Adds SA, renames drd3

Author: miguelgondu

docs/protein-optimization/_toc.yml

@@ -26,6 +26,7 @@ parts:
       - file: using_poli/objective_repository/rdkit_logp.md
       - file: using_poli/objective_repository/ddr3_docking.md
       - file: using_poli/objective_repository/penalized_logp_lambo.md
+      - file: using_poli/objective_repository/sa_tdc.md
       - file: using_poli/objective_repository/foldx_stability.md
       - file: using_poli/objective_repository/foldx_sasa.md
       - file: using_poli/objective_repository/super_mario_bros.md

docs/protein-optimization/index.md

@@ -54,12 +54,18 @@ Computing the log-quotient of solubilities using `RDKit`.
 Computing the penalized log-quotient of solubilities using `lambo`'s implementation.
 :::
 
-:::{grid-item-card} DDR3 (or 3pbl) docking (using `tdc`)
-:link: ./using_poli/objective_repository/ddr3_docking.html
+:::{grid-item-card} DRD3 (or 3pbl) docking (using `tdc`)
+:link: ./using_poli/objective_repository/drd3_docking.html
 :columns: 6
 A wrapper around the Therapeutics Data Commons implmenetation of `3pbl` docking.
 :::
 
+:::{grid-item-card} Synthetic Accessibility (SA, using `tdc`)
+:link: ./using_poli/objective_repository/sa_tdc.html
+:columns: 6
+A wrapper around the Therapeutics Data Commons implmenetation of the synthetic accessibility oracle.
+:::
+
 ::::
 
 ### Proteins
@@ -160,10 +166,3 @@ How to contribute a new black-box optimization algorithm.
 
 ::::
 
-
-<!-- ## References
-
-:::{bibliography}
-:style: alpha
-
-::: -->

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

@@ -53,6 +53,12 @@ Computing the penalized log-quotient of solubilities using `lambo`'s implementat
 A wrapper around the Therapeutics Data Commons implmenetation of 3pbl docking.
 :::
 
+:::{grid-item-card} Synthetic Accessibility (SA, using `tdc`)
+:link: ./using_poli/objective_repository/sa_tdc.html
+:columns: 6
+A wrapper around the Therapeutics Data Commons implmenetation of the synthetic accessibility oracle.
+:::
+
 :::{grid-item-card} TDC oracles [WIP]
 :link: ./using_poli/objective_repository/tdc_oracles.html
 :columns: 6

docs/protein-optimization/using_poli/objective_repository/ddr3_docking.md renamed to docs/protein-optimization/using_poli/objective_repository/drd3_docking.md

@@ -1,4 +1,4 @@
-# DDR3 docking (using TDC)
+# DRD3 docking (using TDC)
 
 ![Type of objective function: discrete](https://img.shields.io/badge/Type-discrete_inputs-blue)
 ![Environment to run this objective function: poli lambo](https://img.shields.io/badge/Environment-poli____lambo-teal
@@ -54,7 +54,7 @@ This can easily be done by running
 
 ```bash
 # From the base of the poli repo
-conda env create --file src/poli/objective_repository/ddr3_docking/environment.yml
+conda env create --file src/poli/objective_repository/drd3_docking/environment.yml
 ```
 
 This particular example _doesn't_ need to have the `lambo` package installed.
@@ -98,7 +98,7 @@ from poli import objective_factory
 
 # How to create
 problem_info, f, x0, y0, run_info = objective_factory.create(
-    name="ddr3_docking",
+    name="drd3_docking",
     force_register=True
 )
 

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

@@ -0,0 +1,62 @@
+# Synthetic Accessibility (using TDC)
+
+![Type of objective function: discrete](https://img.shields.io/badge/Type-discrete_inputs-blue)
+![Environment to run this objective function: poli lambo](https://img.shields.io/badge/Environment-poli____lambo-teal
+)
+
+## About
+
+This objective function computes the synthetic accesibility of a small molecule using [the Therapeutics Data Common's oracle](https://tdcommons.ai/functions/oracles/#synthetic-accessibility-sa) {cite:p}`huang:TDC:2021` (which uses RDKit internally).
+
+## Prerequisites
+
+### Create the `poli__lambo` environment
+
+#### Create the environment from the yml file
+
+This can easily be done by running
+
+```bash
+# From the base of the poli repo
+conda env create --file src/poli/objective_repository/sa_tdc/environment.yml
+```
+
+This particular example _doesn't_ need to have the `lambo` package installed.
+
+## How to run
+
+You can only run this objective function either in the `poli__lambo` environment, or as an isolated process (which runs this environment underneath).
+
+:::{warning}
+Running this objective function will create an `./oracle` folder on your working directory, where it will download the relevant files for the oracle to work.
+:::
+
+::::{tab-set}
+
+:::{tab-item} (Isolated) in the `poli__lambo` environment
+
+After the setup described above, you can simply run the following code from 
+
+```python
+from pathlib import Path
+
+import numpy as np
+
+from poli import objective_factory
+
+# How to create
+problem_info, f, x0, y0, run_info = objective_factory.create(
+    name="sa_tdc",
+    force_register=True
+)
+
+# Example input:
+print(x0)  # [['C' 'C' 'N' 'C' ...]]
+
+# Querying:
+print(y0)  # [[2.8548]]
+```
+
+:::
+
+::::