Spaces:
Running
Running
File size: 3,739 Bytes
907b200 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 | """
SMILES → PDBQT Converter
=========================
Usage: python smiles_to_pdbqt.py <smiles_string> <output_pdbqt_path>
Pipeline:
1. RDKit: parse SMILES → add Hs → 3D embed → energy minimize → write .sdf
2. OpenBabel (obabel): .sdf → .pdbqt (adds partial charges, atom types, torsions)
Output: JSON to stdout {"status": "success"|"error", ...}
"""
import sys
import json
import os
import tempfile
import subprocess
def main():
if len(sys.argv) < 3:
print(json.dumps({
"status": "error",
"message": "Usage: python smiles_to_pdbqt.py <smiles_string> <output_pdbqt_path>"
}))
sys.exit(1)
smiles = sys.argv[1]
output_path = sys.argv[2]
try:
# ---- Step A: RDKit (SMILES → 3D SDF) ----
from rdkit import Chem
from rdkit.Chem import AllChem
mol = Chem.MolFromSmiles(smiles)
if mol is None:
raise ValueError(f"RDKit could not parse SMILES: {smiles}")
# Add hydrogens for proper 3D geometry
mol = Chem.AddHs(mol)
# Generate 3D coordinates (ETKDG v3 for best quality)
embed_result = AllChem.EmbedMolecule(mol, AllChem.ETKDGv3())
if embed_result == -1:
# Fallback: use random coordinates
embed_result = AllChem.EmbedMolecule(mol, AllChem.ETKDGv3())
if embed_result == -1:
raise ValueError("Failed to generate 3D coordinates for molecule")
# Energy minimization with MMFF94 force field
try:
result = AllChem.MMFFOptimizeMolecule(mol, maxIters=2000)
if result == -1:
# MMFF failed, try UFF
AllChem.UFFOptimizeMolecule(mol, maxIters=2000)
except Exception:
# If both fail, proceed with unoptimized geometry
pass
# Write to temporary SDF file
sdf_fd, sdf_path = tempfile.mkstemp(suffix=".sdf")
os.close(sdf_fd)
writer = Chem.SDWriter(sdf_path)
writer.write(mol)
writer.close()
# ---- Step B: OpenBabel (SDF → PDBQT) ----
# Ensure output directory exists
os.makedirs(os.path.dirname(os.path.abspath(output_path)), exist_ok=True)
# Resolve obabel from the same venv bin/ as the Python interpreter
python_dir = os.path.dirname(sys.executable)
obabel_bin = os.path.join(python_dir, "obabel")
if not os.path.exists(obabel_bin):
# Fallback to system obabel
obabel_bin = "obabel"
obabel_cmd = [
obabel_bin,
"-isdf", sdf_path,
"-opdbqt",
"-O", output_path,
"-p", "7.4", # protonate at physiological pH
]
proc = subprocess.run(
obabel_cmd,
capture_output=True,
text=True,
timeout=60
)
# Clean up temp SDF
if os.path.exists(sdf_path):
os.remove(sdf_path)
if proc.returncode != 0:
raise ValueError(f"OpenBabel conversion failed: {proc.stderr.strip()}")
if not os.path.exists(output_path) or os.path.getsize(output_path) == 0:
raise ValueError("OpenBabel produced an empty or missing .pdbqt file")
# Success
print(json.dumps({
"status": "success",
"output_file": output_path,
"smiles": smiles
}))
except Exception as e:
# Clean up on error
if 'sdf_path' in locals() and os.path.exists(sdf_path):
os.remove(sdf_path)
print(json.dumps({
"status": "error",
"message": str(e)
}))
sys.exit(1)
if __name__ == "__main__":
main()
|