size_calculation_v1.py

import os
import subprocess
import pandas as pd
import tempfile
import numpy as np
from rdkit import Chem
from rdkit.Chem import AllChem
from shutil import which

# === Settings ===
csv_file = "/Users/arunrajb/work/methanogenesis_work/sorted_molecules_MCDB.csv"  # input CSV
output_dir = "mol_output_from_csv"
os.makedirs(output_dir, exist_ok=True)

# === Check for Open Babel ===
def check_dependencies():
    if not which("obabel"):
        raise EnvironmentError("❌ Open Babel (obabel) not found in PATH.")

# === Diameter Calculation ===
def calculate_diameter_rdkit(mol):
    """Compute molecular diameter from 3D coordinates"""
    try:
        conf = mol.GetConformer()
        coords = np.array([conf.GetAtomPosition(i) for i in range(mol.GetNumAtoms())])
        dist = np.linalg.norm(coords[:, None, :] - coords[None, :, :], axis=-1)
        return round(np.max(dist), 2)
    except:
        return None

def smiles_to_mol_rdkit(smiles, mol_path):
    try:
        # Convert SMILES to RDKit Mol
        mol = Chem.MolFromSmiles(smiles)
        if mol is None:
            raise ValueError("Invalid SMILES string.")
        mol = Chem.AddHs(mol)

        # 3D Conformer Generation
        params = AllChem.ETKDGv3()
        params.randomSeed = 42
        success = AllChem.EmbedMolecule(mol, params)

        if success != 0:
            print("⚠️ ETKDG embedding failed, retrying with random coordinates...")
            AllChem.EmbedMolecule(mol, useRandomCoords=True)

        # UFF Optimization with increased iterations
        opt_status = AllChem.UFFOptimizeMolecule(mol, maxIters=20000)
        if opt_status != 0:
            print("⚠️ UFF optimization did not converge within max iterations.")

        # Save to .mol file
        Chem.MolToMolFile(mol, mol_path)

        # Calculate diameter
        diameter = calculate_diameter_rdkit(mol)

        return mol, diameter

    except Exception as e:
        print(f"⚠️ RDKit processing failed: {e}")
        return None, None

# === Fallback to Open Babel (.mol) ===
def smiles_to_mol_obabel(smiles, mol_path):
    try:
        with tempfile.NamedTemporaryFile(mode='w', suffix='.smi', delete=False) as tmp:
            tmp.write(smiles)
            tmp_path = tmp.name
        subprocess.run(["obabel", "-ismi", tmp_path, "-O", mol_path, "--gen3d"], check=True)
        os.remove(tmp_path)
        return True
    except Exception as e:
        print(f"⚠️ Open Babel fallback failed: {e}")
        return False

# === Main Processing ===
def process_csv(csv_file):
    check_dependencies()

    df = pd.read_csv(csv_file)  # With header
    diameters = []

    success_count, fail_count = 0, 0
    failures = []

    for idx, row in df.iterrows():
        name = str(row["Molecule Name"]).strip()
        smiles = str(row["Smiles"]).strip()

        if not smiles or pd.isna(smiles) or smiles.lower() == "nan":
            print(f"[{idx+1}] ⚠️ Skipping {name} due to invalid SMILES")
            diameters.append(None)
            continue

        tag = name.replace(" ", "_").replace("/", "_").replace(":", "_")
        mol_path = os.path.join(output_dir, f"{tag}.mol")

        if os.path.exists(mol_path):
            print(f"[{idx+1}] ⏩ Skipping {name} (already exists)")
            mol = Chem.MolFromMolFile(mol_path, removeHs=False)
            if mol:
                diameter = calculate_diameter_rdkit(mol)
                diameters.append(diameter)
                print(f"📏 Diameter (existing): {diameter} Å")
            else:
                diameters.append(None)
            continue

        print(f"[{idx+1}] Processing: {name}")
        mol, diameter = smiles_to_mol_rdkit(smiles, mol_path)
        if mol is None:
            print("⏪ Falling back to Open Babel...")
            if not smiles_to_mol_obabel(smiles, mol_path):
                print(f"❌ Failed: {name}")
                failures.append((name, "3D generation failed"))
                diameters.append(None)
                fail_count += 1
                continue
            print(f"✅ Saved: {mol_path}")
            print(f"📏 Diameter: Not available (Open Babel fallback)")
            diameters.append(None)
        else:
            print(f"✅ Saved: {mol_path}")
            print(f"📏 Diameter: {diameter} Å")
            diameters.append(diameter)

        success_count += 1

    # Add Diameter column and overwrite CSV
    df["Diameter"] = diameters
    df.to_csv(csv_file, index=False)
    print(f"\n✅ Updated CSV saved with Diameter column: {csv_file}")
    print(f"🎉 Done. {success_count} succeeded, {fail_count} failed.")

    if failures:
        fail_log = os.path.join(output_dir, "failed_log.txt")
        with open(fail_log, "w") as f:
            for name, reason in failures:
                f.write(f"{name}\t{reason}\n")
        print(f"📄 Failures logged in: {fail_log}")

# === Run ===
if __name__ == "__main__":
    process_csv(csv_file)