├── CHANGELOG.md ├── CITATION.cff ├── LICENSE ├── MANIFEST.in ├── Moment_Comparison.ipynb ├── README.md ├── docs ├── .buildinfo ├── .nojekyll ├── Makefile ├── _images │ ├── getting_started_10_0.png │ ├── getting_started_11_1.png │ ├── getting_started_14_0.png │ ├── getting_started_15_0.png │ ├── getting_started_16_0.png │ ├── getting_started_17_0.png │ ├── getting_started_18_0.png │ ├── getting_started_8_0.png │ └── getting_started_9_0.png ├── _modules │ ├── geometricus │ │ ├── geometricus.html │ │ ├── moment_utility.html │ │ ├── protein_utility.html │ │ └── utility.html │ ├── index.html │ └── typing.html ├── _sources │ ├── api │ │ ├── geometricus.rst.txt │ │ └── modules.rst.txt │ ├── getting_started.ipynb.txt │ ├── getting_started.rst.txt │ ├── index.rst.txt │ └── install.rst.txt ├── _static │ ├── alabaster.css │ ├── basic.css │ ├── custom.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── geometricus_logo.png │ ├── jquery-3.4.1.js │ ├── jquery-3.5.1.js │ ├── jquery.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── sphinx_highlight.js │ ├── underscore-1.13.1.js │ ├── underscore-1.3.1.js │ └── underscore.js ├── api │ ├── geometricus.html │ └── modules.html ├── build │ ├── doctrees │ │ ├── api │ │ │ ├── geometricus.doctree │ │ │ └── modules.doctree │ │ ├── environment.pickle │ │ ├── getting_started.doctree │ │ ├── index.doctree │ │ ├── install.doctree │ │ └── nbsphinx │ │ │ ├── getting_started.ipynb │ │ │ ├── getting_started_11_1.png │ │ │ ├── getting_started_17_0.png │ │ │ └── getting_started_18_0.png │ └── html │ │ ├── .buildinfo │ │ ├── .nojekyll │ │ ├── _images │ │ ├── getting_started_11_1.png │ │ ├── getting_started_17_0.png │ │ └── getting_started_18_0.png │ │ ├── _modules │ │ ├── geometricus │ │ │ ├── geometricus.html │ │ │ ├── moment_utility.html │ │ │ └── protein_utility.html │ │ ├── index.html │ │ └── typing.html │ │ ├── _sources │ │ ├── api │ │ │ ├── geometricus.rst.txt │ │ │ └── modules.rst.txt │ │ ├── getting_started.ipynb.txt │ │ ├── getting_started.rst.txt │ │ ├── index.rst.txt │ │ └── install.rst.txt │ │ ├── _static │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── jquery-3.4.1.js │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── api │ │ ├── geometricus.html │ │ └── modules.html │ │ ├── genindex.html │ │ ├── getting_started.html │ │ ├── getting_started.ipynb │ │ ├── index.html │ │ ├── install.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ └── searchindex.js ├── genindex.html ├── geometricus.geometricus.rst ├── geometricus.model_utility.rst ├── geometricus.moment_invariants.rst ├── geometricus.moment_utility.rst ├── geometricus.protein_utility.rst ├── geometricus.rst ├── getting_started.html ├── getting_started.ipynb ├── index.html ├── install.html ├── make.bat ├── modules.rst ├── objects.inv ├── py-modindex.html ├── search.html ├── searchindex.js └── source │ ├── api │ ├── geometricus.rst │ └── modules.rst │ ├── conf.py │ ├── getting_started.ipynb │ ├── index.rst │ └── install.rst ├── example_data └── MAPK_KLIFS.tsv ├── geometricus ├── __init__.py ├── geometricus.py ├── istarmap.py ├── model_utility.py ├── models │ └── ShapemerLearn_RADIUS-5_RADIUS-10_KMER-8_KMER-16_68_32_10.pt ├── moment_invariants.py ├── moment_utility.py ├── protein_utility.py └── sampling.py ├── geometricus_logo.png ├── notebooks └── getting_started.ipynb ├── pyproject.toml ├── setup.cfg ├── setup.py └── training ├── 1-generate-training-data.ipynb └── 2-train-shapemerization.ipynb /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/CITATION.cff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/LICENSE -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | recursive-include geometricus/models * -------------------------------------------------------------------------------- /Moment_Comparison.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/Moment_Comparison.ipynb -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/README.md -------------------------------------------------------------------------------- /docs/.buildinfo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/.buildinfo -------------------------------------------------------------------------------- /docs/.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/_images/getting_started_10_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_10_0.png -------------------------------------------------------------------------------- /docs/_images/getting_started_11_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_11_1.png -------------------------------------------------------------------------------- /docs/_images/getting_started_14_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_14_0.png -------------------------------------------------------------------------------- /docs/_images/getting_started_15_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_15_0.png -------------------------------------------------------------------------------- /docs/_images/getting_started_16_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_16_0.png -------------------------------------------------------------------------------- /docs/_images/getting_started_17_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_17_0.png -------------------------------------------------------------------------------- /docs/_images/getting_started_18_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_18_0.png -------------------------------------------------------------------------------- /docs/_images/getting_started_8_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_8_0.png -------------------------------------------------------------------------------- /docs/_images/getting_started_9_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_images/getting_started_9_0.png -------------------------------------------------------------------------------- /docs/_modules/geometricus/geometricus.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_modules/geometricus/geometricus.html -------------------------------------------------------------------------------- /docs/_modules/geometricus/moment_utility.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_modules/geometricus/moment_utility.html -------------------------------------------------------------------------------- /docs/_modules/geometricus/protein_utility.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_modules/geometricus/protein_utility.html -------------------------------------------------------------------------------- /docs/_modules/geometricus/utility.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_modules/geometricus/utility.html -------------------------------------------------------------------------------- /docs/_modules/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_modules/index.html -------------------------------------------------------------------------------- /docs/_modules/typing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_modules/typing.html -------------------------------------------------------------------------------- /docs/_sources/api/geometricus.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_sources/api/geometricus.rst.txt -------------------------------------------------------------------------------- /docs/_sources/api/modules.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_sources/api/modules.rst.txt -------------------------------------------------------------------------------- /docs/_sources/getting_started.ipynb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_sources/getting_started.ipynb.txt -------------------------------------------------------------------------------- /docs/_sources/getting_started.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_sources/getting_started.rst.txt -------------------------------------------------------------------------------- /docs/_sources/index.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_sources/index.rst.txt -------------------------------------------------------------------------------- /docs/_sources/install.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_sources/install.rst.txt -------------------------------------------------------------------------------- /docs/_static/alabaster.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/alabaster.css -------------------------------------------------------------------------------- /docs/_static/basic.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/basic.css -------------------------------------------------------------------------------- /docs/_static/custom.css: -------------------------------------------------------------------------------- 1 | /* This file intentionally left blank. */ 2 | -------------------------------------------------------------------------------- /docs/_static/doctools.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/doctools.js -------------------------------------------------------------------------------- /docs/_static/documentation_options.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/documentation_options.js -------------------------------------------------------------------------------- /docs/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/file.png -------------------------------------------------------------------------------- /docs/_static/geometricus_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/geometricus_logo.png -------------------------------------------------------------------------------- /docs/_static/jquery-3.4.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/jquery-3.4.1.js -------------------------------------------------------------------------------- /docs/_static/jquery-3.5.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/jquery-3.5.1.js -------------------------------------------------------------------------------- /docs/_static/jquery.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/jquery.js -------------------------------------------------------------------------------- /docs/_static/language_data.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/language_data.js -------------------------------------------------------------------------------- /docs/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/minus.png -------------------------------------------------------------------------------- /docs/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/plus.png -------------------------------------------------------------------------------- /docs/_static/pygments.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/pygments.css -------------------------------------------------------------------------------- /docs/_static/searchtools.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/searchtools.js -------------------------------------------------------------------------------- /docs/_static/sphinx_highlight.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/sphinx_highlight.js -------------------------------------------------------------------------------- /docs/_static/underscore-1.13.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/underscore-1.13.1.js -------------------------------------------------------------------------------- /docs/_static/underscore-1.3.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/underscore-1.3.1.js -------------------------------------------------------------------------------- /docs/_static/underscore.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/_static/underscore.js -------------------------------------------------------------------------------- /docs/api/geometricus.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/api/geometricus.html -------------------------------------------------------------------------------- /docs/api/modules.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/api/modules.html -------------------------------------------------------------------------------- /docs/build/doctrees/api/geometricus.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/api/geometricus.doctree -------------------------------------------------------------------------------- /docs/build/doctrees/api/modules.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/api/modules.doctree -------------------------------------------------------------------------------- /docs/build/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/environment.pickle -------------------------------------------------------------------------------- /docs/build/doctrees/getting_started.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/getting_started.doctree -------------------------------------------------------------------------------- /docs/build/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/index.doctree -------------------------------------------------------------------------------- /docs/build/doctrees/install.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/install.doctree -------------------------------------------------------------------------------- /docs/build/doctrees/nbsphinx/getting_started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/nbsphinx/getting_started.ipynb -------------------------------------------------------------------------------- /docs/build/doctrees/nbsphinx/getting_started_11_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/nbsphinx/getting_started_11_1.png -------------------------------------------------------------------------------- /docs/build/doctrees/nbsphinx/getting_started_17_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/nbsphinx/getting_started_17_0.png -------------------------------------------------------------------------------- /docs/build/doctrees/nbsphinx/getting_started_18_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/doctrees/nbsphinx/getting_started_18_0.png -------------------------------------------------------------------------------- /docs/build/html/.buildinfo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/.buildinfo -------------------------------------------------------------------------------- /docs/build/html/.nojekyll: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /docs/build/html/_images/getting_started_11_1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_images/getting_started_11_1.png -------------------------------------------------------------------------------- /docs/build/html/_images/getting_started_17_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_images/getting_started_17_0.png -------------------------------------------------------------------------------- /docs/build/html/_images/getting_started_18_0.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_images/getting_started_18_0.png -------------------------------------------------------------------------------- /docs/build/html/_modules/geometricus/geometricus.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_modules/geometricus/geometricus.html -------------------------------------------------------------------------------- /docs/build/html/_modules/geometricus/moment_utility.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_modules/geometricus/moment_utility.html -------------------------------------------------------------------------------- /docs/build/html/_modules/geometricus/protein_utility.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_modules/geometricus/protein_utility.html -------------------------------------------------------------------------------- /docs/build/html/_modules/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_modules/index.html -------------------------------------------------------------------------------- /docs/build/html/_modules/typing.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_modules/typing.html -------------------------------------------------------------------------------- /docs/build/html/_sources/api/geometricus.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_sources/api/geometricus.rst.txt -------------------------------------------------------------------------------- /docs/build/html/_sources/api/modules.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_sources/api/modules.rst.txt -------------------------------------------------------------------------------- /docs/build/html/_sources/getting_started.ipynb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_sources/getting_started.ipynb.txt -------------------------------------------------------------------------------- /docs/build/html/_sources/getting_started.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_sources/getting_started.rst.txt -------------------------------------------------------------------------------- /docs/build/html/_sources/index.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_sources/index.rst.txt -------------------------------------------------------------------------------- /docs/build/html/_sources/install.rst.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_sources/install.rst.txt -------------------------------------------------------------------------------- /docs/build/html/_static/alabaster.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/alabaster.css -------------------------------------------------------------------------------- /docs/build/html/_static/basic.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/basic.css -------------------------------------------------------------------------------- /docs/build/html/_static/custom.css: -------------------------------------------------------------------------------- 1 | /* This file intentionally left blank. */ 2 | -------------------------------------------------------------------------------- /docs/build/html/_static/doctools.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/doctools.js -------------------------------------------------------------------------------- /docs/build/html/_static/documentation_options.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/documentation_options.js -------------------------------------------------------------------------------- /docs/build/html/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/file.png -------------------------------------------------------------------------------- /docs/build/html/_static/jquery-3.4.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/jquery-3.4.1.js -------------------------------------------------------------------------------- /docs/build/html/_static/jquery-3.5.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/jquery-3.5.1.js -------------------------------------------------------------------------------- /docs/build/html/_static/jquery.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/jquery.js -------------------------------------------------------------------------------- /docs/build/html/_static/language_data.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/language_data.js -------------------------------------------------------------------------------- /docs/build/html/_static/minus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/minus.png -------------------------------------------------------------------------------- /docs/build/html/_static/plus.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/plus.png -------------------------------------------------------------------------------- /docs/build/html/_static/pygments.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/pygments.css -------------------------------------------------------------------------------- /docs/build/html/_static/searchtools.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/searchtools.js -------------------------------------------------------------------------------- /docs/build/html/_static/underscore-1.3.1.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/underscore-1.3.1.js -------------------------------------------------------------------------------- /docs/build/html/_static/underscore.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/_static/underscore.js -------------------------------------------------------------------------------- /docs/build/html/api/geometricus.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/api/geometricus.html -------------------------------------------------------------------------------- /docs/build/html/api/modules.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/api/modules.html -------------------------------------------------------------------------------- /docs/build/html/genindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/genindex.html -------------------------------------------------------------------------------- /docs/build/html/getting_started.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/getting_started.html -------------------------------------------------------------------------------- /docs/build/html/getting_started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/getting_started.ipynb -------------------------------------------------------------------------------- /docs/build/html/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/index.html -------------------------------------------------------------------------------- /docs/build/html/install.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/install.html -------------------------------------------------------------------------------- /docs/build/html/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/objects.inv -------------------------------------------------------------------------------- /docs/build/html/py-modindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/py-modindex.html -------------------------------------------------------------------------------- /docs/build/html/search.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/search.html -------------------------------------------------------------------------------- /docs/build/html/searchindex.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/build/html/searchindex.js -------------------------------------------------------------------------------- /docs/genindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/genindex.html -------------------------------------------------------------------------------- /docs/geometricus.geometricus.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/geometricus.geometricus.rst -------------------------------------------------------------------------------- /docs/geometricus.model_utility.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/geometricus.model_utility.rst -------------------------------------------------------------------------------- /docs/geometricus.moment_invariants.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/geometricus.moment_invariants.rst -------------------------------------------------------------------------------- /docs/geometricus.moment_utility.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/geometricus.moment_utility.rst -------------------------------------------------------------------------------- /docs/geometricus.protein_utility.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/geometricus.protein_utility.rst -------------------------------------------------------------------------------- /docs/geometricus.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/geometricus.rst -------------------------------------------------------------------------------- /docs/getting_started.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/getting_started.html -------------------------------------------------------------------------------- /docs/getting_started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/getting_started.ipynb -------------------------------------------------------------------------------- /docs/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/index.html -------------------------------------------------------------------------------- /docs/install.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/install.html -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/modules.rst -------------------------------------------------------------------------------- /docs/objects.inv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/objects.inv -------------------------------------------------------------------------------- /docs/py-modindex.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/py-modindex.html -------------------------------------------------------------------------------- /docs/search.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/search.html -------------------------------------------------------------------------------- /docs/searchindex.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/searchindex.js -------------------------------------------------------------------------------- /docs/source/api/geometricus.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/source/api/geometricus.rst -------------------------------------------------------------------------------- /docs/source/api/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/source/api/modules.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/getting_started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/source/getting_started.ipynb -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/install.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/docs/source/install.rst -------------------------------------------------------------------------------- /example_data/MAPK_KLIFS.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/example_data/MAPK_KLIFS.tsv -------------------------------------------------------------------------------- /geometricus/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/__init__.py -------------------------------------------------------------------------------- /geometricus/geometricus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/geometricus.py -------------------------------------------------------------------------------- /geometricus/istarmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/istarmap.py -------------------------------------------------------------------------------- /geometricus/model_utility.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/model_utility.py -------------------------------------------------------------------------------- /geometricus/models/ShapemerLearn_RADIUS-5_RADIUS-10_KMER-8_KMER-16_68_32_10.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/models/ShapemerLearn_RADIUS-5_RADIUS-10_KMER-8_KMER-16_68_32_10.pt -------------------------------------------------------------------------------- /geometricus/moment_invariants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/moment_invariants.py -------------------------------------------------------------------------------- /geometricus/moment_utility.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/moment_utility.py -------------------------------------------------------------------------------- /geometricus/protein_utility.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/protein_utility.py -------------------------------------------------------------------------------- /geometricus/sampling.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus/sampling.py -------------------------------------------------------------------------------- /geometricus_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/geometricus_logo.png -------------------------------------------------------------------------------- /notebooks/getting_started.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/notebooks/getting_started.ipynb -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/pyproject.toml -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/setup.cfg -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/setup.py -------------------------------------------------------------------------------- /training/1-generate-training-data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/training/1-generate-training-data.ipynb -------------------------------------------------------------------------------- /training/2-train-shapemerization.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/TurtleTools/geometricus/HEAD/training/2-train-shapemerization.ipynb --------------------------------------------------------------------------------