Adds a page with all the objectives

Author: miguelgondu

docs/protein-optimization/index.md

@@ -9,7 +9,7 @@ Our promise is: if you can run your objective function reliably in a `conda` env
 
 ## Black-box objective functions
 
-These are some objective functions available on `poli`. **For a full list**, check [getting started](./getting_started/getting_started.md).
+These are some objective functions available on `poli`. **For a full list**, [check here](./using_poli/objective_repository/all_objectives.md).
 
 
 ### Toy problems
@@ -81,18 +81,7 @@ Rapid Stability Predictions of single mutations from a wildtype. [WIP]
 
 ::::
 
-### Other
 
-::::{grid}
-:gutter: 3
-
-:::{grid-item-card} Mario jumps
-:link: ./using_poli/objective_repository/super_mario_bros.html
-:columns: 6
-Optimizing the number of jumps on a Super Mario Bros level
-:::
-
-::::
 ## Black-box optimization algorithms
 
 On top of `poli`, we provide `poli-baselines`, a collection of **black-box optimization algorithms** (focusing especially on *discrete* sequences). Examples include
@@ -136,10 +125,6 @@ Graph Genetic Algorithms for small molecules. [WIP]
 
 A good place to start is the next chapter! [Go to Getting Started](./getting_started/getting_started.md).
 
-<!-- ## Contents of the book
-
-```{tableofcontents}
-``` -->
 
 ## Contribute problems or solvers
 

docs/protein-optimization/using_poli/objective_repository/all_objectives.md

@@ -0,0 +1,92 @@
+# All objective functions
+
+These are all the objective functions available on `poli`. Click on one of them to get a minimal working example of how to use it.
+
+
+### Toy problems
+
+::::{grid}
+:gutter: 3
+
+:::{grid-item-card} White noise
+:link: ./using_poli/objective_repository/white_noise.html
+:columns: 6
+White noise drawn from a unit Gaussian
+:::
+
+:::{grid-item-card} Aloha
+:link: ./using_poli/objective_repository/aloha.html
+:columns: 6
+A toy example about optimizing 5-letter words to spell "ALOHA"
+:::
+
+::::
+
+### Small molecules
+
+Most of our problems are based on the [PMO]() benchmark, by Gao et al [TODO: add cite].
+
+::::{grid}
+:gutter: 3
+
+:::{grid-item-card} Quantitative Estimate of Druglikeness (QED)
+:link: ./using_poli/objective_repository/rdkit_qed.html
+:columns: 6
+Computing the QED using `RDKit`.
+:::
+
+:::{grid-item-card} Log-solubility (LogP)
+:link: ./using_poli/objective_repository/rdkit_logp.html
+:columns: 6
+Computing the log-quotient of solubilities using `RDKit`.
+:::
+
+:::{grid-item-card} TDC oracles [WIP]
+:link: ./using_poli/objective_repository/tdc_oracles.html
+:columns: 6
+Some of the oracles provided by the Therapeutics Data Commons. [WIP]
+:::
+
+:::{grid-item-card} GuacaMol [WIP]
+:link: ./using_poli/objective_repository/tdc_oracles.html
+:columns: 6
+Some of the oracles provided by GuacaMol. [WIP]
+:::
+
+::::
+
+### Proteins
+
+::::{grid}
+:gutter: 3
+
+:::{grid-item-card} Protein Stability (using `foldx`)
+:link: ./using_poli/objective_repository/foldx_stability.html
+:columns: 6
+Stability of mutations of a wildtype using `foldx`
+:::
+
+:::{grid-item-card} Protein SASA score (using `foldx`)
+:link: ./using_poli/objective_repository/foldx_sasa.html
+:columns: 6
+Solvent accessibility of mutations of a wildtype using `foldx`
+:::
+
+:::{grid-item-card} Protein Stability (using `RaSP`) [WIP]
+:link: ./using_poli/objective_repository/RaSP.html
+:columns: 6
+Rapid Stability Predictions of single mutations from a wildtype. [WIP]
+:::
+
+::::
+
+### Other
+
+::::{grid}
+:gutter: 3
+
+:::{grid-item-card} Mario jumps
+:link: ./using_poli/objective_repository/super_mario_bros.html
+:columns: 6
+Optimizing the number of jumps on a Super Mario Bros level
+:::