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"""
standalone_show_generated.py
--------------------------------
Runs Gen_PartialSMILES2.py with a user scaffold SMILES, loads the
generated_molecules.csv file, displays a 2D grid of molecules, and
creates small icon images for each generated molecule.
Usage:
python standalone_show_generated.py "CC(N)C(=O)O"
"""
import subprocess
import sys
import os
import pandas as pd
from rdkit import Chem
from rdkit.Chem import Draw
# ---------------------------------------------------------
# 1. Ensure scaffold has attachment point [*]
# ---------------------------------------------------------
def ensure_attachment_point(smiles):
"""
Ensures the scaffold contains the required [*] wildcard.
If missing, add [*] to the front.
"""
if "[*]" in smiles:
return smiles
return "[*]" + smiles
# ---------------------------------------------------------
# 2. Run the generator script (Gen_PartialSMILES2.py)
# ---------------------------------------------------------
def run_generator(scaffold_smiles, n_to_gen=16):
"""
Runs the molecule generator and produces generated_molecules.csv.
"""
scaffold_smiles = ensure_attachment_point(scaffold_smiles)
cmd = [
sys.executable,
"Gen_PartialSMILES2.py",
"--scaffold", scaffold_smiles,
"--n_to_gen", str(n_to_gen)
]
print(f"\nRunning generator with scaffold: {scaffold_smiles}")
print("Command:", " ".join(cmd), "\n")
subprocess.run(cmd, check=True)
if not os.path.exists("generated_molecules.csv"):
raise FileNotFoundError("generated_molecules.csv not found after generator run.")
print("Generation complete!\n")
# ---------------------------------------------------------
# 3. Render full RDKit grid image & save as PNG
# ---------------------------------------------------------
def load_and_draw_generated(csv_path="generated_molecules.csv"):
"""
Reads generated_molecules.csv and displays a 2D RDKit structure grid.
Saves the grid as generated_molecules.png.
"""
df = pd.read_csv(csv_path)
smiles_list = df["smiles"].tolist()
mols = []
legends = []
for smi in smiles_list:
mol = Chem.MolFromSmiles(smi)
if mol:
mols.append(mol)
legends.append(smi)
if not mols:
print("No valid molecules found in CSV.")
return None, []
print(f"Rendering {len(mols)} molecules into grid...")
img = Draw.MolsToGridImage(
mols,
molsPerRow=4,
subImgSize=(250, 250),
legends=legends
)
img.show()
img.save("generated_molecules.png")
print("Saved structure grid → generated_molecules.png\n")
return mols, smiles_list
# ---------------------------------------------------------
# 4. Create 150×150 PNG icons from each molecule
# ---------------------------------------------------------
def generate_icons(mols, smiles_list, save_folder="icons"):
"""
Converts each RDKit Mol into a small 150×150 PNG icon.
Saves them in icons/, returns PIL images and labels.
"""
os.makedirs(save_folder, exist_ok=True)
print("Creating icons...")
icons = []
labels = []
for i, mol in enumerate(mols):
img = Draw.MolToImage(mol, size=(150, 150), kekulize=True)
icon_path = os.path.join(save_folder, f"icon_{i+1}.png")
img.save(icon_path)
icons.append(img)
labels.append(smiles_list[i])
print(f"Saved {len(icons)} icons → {save_folder}/")
return icons, labels
# ---------------------------------------------------------
# 5. Main execution
# ---------------------------------------------------------
if __name__ == "__main__":
if len(sys.argv) < 2:
print("Usage: python standalone_show_generated.py \"SMILES_STRING\"")
sys.exit(1)
scaffold = sys.argv[1]
# Step 1: Run generator
run_generator(scaffold, n_to_gen=16)
# Step 2: Show big RDKit grid
mols, smiles_out = load_and_draw_generated()
# Step 3: Create icon images
if mols:
icons, labels = generate_icons(mols, smiles_out)
print("\nIcons ready! You can now use them in your Gradio grid.")
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