GDEE Package
- class gdee.ProteinEngineering(protein_name, database)[source]
Main interface for the GDEE protein engineering platform.
Orchestrates variant generation, 3D modeling, quality assessment, molecular docking, and result storage in SQLite database.
- __init__(protein_name, database)[source]
Initialize protein engineering workflow.
- Parameters:
protein_name – Name identifier for target protein
database – Path to SQLite database file
- add_ligand(name, filename)[source]
Add a ligand for docking calculations.
- Parameters:
name – Unique ligand identifier
filename – Path to PDBQT format ligand file
- Returns:
Created ligand object for adding measurements
- Return type:
Ligand
- Raises:
RuntimeError – If ligand name already exists
- run()[source]
Execute the complete protein engineering workflow.
Runs variant generation, 3D modeling, quality assessment, docking, and saves results to database.
- Raises:
RuntimeError – If processing fails or is interrupted
- class gdee.RescoreVariants(in_db, out_db, table, functions, files_path)[source]
Re-evaluate existing docking results with trained metamodel.
- __init__(in_db, out_db, table, functions, files_path)[source]
Initialize rescoring workflow.
- Parameters:
in_db – Input database path with docking results
out_db – Output database path for rescored results
table – Table name for rescored poses
functions – Path to pickle file with scoring functions
files_path – Path to structure files directory
- run()[source]
Execute the rescoring workflow.
Re-scores poses from input database and saves to output database.
- Raises:
RuntimeError – If processing fails or is interrupted