Merge pull request #1 from MachineLearningLifeScience/add_rfp_lambo_docs

Add rfp lambo docs

Author: RMichae1

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

@@ -78,6 +78,12 @@ Solvent accessibility of mutations of a wildtype using `foldx`
 Rapid Stability Predictions of single mutations from a wildtype. [WIP]
 :::
 
+:::{grid-item-card} RFP Fluorescence Protein Stability (using `lambo`)
+:link: ./using_poli/objective_repository/foldx_rfp_lambo.html
+:columns: 6
+LaMBO Fluorescence (RFP) by stability and solvent-accessible surface area.
+:::
+
 ::::
 
 ### Other

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

@@ -0,0 +1,60 @@
+# Protein (RFP) stability and SASA (using `foldx`,`lambo`)
+![Type of objective function: discrete](https://img.shields.io/badge/Type-discrete_inputs-blue)
+![Environment to run this objective function: poli protein](https://img.shields.io/badge/Environment-poli____lambo
+)
+
+## About
+
+This objective function returns stability using `foldx` and SASA, _exactly_ as done in the `lambo` implementation.
+
+## Prerequisites
+
+- Have `foldx` installed, and available in your home directory. We expect the following files to be there:
+  - `~/foldx/foldx`: the binary. You might need to rename it.
+  - `~/foldx/rotabase.txt`: a text file necessary for `foldx` to run.
+- Have `lambo` checked out, preferrably in the home directory, specifically containing: 
+  - `lambo.tasks.proxy_rfp.proxy_rfp.ProxyRFPTask`
+  - the rfp data: see `~/lambo/assets/fpbase`
+
+## How to run
+
+You can either run this objective function in your current environment (assuming that you have the correct dependencies installed), or you can run it in an isolated environment.
+
+::::{tab-set}
+
+:::{tab-item} In current environment
+
+You will have to install the following two dependencies:
+
+```bash
+pip install -r ~/lambo/requirements.txt
+```
+
+This contains: `pytorch botorch python-levenshtein wandb biopython hydra-core pymoo pandas deepchem transformers selfies jupyter seaborn pyscreener` and other packages.
+
+Then run
+
+```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="foldx_rfp",
+)
+
+# Example input:
+print(x0)
+
+# Querying:
+print(y0)  # The stability of your wildtype
+```
+
+You could also pass an `problem: ProblemSetupInformation` to the create method. For the alphabet reference by default, [we use this encoding](https://github.com/MachineLearningLifeScience/poli/blob/44cad2a5c95f209aeb24d4893d162b3359ca91a3/src/poli/core/util/proteins/defaults.py#L1).
+
+:::
+
+::::