added GFP CBas documentation

docs/protein-optimization/index.md

@@ -79,6 +79,18 @@ 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.
+:::
+
+:::{grid-item-card} Protein Fluorescence (using `CBas`) [WIP]
+:link: ./using_poli/objective_repository/gfp_cbas.html
+:columns: 6
+Surrogate fluorescence prediction of mutations from a GFP sequence. [WIP]
+:::
+
 ::::
 
 

docs/protein-optimization/understanding_foldx/01-single-mutation-using-foldx/tmp/Raw_101m_Repair.fxout

@@ -11,3 +11,5 @@ Pdb	total energy	Backbone Hbond	Sidechain Hbond	Van der Waals	Electrostatics	Sol
 WT_101m_Repair_1.pdb	-34.3436	-141.831	-47.9784	-179.662	-8.13848	243.99	-239.232	3.40664	105.266	231.722	0	0	0	5.28162	157.882	-8.73035	0	0	0	0	1.56224	0
 101m_Repair_1.pdb	-31.7457	-141.841	-48.2413	-177.827	-8.5183	243.998	-235.896	3.3294	104.051	231.196	0	0	0	5.25497	157.841	-8.81857	0	0	0	0	1.5666	0
 WT_101m_Repair_1.pdb	-34.3436	-141.831	-47.9784	-179.662	-8.13848	243.99	-239.232	3.40664	105.266	231.722	0	0	0	5.28162	157.882	-8.73035	0	0	0	0	1.56224	0
+101m_Repair_1.pdb	-31.7457	-141.841	-48.2413	-177.827	-8.5183	243.998	-235.896	3.3294	104.051	231.196	0	0	0	5.25497	157.841	-8.81857	0	0	0	0	1.5666	0
+WT_101m_Repair_1.pdb	-34.3436	-141.831	-47.9784	-179.662	-8.13848	243.99	-239.232	3.40664	105.266	231.722	0	0	0	5.28162	157.882	-8.73035	0	0	0	0	1.56224	0

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

@@ -84,6 +84,12 @@ Rapid Stability Predictions of single mutations from a wildtype. [WIP]
 LaMBO Fluorescence (RFP) by stability and solvent-accessible surface area.
 :::
 
+:::{grid-item-card} GFP Fluorescence Protein Surrogate (using `CBas`)
+:link: ./using_poli/objective_repository/gfp_cbas.html
+:columns: 6
+CBas Fluorescence (GFP) median brightness by latent encoding surrogate under the assumption that the encoder mean correlates sufficiently with target brightness.
+:::
+
 ::::
 
 ### Other

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

@@ -0,0 +1,84 @@
+# Protein Fluorescence (using `CBas`)
+![Type of objective function: discrete](https://img.shields.io/badge/Type-discrete_inputs-blue)
+![Environment to run this objective function: poli protein_cbas](https://img.shields.io/badge/Environment-poli____protein-teal
+)
+
+[TODO: revise]
+
+## About
+
+This objective function returns the mean encoding (i.e. median brightness surrogate) using `CBas`.
+
+## Prerequisites
+
+- Assets: GFP dataframe, and model checkpoints as provided in the `poli` module
+
+## 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 dependencies:
+
+```bash
+pip install biopython python-levenshtein numpy pandas scipy torch torchvision torchaudio keras-core tensorflow
+```
+
+Then run
+
+```python
+from pathlib import Path
+
+import numpy as np
+
+from poli import objective_factory
+
+# How to create
+f, x0, y0 = objective_factory.create(
+    name="gfp_cbas",
+)
+
+# Example input:
+print(x0)
+
+# Querying:
+print(y0)  # The encoding of the first batch of GFP sequences
+```
+
+:::
+
+:::{tab-item} In isolation
+
+If you want us to handle dependencies, run
+
+```python
+from pathlib import Path
+
+import numpy as np
+
+from poli import objective_factory
+
+# How to create
+f, x0, y0 = objective_factory.create(
+    name="gfp_cbas",
+    wildtype_pdb_file=wildtype_pdb_file,
+    force_register=True,
+)
+
+# Example input:
+print(x0)
+
+# Querying:
+print(y0)  # The stability of your wildtype
+```
+
+```{warning}
+Registering the objective function in this way will create a `conda` environment called `poli__protein_cbas` with the relevant dependencies.
+```
+
+:::
+
+::::