diff --git a/README.md b/README.md index 61bae83..dbc2a58 100644 --- a/README.md +++ b/README.md @@ -51,7 +51,8 @@ Then, to run a command in your normal terminal, simply point to the PyMOL Python Here are the example install commands for the supported models: - ESM3: `pip install esm` -- Boltz-1: `pip install boltz` +- Boltz v2.2.0: `pip install boltz[cuda] -U or git clone https://github.com/jwohlwend/boltz.git +cd boltz; pip install -e .[cuda]` - Chai-1: `pip install chai_lab==0.5.0` - Protenix: `pip install --extra-index-url=https://pypi.nvidia.com --trusted-host pypi.nvidia.com nvidia-cublas-cu12 deepspeed==0.14.4 protenix` diff --git a/pymolfold/__init__.py b/pymolfold/__init__.py index b040e04..336b282 100644 --- a/pymolfold/__init__.py +++ b/pymolfold/__init__.py @@ -1,7 +1,7 @@ ''' PyMOL Protein Folding Plugin -By Colby T. Ford, Ph.D. +By Colby T. Ford, Ph.D License: GPLv3 ''' @@ -249,9 +249,20 @@ def fold_boltz( if os.path.exists(affinity_json_path): with open(affinity_json_path, 'r') as f: affinity_data = json.load(f) - affinity_results = (f"Affinity Prediction Results:\n\n" - f"Predicted Affinity (log(IC50), µM): {affinity_data.get('affinity_pred_value', 'N/A')}\n" - f"Binding Probability: {affinity_data.get('affinity_probability_binary', 'N/A')}") + y = affinity_data.get('affinity_pred_value') + prob = affinity_data.get('affinity_probability_binary') + + kcal_mol_str = "N/A" + if isinstance(y, (int, float)): + # Convert log(IC50) to kcal/mol using the provided formula + kcal_mol = (6 - y) * 1.364 + kcal_mol_str = f"{kcal_mol:.2f}" + + prob_str = f"{prob:.2f}" if isinstance(prob, (int, float)) else "N/A" + + # Format the result string to match the user's request + affinity_results = (f"IC50: {kcal_mol_str} kcal/mol " + f"Binding Affinity Likelihood: {prob_str}") return folded_path, affinity_results diff --git a/pymolfold_v0.4.2.zip b/pymolfold_v0.4.2.zip deleted file mode 100644 index 685330f..0000000 Binary files a/pymolfold_v0.4.2.zip and /dev/null differ diff --git a/pymolfold_v0.4.3.zip b/pymolfold_v0.4.3.zip new file mode 100644 index 0000000..da34750 Binary files /dev/null and b/pymolfold_v0.4.3.zip differ