refactor: Cleaned Enzeptional

Signed-off-by: nanayves <[email protected]>

examples/enzeptional/README.md

@@ -0,0 +1,97 @@
+# Enzyme Optimization Experiment
+
+## Description
+This script performs an optimization experiment for enzyme sequences using different mutation strategies.
+
+## Import modules
+```python
+import logging
+import pandas as pd
+from gt4sd.frameworks.enzeptional.processing import HFandTAPEModelUtility
+from gt4sd.frameworks.enzeptional.core import SequenceMutator, EnzymeOptimizer
+from gt4sd.configuration import sync_algorithm_with_s3
+from gt4sd.configuration import GT4SDConfiguration
+configuration = GT4SDConfiguration.get_instance()
+```
+
+## Load datasets and scorers
+```python
+sync_algorithm_with_s3("proteins/enzeptional/scorers", module="properties")
+```
+Feasibility scorer path
+```python
+scorer_path = f"{configuration.gt4sd_local_cache_path}/properties/proteins/enzeptional/scorers/feasibility/model.pkl"
+```
+## Set embedding model/tokenizer paths
+```python
+language_model_path = "facebook/esm2_t33_650M_UR50D"
+tokenizer_path = "facebook/esm2_t33_650M_UR50D"
+unmasking_model_path = "facebook/esm2_t33_650M_UR50D"
+chem_model_path = "seyonec/ChemBERTa-zinc-base-v1"
+chem_tokenizer_path = "seyonec/ChemBERTa-zinc-base-v1"
+```
+## Load protein embedding model
+```python
+protein_model = HFandTAPEModelUtility(
+ embedding_model_path=language_model_path, tokenizer_path=tokenizer_path
+ )
+```
+## Create mutation config 
+```python
+mutation_config = {
+ "type": "language-modeling",
+ "embedding_model_path": language_model_path,
+ "tokenizer_path": tokenizer_path,
+ "unmasking_model_path": unmasking_model_path,
+ }
+```
+## Set key parameters
+```python
+intervals = [(5, 10), (20, 25)]
+batch_size = 5
+top_k = 3
+substrate_smiles = "NC1=CC=C(N)C=C1"
+product_smiles = "CNC1=CC=C(NC(=O)C2=CC=C(C=C2)C(C)=O)C=C1"
+
+sample_sequence = "MSKLLMIGTGPVAIDQFLTRYEASCQAYKDMHQDQQLSSQFNTNLFEGDKALVTKFLEINRTLS"
+```
+## Load mutator
+```python
+mutator = SequenceMutator(sequence=sample_sequence, mutation_config=mutation_config)
+```
+## Set Optimizer
+```python
+optimizer = EnzymeOptimizer(
+ sequence=sample_sequence,
+ protein_model=protein_model,
+ substrate_smiles=substrate_smiles,
+ product_smiles=product_smiles,
+ chem_model_path=chem_model_path,
+ chem_tokenizer_path=chem_tokenizer_path,
+ scorer_filepath=scorer_path,
+ mutator=mutator,
+ intervals=intervals,
+ batch_size=batch_size,
+ top_k=top_k,
+ selection_ratio=0.25,
+ perform_crossover=True,
+ crossover_type="single_point",
+ concat_order=["substrate", "sequence", "product"],
+)
+```
+## Define optmization parameters
+```python
+num_iterations = 3
+num_sequences = 5
+num_mutations = 5
+time_budget = 3600
+```
+## Optimize
+```python
+optimized_sequences, iteration_info = optimizer.optimize(
+ num_iterations=num_iterations,
+ num_sequences=num_sequences,
+ num_mutations=num_mutations,
+ time_budget=time_budget,
+)
+```

src/gt4sd/frameworks/enzeptional/__init__.py

@@ -1,7 +1,7 @@
 #
 # MIT License
 #
-# Copyright (c) 2023 GT4SD team
+# Copyright (c) 2024 GT4SD team
 #
 # Permission is hereby granted, free of charge, to any person obtaining a copy
 # of this software and associated documentation files (the "Software"), to deal
@@ -27,3 +27,4 @@
 """
 
 from .core import EnzymeOptimizer # noqa: F401
+from .core import EnzymeOptimizer # noqa: F401