Add documentation

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/build/.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 8c850b00a149de6b99241066413f4df7
+tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/_sources/coconut.Externals.rst.txt

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+coconut.Externals package
+=========================
+
+Module contents
+---------------
+
+.. automodule:: coconut.Externals
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/_sources/coconut.example.rst.txt

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+coconut.example package
+=======================
+
+Module contents
+---------------
+
+.. automodule:: coconut.example
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/_sources/coconut.rst.txt

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+coconut package
+===============
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   coconut.Externals
+   coconut.example
+   coconut.src
+
+Submodules
+----------
+
+coconut.version module
+----------------------
+
+.. automodule:: coconut.version
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: coconut
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/_sources/coconut.src.Core.rst.txt

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+coconut.src.Core package
+========================
+
+Submodules
+----------
+
+coconut.src.Core.BaseScores module
+----------------------------------
+
+.. automodule:: coconut.src.Core.BaseScores
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.CoiledCoilAlignClass module
+--------------------------------------------
+
+.. automodule:: coconut.src.Core.CoiledCoilAlignClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.CoiledCoilClass module
+---------------------------------------
+
+.. automodule:: coconut.src.Core.CoiledCoilClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.ExtendCCClass module
+-------------------------------------
+
+.. automodule:: coconut.src.Core.ExtendCCClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.InputClass module
+----------------------------------
+
+.. automodule:: coconut.src.Core.InputClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.PairCoilClass module
+-------------------------------------
+
+.. automodule:: coconut.src.Core.PairCoilClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.ScoringClass module
+------------------------------------
+
+.. automodule:: coconut.src.Core.ScoringClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.SlidingWindowsClass module
+-------------------------------------------
+
+.. automodule:: coconut.src.Core.SlidingWindowsClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.ml\_prediction module
+--------------------------------------
+
+.. automodule:: coconut.src.Core.ml_prediction
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.predict\_cc module
+-----------------------------------
+
+.. automodule:: coconut.src.Core.predict_cc
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.read\_CC\_properties module
+--------------------------------------------
+
+.. automodule:: coconut.src.Core.read_CC_properties
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.read\_frequency\_scores module
+-----------------------------------------------
+
+.. automodule:: coconut.src.Core.read_frequency_scores
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.test\_model\_database module
+---------------------------------------------
+
+.. automodule:: coconut.src.Core.test_model_database
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+coconut.src.Core.train\_models module
+-------------------------------------
+
+.. automodule:: coconut.src.Core.train_models
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: coconut.src.Core
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/_sources/coconut.src.Models.rst.txt

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+coconut.src.Models package
+==========================
+
+Submodules
+----------
+
+coconut.src.Models.ModelClass module
+------------------------------------
+
+.. automodule:: coconut.src.Models.ModelClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: coconut.src.Models
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/_sources/coconut.src.rst.txt

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+coconut.src package
+===================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   coconut.src.Core
+   coconut.src.Models
+
+Submodules
+----------
+
+coconut.src.CoconutClass module
+-------------------------------
+
+.. automodule:: coconut.src.CoconutClass
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: coconut.src
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/build/_sources/index.rst.txt

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+.. COCONUT documentation master file, created by
+   sphinx-quickstart on Sun Mar 24 17:44:49 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to COCONUT's documentation!
+===================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/build/_sources/modules.rst.txt

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+coconut
+=======
+
+.. toctree::
+   :maxdepth: 4
+
+   coconut