Initial commit, writes a chapter on optimizing energy in single mutants

Author: miguelgondu

.gitignore

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+.DS_Store
+
+# Example's working directory
+examples/understanding_foldx/tmp
+docs/protein-optimization/understanding_foldx/01-single-mutation-using-foldx/tmp/*
+!docs/protein-optimization/understanding_foldx/01-single-mutation-using-foldx/tmp/101m_Repair.pdb
+!docs/protein-optimization/understanding_foldx/01-single-mutation-using-foldx/tmp/101m.pdb
+!docs/protein-optimization/understanding_foldx/01-single-mutation-using-foldx/tmp/Raw_101m_Repair.fxout
+!docs/protein-optimization/understanding_foldx/01-single-mutation-using-foldx/tmp/individual_list.txt
+
+# Build directory
+docs/protein-optimization/_build

docs/protein-optimization/_config.yml

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+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: Protein optimization
+author: Miguel González-Duque
+logo: logo_protein_opt.png
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.tex
+
+# Add a bibtex file so that we can create citations
+bibtex_bibfiles:
+  - references.bib
+
+# Information about where the book exists on the web
+# repository:
+#   url: https://github.com/executablebooks/jupyter-book  # Online location of your book
+#   path_to_book: docs  # Optional path to your book, relative to the repository root
+#   branch: master  # Which branch of the repository should be used when creating links (optional)
+
+# # Add GitHub buttons to your book
+# # See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+# html:
+#   use_issues_button: true
+#   use_repository_button: true

docs/protein-optimization/_toc.yml

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+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: index.md
+parts:
+  - caption: Understanding FoldX
+    numbered: true
+    chapters:
+    - file: understanding_foldx/00-installing-foldx.md
+    - file: understanding_foldx/01-single-mutation-using-foldx/index.ipynb

docs/protein-optimization/index.md

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+# Tutorials on protein optimization
+
+This book contains documentation on how to measure protein's properties (e.g. stability, solubility...) using tools like FoldX. [Work in Progress]
+
+```{tableofcontents}
+```

docs/protein-optimization/logo_protein_opt.png

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+---
+---
+
+@article{stanton2022accelerating,
+  title={Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders},
+  author={Stanton, Samuel and Maddox, Wesley and Gruver, Nate and Maffettone, Phillip and Delaney, Emily and Greenside, Peyton and Wilson, Andrew Gordon},
+  journal={arXiv preprint arXiv:2203.12742},
+  year={2022}
+}

docs/protein-optimization/references.bib

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+jupyter-book
+matplotlib
+numpy
+biopython
+pandas

docs/protein-optimization/requirements.txt

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+# Installing FoldX
+
+[TODO: write]