21 | 22 | from faerun import host 23 | 24 | host('helix.faerun', label_type='default', 25 | theme='dark') 26 | 27 | Formatting Labels 28 | ^^^^^^^^^^^^^^^^^ 29 | Labels can be formatted by defining a custom ``label_formatter``. If no ``label_formatter`` is provided to the ``host`` function, the default is used: 30 | 31 | .. code-block:: python 32 | 33 | label_formatter = lambda label, index, name: label.split('__')[0] 34 | 35 | This default splits the label value on ``'__'`` to store different labels and enable search on different values the the displayed labels. See "Searching" for details. Defining a custom label formatter is straight forward. As an example, let's prefix each label with a string and add their index and layer name: 36 | 37 | .. code-block:: python 38 | 39 | def custom_label_formatter(label, index, name): 40 | return f'Example: {label} ({index}, {name})' 41 | 42 | host('helix.faerun', label_type='default', 43 | theme='dark', label_formatter=custom_label_formatter) 44 | 45 | This function is then called whenever a label is requested from the server. In addition to the argument ``label``, the arguments ``index`` and ``name`` can be used to further customize the displayed label and represent the integer index of the data point and the data layer they belong to (e.g. the name defined with ``add_scatter``). 46 | 47 | .. image:: _static/tutorial_host_label.png 48 | :alt: Example of a custom label formatter. 49 | 50 | Adding Hyperlinks 51 | ^^^^^^^^^^^^^^^^^ 52 | Faerun allows to link the data to an arbitrary URL which can be visited upon double-clicking a data point. In order to do this, a ``link_formatter`` has to be provided. This works similar to customizing the label. 53 | 54 | .. code-block:: python 55 | 56 | def custom_link_formatter(label, index, name): 57 | return f'https://www.google.com/search?q={label}' 58 | 59 | host('helix.faerun', label_type='default', 60 | theme='dark', link_formatter=custom_link_formatter) 61 | 62 | 63 | Searching 64 | ^^^^^^^^^ 65 | The hosted version of a Faerun visualization also allows for searching. As a default, the search searches for exact matches in labels (substring or regex searches are not possible at this time). 66 | 67 | .. image:: _static/tutorial_host_search.png 68 | :alt: The result of a search. 69 | 70 | However, the search can be customized. As described in "Formatting Labels", additional label values can be added by separating them using ``'__'``. 71 | 72 | .. code-block:: python 73 | 74 | c = np.random.randint(0, 2, len(x)) 75 | labels = [''] * len(c) 76 | 77 | for i, e in enumerate(c): 78 | labels[i] = str(e) + '__' + str(i % 20) 79 | 80 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': labels} 81 | 82 | The above examples adds an additional label value and as default, the second label value is then used by the search. 83 | 84 | .. image:: _static/tutorial_host_search_2.png 85 | :alt: The result of a custom search. 86 | 87 | If there are additional label values, the search index can be set using the ``search_index`` argument. 88 | 89 | Add Info / Documentation 90 | ^^^^^^^^^^^^^^^^^^^^^^^^ 91 | As the visualization is ready to be deployed to a publicly accessible web server, it might be of interest to add a documentation. The ``host`` method supports the argument ``info`` that accepts a (markdown formatted) string. This information is the desplayed on the generated web page. 92 | 93 | .. code-block:: python 94 | 95 | info = ('#Welcome to Fearun', 96 | 'This is a small Faerun example.' 97 | '', 98 | 'Yay markdown! This means that you can easily:', 99 | '- Add lists', 100 | '- Build tables', 101 | '- Insert images and links', 102 | '- Add code examples', 103 | '- ...' 104 | ) 105 | 106 | host('helix.faerun', label_type='default', theme='dark', 107 | label_formatter=custom_label_formatter, link_formatter=custom_link_formatter, 108 | info='\n'.join(info)) 109 | 110 | An info button is then shown next to the screenshot button, which upon click opens a window containing the info. 111 | 112 | Complete Example 113 | ^^^^^^^^^^^^^^^^ 114 | 115 | .. code-block:: python 116 | 117 | import pickle 118 | import numpy as np 119 | from faerun import Faerun, host 120 | 121 | 122 | def main(): 123 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 124 | 125 | x = np.linspace(0, 12.0, 326) 126 | y = np.sin(np.pi * x) 127 | z = np.cos(np.pi * x) 128 | c = np.random.randint(0, 2, len(x)) 129 | 130 | labels = [''] * len(c) 131 | 132 | for i, e in enumerate(c): 133 | labels[i] = str(e) + '__' + str(i % 20) 134 | 135 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': labels} 136 | 137 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 138 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 139 | 140 | f.plot('helix') 141 | 142 | with open('helix.faerun', 'wb+') as handle: 143 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 144 | 145 | def custom_label_formatter(label, index, name): 146 | return f'Example: {label} ({index}, {name})' 147 | 148 | def custom_link_formatter(label, index, name): 149 | return f'https://www.google.com/search?q={label}' 150 | 151 | info = ('#Welcome to Fearun', 152 | 'This is a small Faerun example.' 153 | '', 154 | 'Yay markdown! This means that you can easily:', 155 | '- Add lists', 156 | '- Build tables', 157 | '- Insert images and links', 158 | '- Add code examples', 159 | '- ...' 160 | ) 161 | 162 | host('helix.faerun', label_type='default', theme='dark', 163 | label_formatter=custom_label_formatter, link_formatter=custom_link_formatter, 164 | info='\n'.join(info)) 165 | 166 | 167 | if __name__ == '__main__': 168 | main() 169 | 170 | -------------------------------------------------------------------------------- /doc/index.rst: -------------------------------------------------------------------------------- 1 | Welcome to Faerun's documentation! 2 | ================================== 3 | Here are some teasers. 4 | 5 | .. image:: _static/drugbank_2d_light.png 6 | :alt: Example of Drugbank compounds in 2d with the light theme. 7 | 8 | .. image:: _static/drugbank_2d_dark.png 9 | :alt: Example of Drugbank compounds in 2d with the dark theme. 10 | 11 | Table of Contents 12 | ----------------- 13 | 14 | .. toctree:: 15 | 16 | tutorial 17 | host 18 | documentation 19 | -------------------------------------------------------------------------------- /doc/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=. 11 | set BUILDDIR=_build 12 | 13 | if "%1" == "" goto help 14 | 15 | %SPHINXBUILD% >NUL 2>NUL 16 | if errorlevel 9009 ( 17 | echo. 18 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 19 | echo.installed, then set the SPHINXBUILD environment variable to point 20 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 21 | echo.may add the Sphinx directory to PATH. 22 | echo. 23 | echo.If you don't have Sphinx installed, grab it from 24 | echo.http://sphinx-doc.org/ 25 | exit /b 1 26 | ) 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /doc/tutorial.rst: -------------------------------------------------------------------------------- 1 | Getting Started 2 | --------------- 3 | 4 | Installation 5 | ^^^^^^^^^^^^ 6 | Faerun can be installed using pip. 7 | 8 | .. code-block:: bash 9 | 10 | pip install faerun 11 | 12 | In order to use it in a script, the class ``Faerun`` has to be imported from the package. 13 | 14 | .. code-block:: python 15 | 16 | from faerun import Faerun 17 | 18 | That's it for the installation. 19 | 20 | Create a Plot Document 21 | ^^^^^^^^^^^^^^^^^^^^^^ 22 | In order to plot, a plot document has to be created. To do so, create an instance of the class ``Faerun`` 23 | 24 | .. code-block:: python 25 | 26 | from faerun import Faerun 27 | 28 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 29 | 30 | Here, we set the ``title`` of the plot document. This will be used as the title of the HTML document. The clear color of the canvas, which is the background color of the plot, is set to ``'#222222'`` (which is the hex-code for a dark gray). 31 | The drawing of coordinate axes is disabled by setting ``coords=False`` and since we want to draw 3D data, the argument ``view`` is set to ``'free'`` to enable the user to pan and rotate the plot. 32 | 33 | Preparing Data for Plotting 34 | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 35 | The next step is to prepare the data which is to be plotted. In the tutorial, we will just generate some nice looking data using ``numpy``. 36 | 37 | .. code-block:: python 38 | 39 | import numpy as np 40 | 41 | x = np.linspace(0, 12.0, 326) 42 | y = np.sin(np.pi * x) 43 | z = np.cos(np.pi * x) 44 | c = np.random.randint(0, 6, len(x)) 45 | 46 | This data can then be wrapped in a ``dict``. In addition, ``DataFrame`` from the ``pandas`` package are also supported by faerun. 47 | In the example, the same values are used for the colors ``c`` and labels ``labels``. 48 | 49 | .. code-block:: python 50 | 51 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': c} 52 | 53 | Adding a Scatter Layer 54 | ^^^^^^^^^^^^^^^^^^^^^^ 55 | Given the ``Faerun`` instance and the data, a scatter plot can be created using the method ``add_scatter``. 56 | 57 | .. code-block:: python 58 | 59 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 60 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 61 | 62 | The data is added as a scatter layer named helix. The chose shader will render the data points as 63 | spheres (with diffuse and specular lighting) of size 5.0 with colors from the ``matplotlib`` colormap ``'Dark2'``. 64 | As the ``c`` is categorical, the parameter ``categorical`` is set to ``True``, otherwise ``matplotlib`` will mess up the values. 65 | 66 | Finally, ``has_legend=True`` adds the scatter layer to the legend and ``legend_labels`` is a ``list`` of ``tuple``, associating values with a label. 67 | 68 | Saving to HTML 69 | ^^^^^^^^^^^^^^ 70 | The faerun document can the be plotted to an HTML document with an accompanying JavaScript data file. 71 | 72 | .. code-block:: python 73 | 74 | f.plot('helix') 75 | 76 | This saves the plot as ``helix.html` and ``helix.js``. The files can be opened locally or hosted on any web server. 77 | 78 | .. image:: _static/tutorial.png 79 | :alt: A helix drawn using faerun. 80 | 81 | Saving to Faerun Data File 82 | ^^^^^^^^^^^^^^^^^^^^^^^^^^ 83 | The faerun document can also be exported to a faerun data file, which in turn can then be hosted using the ``web`` module. 84 | 85 | .. code-block:: python 86 | 87 | import pickle 88 | 89 | with open('helix.faerun', 'wb+') as handle: 90 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 91 | 92 | Complete Example 93 | ^^^^^^^^^^^^^^^^ 94 | .. code-block:: python 95 | 96 | import pickle 97 | import numpy as np 98 | from faerun import Faerun 99 | 100 | def main(): 101 | f = Faerun(title='faerun-example', clear_color='#222222', coords=False, view='free') 102 | 103 | x = np.linspace(0, 12.0, 326) 104 | y = np.sin(np.pi * x) 105 | z = np.cos(np.pi * x) 106 | c = np.random.randint(0, 2, len(x)) 107 | 108 | data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': c} 109 | 110 | f.add_scatter('helix', data, shader='sphere', colormap='Dark2', point_scale=5.0, 111 | categorical=True, has_legend=True, legend_labels=[(0, 'Zero'), (1, 'One')]) 112 | 113 | f.plot('helix') 114 | 115 | with open('helix.faerun', 'wb+') as handle: 116 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 117 | 118 | if __name__ == '__main__': 119 | main() 120 | 121 | -------------------------------------------------------------------------------- /examples/example.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import pandas as pd 3 | import tmap as tm 4 | from faerun import Faerun, FaerunPlot 5 | from rdkit.Chem import AllChem 6 | from rdkit.Chem import rdMolDescriptors as Descriptors 7 | from sklearn.decomposition import PCA 8 | 9 | 10 | def get_fingerprint(in_smiles): 11 | results = [] 12 | smiles = [] 13 | for s in in_smiles: 14 | mol = AllChem.MolFromSmiles(s) 15 | if mol is not None: 16 | if mol.GetNumAtoms() > 100: 17 | continue 18 | mqn = Descriptors.MQNs_(mol) 19 | results.append(np.array(mqn)) 20 | smiles.append(s) 21 | 22 | return results, smiles 23 | 24 | 25 | def load(): 26 | drugbank = [] 27 | with open("drugbank.smi") as f: 28 | for line in f.readlines(): 29 | drugbank.append(line.split()[0].strip()) 30 | 31 | mqns, smiles = get_fingerprint(drugbank) 32 | mqns = np.array(mqns) 33 | 34 | pca = PCA(n_components=3) 35 | result = pca.fit_transform(mqns) 36 | return result, mqns, smiles 37 | 38 | 39 | def load_tmap(): 40 | drugbank = [] 41 | with open("drugbank.smi") as f: 42 | for line in f.readlines(): 43 | drugbank.append(line.split()[0].strip()) 44 | 45 | mqns, smiles = get_fingerprint(drugbank) 46 | mqns = np.array(mqns) 47 | 48 | return tm.embed(mqns) 49 | 50 | 51 | coords, mqns, smiles = load() 52 | smiles = [s + "__This is a Test" for s in smiles] 53 | 54 | data = {"x": [], "y": [], "z": [], "c": [], "labels": smiles} 55 | 56 | for i, e in enumerate(coords): 57 | data["x"].append(coords[i][0]) 58 | data["y"].append(coords[i][1]) 59 | data["z"].append(coords[i][2]) 60 | data["c"].append(mqns[i][0]) 61 | 62 | df = pd.DataFrame.from_dict(data) 63 | 64 | # plot = FaerunPlot() 65 | # plot.add_series(x=df.x, y=df.y, z=df.z, c=df.c, labels=df.labels) 66 | # plot.save("test", "smiles") 67 | 68 | te = load_tmap() 69 | 70 | plot = FaerunPlot(view="front") 71 | plot.add_tmap_series(te, c=df.c) 72 | plot.save("test", "smiles") 73 | -------------------------------------------------------------------------------- /examples/example_sin.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import pandas as pd 3 | from faerun import Faerun 4 | import pickle 5 | 6 | 7 | faerun = Faerun(view="free", clear_color="#222222") 8 | 9 | t = np.linspace(0, 12.0, 326) 10 | s = np.sin(np.pi * t) 11 | c = np.cos(np.pi * t) 12 | sizes = np.linspace(0.1, 2.0, 326) 13 | 14 | data = {"x": t, "y": s, "z": c, "c": t / max(t) * 100.0, "s": sizes} 15 | 16 | data2 = {"x": t, "y": c, "z": s, "c": t / max(t), "s": sizes, "labels": sizes} 17 | 18 | x = np.linspace(0, 12.0, 326) 19 | c = np.random.randint(0, 6, len(x)) 20 | data3 = { 21 | "x": x, 22 | "y": np.random.rand(len(x)) - 0.5, 23 | "z": np.random.rand(len(x)) - 0.5, 24 | "c": [c, x], 25 | "cs": np.random.rand(len(x)), 26 | "s": [np.random.rand(len(x)), np.random.rand(len(x))], 27 | "labels": c, 28 | } 29 | 30 | legend_labels = [(0, "A"), (1, "B"), (2, "C"), (3, "D"), (4, "E"), (5, "F")] 31 | 32 | df = pd.DataFrame.from_dict(data) 33 | df2 = pd.DataFrame.from_dict(data2) 34 | 35 | faerun.add_scatter( 36 | "sinus", 37 | df, 38 | shader="circle", 39 | point_scale=5.0, 40 | has_legend=True, 41 | legend_labels=[(0.0, "Low"), (50.0, "Inbetween"), (df["c"].max(), "High")], 42 | ) 43 | faerun.add_scatter( 44 | "cosinus", df2, shader="sphere", point_scale=5.0, colormap="jet", has_legend=True 45 | ) 46 | faerun.add_scatter( 47 | "categorical", 48 | data3, 49 | shader="sphere", 50 | point_scale=5.0, 51 | colormap=["Set1", "viridis"], 52 | has_legend=True, 53 | categorical=[True, False], 54 | legend_labels=legend_labels, 55 | series_title=["A", "B"], 56 | ondblclick=["console.log(labels[0])", "console.log('B:' + labels[0])"], 57 | ) 58 | 59 | with open("index.pickle", "wb+") as handle: 60 | pickle.dump(faerun.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 61 | 62 | file = open("index.pickle", "rb") 63 | obj = pickle.load(file) 64 | file.close() 65 | 66 | faerun.plot(template="default") 67 | -------------------------------------------------------------------------------- /examples/example_web.py: -------------------------------------------------------------------------------- 1 | import pickle 2 | import random 3 | import numpy as np 4 | import pandas as pd 5 | from faerun import Faerun, host 6 | from rdkit.Chem import AllChem 7 | from rdkit.Chem import rdMolDescriptors as Descriptors 8 | from sklearn.decomposition import PCA 9 | 10 | 11 | def get_fingerprint(in_smiles): 12 | results = [] 13 | smiles = [] 14 | for s in in_smiles: 15 | mol = AllChem.MolFromSmiles(s) 16 | if mol is not None: 17 | if mol.GetNumAtoms() > 100: 18 | continue 19 | mqn = Descriptors.MQNs_(mol) 20 | results.append(np.array(mqn)) 21 | smiles.append(s) 22 | 23 | return results, smiles 24 | 25 | 26 | def load(): 27 | drugbank = [] 28 | with open("drugbank.smi") as f: 29 | for line in f.readlines(): 30 | drugbank.append(line.split()[0].strip()) 31 | 32 | mqns, smiles = get_fingerprint(drugbank) 33 | mqns = np.array(mqns) 34 | 35 | pca = PCA(n_components=2) 36 | result = pca.fit_transform(mqns) 37 | return result, mqns, smiles 38 | 39 | 40 | def main(): 41 | coords, mqns, smiles = load() 42 | 43 | data = {"x": [], "y": [], "c": [], "s": [], "labels": smiles} 44 | 45 | for i, _ in enumerate(coords): 46 | data["x"].append(coords[i][0]) 47 | data["y"].append(coords[i][1]) 48 | data["c"].append(mqns[i][0]) 49 | data["s"].append(random.randint(1, 5)) 50 | 51 | df = pd.DataFrame.from_dict(data) 52 | 53 | faerun = Faerun() 54 | faerun.add_scatter( 55 | "drugbank", 56 | df, 57 | shader="smoothCircle", 58 | point_scale=2.0, 59 | colormap="jet", 60 | has_legend=True, 61 | categorical=False, 62 | ) 63 | 64 | with open("example.faerun", "wb+") as f: 65 | pickle.dump(faerun.create_python_data(), f, protocol=pickle.HIGHEST_PROTOCOL) 66 | 67 | info = ( 68 | "#Welcome to Fearun", 69 | "This is a small demonstration visualising drugs stored in [Drugbank](http://drugbank.ca) using coordinates generated by a PCA projection." 70 | "", 71 | "By the way, this info was generated using markdown, this means that you can easily:", 72 | "- Add lists", 73 | "- Build tables", 74 | "- Insert images and links", 75 | "- Add code examples", 76 | "- ...", 77 | ) 78 | 79 | host( 80 | "example.faerun", 81 | label_type="smiles", 82 | legend=True, 83 | theme="light", 84 | info="\n".join(info), 85 | ) 86 | 87 | 88 | if __name__ == "__main__": 89 | main() 90 | -------------------------------------------------------------------------------- /examples/example_web_3d.py: -------------------------------------------------------------------------------- 1 | import pickle 2 | import numpy as np 3 | import pandas as pd 4 | from faerun import Faerun, host 5 | from rdkit.Chem import AllChem 6 | from rdkit.Chem import rdMolDescriptors as Descriptors 7 | from sklearn.decomposition import PCA 8 | 9 | 10 | def get_fingerprint(in_smiles): 11 | results = [] 12 | smiles = [] 13 | for s in in_smiles: 14 | mol = AllChem.MolFromSmiles(s) 15 | if mol is not None: 16 | if mol.GetNumAtoms() > 100: 17 | continue 18 | mqn = Descriptors.MQNs_(mol) 19 | results.append(np.array(mqn)) 20 | smiles.append(s) 21 | 22 | return results, smiles 23 | 24 | 25 | def load(): 26 | drugbank = [] 27 | with open('drugbank.smi') as f: 28 | for line in f.readlines(): 29 | drugbank.append(line.split()[0].strip()) 30 | 31 | mqns, smiles = get_fingerprint(drugbank) 32 | mqns = np.array(mqns) 33 | 34 | pca = PCA(n_components=3) 35 | result = pca.fit_transform(mqns) 36 | return result, mqns, smiles 37 | 38 | def main(): 39 | coords, mqns, smiles = load() 40 | 41 | data = { 42 | 'x': [], 'y': [], 'z': [], 43 | 'c': [], 44 | 'labels': smiles 45 | } 46 | 47 | for i, _ in enumerate(coords): 48 | data['x'].append(coords[i][0]) 49 | data['y'].append(coords[i][1]) 50 | data['z'].append(coords[i][2]) 51 | data['c'].append(mqns[i][0]) 52 | 53 | df = pd.DataFrame.from_dict(data) 54 | 55 | faerun = Faerun() 56 | faerun.add_scatter('drugbank', df, shader='sphere', point_scale=5.0, colormap='jet', has_legend=True, categorical=False) 57 | 58 | with open('example.faerun', 'wb+') as f: 59 | pickle.dump(faerun.create_python_data(), f, protocol=pickle.HIGHEST_PROTOCOL) 60 | 61 | info = ('#Welcome to Fearun', 62 | 'This is a small demonstration visualising drugs stored in [Drugbank](http://drugbank.ca) using coordinates generated by a PCA projection.' 63 | '', 64 | 'By the way, this info was generated using markdown, this means that you can easily:', 65 | '- Add lists', 66 | '- Build tables', 67 | '- Insert images and links', 68 | '- Add code examples', 69 | '- ...' 70 | ) 71 | 72 | host('example.faerun', label_type='default', legend=True, theme='dark', 73 | info='\n'.join(info), view='free') 74 | 75 | if __name__ == '__main__': 76 | main() 77 | -------------------------------------------------------------------------------- /examples/index.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/reymond-group/faerun-python/f656b8d04bedd00f3f7943dfbe4b882f7bb72a6c/examples/index.pickle -------------------------------------------------------------------------------- /examples/tutorial.py: -------------------------------------------------------------------------------- 1 | import pickle 2 | import numpy as np 3 | from faerun import Faerun 4 | 5 | 6 | def main(): 7 | f = Faerun(clear_color="#222222", coords=True, view="front") 8 | 9 | x = np.linspace(0, 12.0, 326) 10 | y = np.sin(np.pi * x) 11 | z = np.cos(np.pi * x) 12 | c = np.random.randint(0, 2, len(x)) 13 | 14 | labels = [str(l) + "__Test" for l in c] 15 | 16 | data = {"x": x, "y": y, "z": z, "c": c, "labels": labels} 17 | 18 | f.add_scatter( 19 | "helix", 20 | data, 21 | shader="smoothCircle", 22 | colormap="Dark2", 23 | point_scale=5.0, 24 | categorical=True, 25 | has_legend=True, 26 | legend_labels=[(0, "Zero"), (1, "One")], 27 | selected_labels=["None", "Just a Small Test"], 28 | ) 29 | 30 | f.add_tree( 31 | "helixtree", {"from": [1, 5, 6, 7], "to": [2, 7, 8, 9]}, point_helper="helix" 32 | ) 33 | 34 | f.plot("helix") 35 | 36 | with open("helix.faerun", "wb+") as handle: 37 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 38 | 39 | 40 | if __name__ == "__main__": 41 | main() 42 | -------------------------------------------------------------------------------- /examples/tutorial_host.py: -------------------------------------------------------------------------------- 1 | import pickle 2 | import numpy as np 3 | from faerun import Faerun, host 4 | 5 | 6 | def main(): 7 | f = Faerun(title="faerun-example", clear_color="#222222", coords=False, view="free") 8 | 9 | x = np.linspace(0, 12.0, 326) 10 | y = np.sin(np.pi * x) 11 | z = np.cos(np.pi * x) 12 | c = np.random.randint(0, 2, len(x)) 13 | 14 | labels = [""] * len(c) 15 | 16 | for i, e in enumerate(c): 17 | labels[i] = str(e) + "__" + str(i % 20) 18 | 19 | data = {"x": x, "y": y, "z": z, "c": c, "labels": labels} 20 | 21 | f.add_scatter( 22 | "helix", 23 | data, 24 | shader="sphere", 25 | colormap="Dark2", 26 | point_scale=5.0, 27 | categorical=True, 28 | has_legend=True, 29 | legend_labels=[(0, "Zero"), (1, "One")], 30 | ) 31 | 32 | f.plot("helix") 33 | 34 | with open("helix.faerun", "wb+") as handle: 35 | pickle.dump(f.create_python_data(), handle, protocol=pickle.HIGHEST_PROTOCOL) 36 | 37 | def custom_label_formatter(label, index, name): 38 | return f"Example: {label} ({index}, {name})" 39 | 40 | def custom_link_formatter(label, index, name): 41 | return f"https://www.google.com/search?q={label}" 42 | 43 | info = ( 44 | "#Welcome to Fearun", 45 | "This is a small Faerun example." "", 46 | "Yay markdown! This means that you can easily:", 47 | "- Add lists", 48 | "- Build tables", 49 | "- Insert images and links", 50 | "- Add code examples", 51 | "- ...", 52 | ) 53 | 54 | host( 55 | "helix.faerun", 56 | label_type="default", 57 | title="Helix", 58 | theme="dark", 59 | label_formatter=custom_label_formatter, 60 | link_formatter=custom_link_formatter, 61 | info="\n".join(info), 62 | ) 63 | 64 | 65 | if __name__ == "__main__": 66 | main() 67 | -------------------------------------------------------------------------------- /faerun/__init__.py: -------------------------------------------------------------------------------- 1 | import os 2 | from faerun.faerun import Faerun 3 | from faerun.web import host 4 | 5 | try: 6 | from .plot import FaerunPlot 7 | except: 8 | ... 9 | 10 | _ROOT = os.path.abspath(os.path.dirname(__file__)) 11 | 12 | 13 | def get_asset(path): 14 | """Gets the path to the assets folder 15 | 16 | Arguments: 17 | path {str} -- The path of the asset within the asset folder 18 | 19 | Returns: 20 | str -- The full path to the asset 21 | """ 22 | return os.path.join(_ROOT, "assets", path) 23 | -------------------------------------------------------------------------------- /faerun/plot.py: -------------------------------------------------------------------------------- 1 | from cProfile import label 2 | from typing import Union, List, Iterable, Optional 3 | from tmap.core import TMAPEmbedding 4 | from faerun import Faerun 5 | from matplotlib.colors import Colormap 6 | 7 | 8 | class FaerunPlot: 9 | def __init__( 10 | self, 11 | clear_color: str = "#222222", 12 | coords: bool = False, 13 | view: str = "front", 14 | thumbnail_fixed: bool = False, 15 | impress: Optional[str] = None, 16 | ): 17 | if impress is None: 18 | impress = 'made with tmap
and faerun
source' 19 | 20 | self.f = Faerun( 21 | clear_color=clear_color, 22 | coords=coords, 23 | view=view, 24 | impress=impress, 25 | thumbnail_fixed=thumbnail_fixed, 26 | ) 27 | 28 | def add_series( 29 | self, 30 | x: Iterable, 31 | y: Iterable, 32 | c: Union[List, List[List]], 33 | z: Optional[Iterable] = None, 34 | labels: Optional[List] = None, 35 | cmap: Union[Union[str, Colormap], List[Union[str, Colormap]]] = "viridis", 36 | categorical: Union[bool, List[bool]] = False, 37 | shader: str = "smoothCircle", 38 | point_scale: float = 2.0, 39 | title: Optional[Union[str, List[str]]] = None, 40 | show_legend: bool = True, 41 | legend_title: str = "", 42 | name: Optional[str] = None, 43 | ) -> str: 44 | multiple_c = any(isinstance(el, list) for el in c) 45 | n_c = 1 46 | 47 | if multiple_c: 48 | n_c = len(c) 49 | 50 | if title is None: 51 | if multiple_c: 52 | title = [str(i + 1) for i in range(n_c)] 53 | else: 54 | title = "1" 55 | 56 | if name is None: 57 | name = "Series" + str(len(self.f.scatters) + 1) 58 | 59 | data = { 60 | "x": x, 61 | "y": y, 62 | "c": c, 63 | } 64 | 65 | if z is not None: 66 | data["z"] = z 67 | 68 | if labels is not None: 69 | data["labels"] = labels 70 | 71 | self.f.add_scatter( 72 | name, 73 | data, 74 | shader=shader, 75 | colormap=cmap, 76 | point_scale=point_scale, 77 | categorical=categorical, 78 | has_legend=show_legend, 79 | # legend_labels=[], 80 | # selected_labels=["SMILES", "Drugbank ID", "Name"], 81 | series_title=title, 82 | # max_legend_label=[ 83 | # None, 84 | # None, 85 | # None, 86 | # None, 87 | # None, 88 | # str(round(max(tpsa))), 89 | # str(round(max(logp))), 90 | # str(round(max(mw))), 91 | # str(round(max(h_acceptors))), 92 | # str(round(max(h_donors))), 93 | # str(round(max(ring_count))), 94 | # ], 95 | # min_legend_label=[ 96 | # None, 97 | # None, 98 | # None, 99 | # None, 100 | # None, 101 | # str(round(min(tpsa))), 102 | # str(round(min(logp))), 103 | # str(round(min(mw))), 104 | # str(round(min(h_acceptors))), 105 | # str(round(min(h_donors))), 106 | # str(round(min(ring_count))), 107 | # ], 108 | # title_index=2, 109 | legend_title=legend_title, 110 | ) 111 | 112 | return name 113 | 114 | def add_tree(self, target: str, s: Iterable, t: Iterable, color: str = "#666666"): 115 | self.f.add_tree( 116 | target + "Tree", {"from": s, "to": t}, point_helper=target, color=color 117 | ) 118 | 119 | def add_tmap_series( 120 | self, 121 | tmap_embedding: TMAPEmbedding, 122 | c: Union[List, List[List]], 123 | z: Optional[Iterable] = None, 124 | labels: Optional[List] = None, 125 | cmap: Union[str, Colormap] = "viridis", 126 | categorical: bool = False, 127 | shader: str = "smoothCircle", 128 | point_scale: float = 2.0, 129 | title: str = None, 130 | show_legend: bool = True, 131 | legend_title: str = "", 132 | name: Optional[str] = None, 133 | add_tree: bool = True, 134 | tree_color: str = "#888888", 135 | ): 136 | 137 | series_name = self.add_series( 138 | tmap_embedding.x, 139 | tmap_embedding.y, 140 | c=c, 141 | z=z, 142 | labels=labels, 143 | cmap=cmap, 144 | categorical=categorical, 145 | shader=shader, 146 | point_scale=point_scale, 147 | title=title, 148 | show_legend=show_legend, 149 | legend_title=legend_title, 150 | name=name, 151 | ) 152 | 153 | if add_tree: 154 | self.add_tree(series_name, tmap_embedding.s, tmap_embedding.t, tree_color) 155 | 156 | def save(self, name, template="default"): 157 | self.f.plot(name, template=template) 158 | -------------------------------------------------------------------------------- /notebook/faerun.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": 1, 6 | "metadata": {}, 7 | "outputs": [ 8 | { 9 | "data": { 10 | "text/html": [ 11 | "\n", 12 | " \n", 19 | " " 20 | ], 21 | "text/plain": [ 22 | "" 23 | ] 24 | }, 25 | "metadata": {}, 26 | "output_type": "display_data" 27 | }, 28 | { 29 | "data": { 30 | "text/html": [ 31 | "./sine.html
" 32 | ], 33 | "text/plain": [ 34 | "/home/daenu/Code/faerun-python/notebook/sine.html" 35 | ] 36 | }, 37 | "metadata": {}, 38 | "output_type": "display_data" 39 | } 40 | ], 41 | "source": [ 42 | "import numpy as np\n", 43 | "from faerun import Faerun\n", 44 | "from IPython.core.display import HTML\n", 45 | "from IPython.display import IFrame\n", 46 | "\n", 47 | "f = Faerun(view='front', clear_color='#fff')\n", 48 | "\n", 49 | "x = np.linspace(0, 12.0, 326)\n", 50 | "y = np.sin(np.pi * x)\n", 51 | "c = np.sin(np.pi * x)\n", 52 | "\n", 53 | "data = {'x': x, 'y': y, 'c': c, 'labels': c}\n", 54 | "\n", 55 | "f.add_scatter('Sine', data, shader='smoothCircle', colormap='viridis', point_scale=2.5,\n", 56 | " has_legend=True)\n", 57 | "\n", 58 | "f.plot('sine')" 59 | ] 60 | }, 61 | { 62 | "cell_type": "code", 63 | "execution_count": 2, 64 | "metadata": { 65 | "scrolled": false 66 | }, 67 | "outputs": [ 68 | { 69 | "data": { 70 | "text/html": [ 71 | "\n", 72 | " \n", 79 | " " 80 | ], 81 | "text/plain": [ 82 | "" 83 | ] 84 | }, 85 | "metadata": {}, 86 | "output_type": "display_data" 87 | }, 88 | { 89 | "data": { 90 | "text/html": [ 91 | "./helix.html
" 92 | ], 93 | "text/plain": [ 94 | "/home/daenu/Code/faerun-python/notebook/helix.html" 95 | ] 96 | }, 97 | "metadata": {}, 98 | "output_type": "display_data" 99 | } 100 | ], 101 | "source": [ 102 | "f = Faerun(view='free', clear_color='#262626')\n", 103 | "\n", 104 | "x = np.linspace(0, 12.0, 326)\n", 105 | "y = np.sin(np.pi * x)\n", 106 | "z = np.cos(np.pi * x)\n", 107 | "c = np.random.randint(0, 2, len(x))\n", 108 | "\n", 109 | "data = {'x': x, 'y': y, 'z': z, 'c': c, 'labels': c}\n", 110 | "\n", 111 | "f.add_scatter('Helix', data, shader='sphere', colormap='Dark2', point_scale=5.0,\n", 112 | " categorical=True, has_legend=True, legend_labels=[(1, 'One'), (0, 'Zero')])\n", 113 | "\n", 114 | "f.plot('helix')" 115 | ] 116 | }, 117 | { 118 | "cell_type": "code", 119 | "execution_count": null, 120 | "metadata": { 121 | "scrolled": true 122 | }, 123 | "outputs": [], 124 | "source": [] 125 | }, 126 | { 127 | "cell_type": "code", 128 | "execution_count": null, 129 | "metadata": {}, 130 | "outputs": [], 131 | "source": [] 132 | } 133 | ], 134 | "metadata": { 135 | "kernelspec": { 136 | "display_name": "Python 3", 137 | "language": "python", 138 | "name": "python3" 139 | }, 140 | "language_info": { 141 | "codemirror_mode": { 142 | "name": "ipython", 143 | "version": 3 144 | }, 145 | "file_extension": ".py", 146 | "mimetype": "text/x-python", 147 | "name": "python", 148 | "nbconvert_exporter": "python", 149 | "pygments_lexer": "ipython3", 150 | "version": "3.7.3" 151 | } 152 | }, 153 | "nbformat": 4, 154 | "nbformat_minor": 2 155 | } 156 | -------------------------------------------------------------------------------- /notebook/requirements.txt: -------------------------------------------------------------------------------- 1 | matplotlib>=3.0.2 2 | Jinja2>=2.10 3 | ujson>=1.35 4 | numpy>=1.15.4 5 | colour>=0.1.5 6 | CherryPy>=18.1.0 7 | pandas>=0.24.2 8 | faerun>=0.2.4 -------------------------------------------------------------------------------- /notebook/runtime.txt: -------------------------------------------------------------------------------- 1 | python-3.6 -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- 1 | matplotlib>=3.0.2 2 | Jinja2>=2.10 3 | ujson>=1.35 4 | numpy>=1.15.4 5 | colour>=0.1.5 6 | CherryPy>=18.1.0 7 | Sphinx>=1.8.3 8 | autodoc>=0.5.0 9 | sphinx-markdown-builder>=0.4.1 10 | sphinx-rtd-theme>=0.4.3 11 | pandas>=0.24.2 12 | tmap-viz>=1.0.16 -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import os 3 | from setuptools import setup 4 | from setuptools import Command 5 | from setuptools.command.test import test as TestCommand 6 | from datetime import datetime 7 | 8 | 9 | with open("README.md", "r") as fh: 10 | LONG_DESCRIPTION = fh.read() 11 | 12 | NAME = "faerun" 13 | VERSION = "0.4.6" 14 | AUTHOR = "Daniel Probst" 15 | DESCRIPTION = "A python package for generating interactive views of chemical spaces." 16 | URL = "https://github.com/reymond-group/faerun-python" 17 | REQUIRED_PYTHON_VERSION = (3, 0) 18 | PACKAGES = ["faerun"] 19 | INSTALL_DEPENDENCIES = [ 20 | "matplotlib>=3.0.2", 21 | "Jinja2>=2.10", 22 | "ujson>=1.35", 23 | "numpy>=1.15.4", 24 | "colour>=0.1.5", 25 | "CherryPy>=18.1.0", 26 | "pandas>=0.24.2", 27 | ] 28 | SETUP_DEPENDENCIES = [] 29 | TEST_DEPENDENCIES = ["pytest"] 30 | EXTRA_DEPENDENCIES = {"dev": ["pytest"]} 31 | 32 | if sys.version_info < REQUIRED_PYTHON_VERSION: 33 | sys.exit("Python >= 3.0 is required. Your version:\n" + sys.version) 34 | 35 | 36 | class PyTest(TestCommand): 37 | """ 38 | Use pytest to run tests 39 | """ 40 | 41 | user_options = [("pytest-args=", "a", "Arguments to pass into py.test")] 42 | 43 | def initialize_options(self): 44 | TestCommand.initialize_options(self) 45 | self.pytest_args = [] 46 | 47 | def finalize_options(self): 48 | TestCommand.finalize_options(self) 49 | self.test_args = [] 50 | self.test_suite = True 51 | 52 | def run_tests(self): 53 | import pytest 54 | 55 | errno = pytest.main(self.pytest_args) 56 | sys.exit(errno) 57 | 58 | 59 | setup( 60 | name=NAME, 61 | description=DESCRIPTION, 62 | long_description=LONG_DESCRIPTION, 63 | long_description_content_type="text/markdown", 64 | url=URL, 65 | version=VERSION, 66 | author=AUTHOR, 67 | packages=PACKAGES, 68 | include_package_data=True, 69 | python_requires=">=3", 70 | install_requires=INSTALL_DEPENDENCIES, 71 | setup_requires=SETUP_DEPENDENCIES, 72 | tests_require=TEST_DEPENDENCIES, 73 | extras_require=EXTRA_DEPENDENCIES, 74 | cmdclass={"test": PyTest}, 75 | ) 76 | --------------------------------------------------------------------------------