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Zhongwei Li
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skills/rdkit/scripts/molecular_properties.py
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243
skills/rdkit/scripts/molecular_properties.py
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#!/usr/bin/env python3
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"""
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Molecular Properties Calculator
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Calculate comprehensive molecular properties and descriptors for molecules.
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Supports single molecules or batch processing from files.
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Usage:
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python molecular_properties.py "CCO"
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python molecular_properties.py --file molecules.smi --output properties.csv
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"""
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import argparse
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import sys
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from pathlib import Path
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try:
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from rdkit import Chem
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from rdkit.Chem import Descriptors, Lipinski
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except ImportError:
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print("Error: RDKit not installed. Install with: conda install -c conda-forge rdkit")
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sys.exit(1)
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def calculate_properties(mol):
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"""Calculate comprehensive molecular properties."""
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if mol is None:
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return None
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properties = {
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# Basic properties
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'SMILES': Chem.MolToSmiles(mol),
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'Molecular_Formula': Chem.rdMolDescriptors.CalcMolFormula(mol),
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# Molecular weight
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'MW': Descriptors.MolWt(mol),
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'ExactMW': Descriptors.ExactMolWt(mol),
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# Lipophilicity
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'LogP': Descriptors.MolLogP(mol),
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'MR': Descriptors.MolMR(mol),
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# Polar surface area
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'TPSA': Descriptors.TPSA(mol),
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'LabuteASA': Descriptors.LabuteASA(mol),
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# Hydrogen bonding
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'HBD': Descriptors.NumHDonors(mol),
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'HBA': Descriptors.NumHAcceptors(mol),
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# Atom counts
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'Heavy_Atoms': Descriptors.HeavyAtomCount(mol),
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'Heteroatoms': Descriptors.NumHeteroatoms(mol),
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'Valence_Electrons': Descriptors.NumValenceElectrons(mol),
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# Ring information
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'Rings': Descriptors.RingCount(mol),
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'Aromatic_Rings': Descriptors.NumAromaticRings(mol),
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'Saturated_Rings': Descriptors.NumSaturatedRings(mol),
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'Aliphatic_Rings': Descriptors.NumAliphaticRings(mol),
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'Aromatic_Heterocycles': Descriptors.NumAromaticHeterocycles(mol),
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# Flexibility
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'Rotatable_Bonds': Descriptors.NumRotatableBonds(mol),
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'Fraction_Csp3': Descriptors.FractionCsp3(mol),
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# Complexity
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'BertzCT': Descriptors.BertzCT(mol),
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# Drug-likeness
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'QED': Descriptors.qed(mol),
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}
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# Lipinski's Rule of Five
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properties['Lipinski_Pass'] = (
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properties['MW'] <= 500 and
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properties['LogP'] <= 5 and
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properties['HBD'] <= 5 and
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properties['HBA'] <= 10
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)
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# Lead-likeness
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properties['Lead-like'] = (
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250 <= properties['MW'] <= 350 and
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properties['LogP'] <= 3.5 and
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properties['Rotatable_Bonds'] <= 7
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)
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return properties
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def process_single_molecule(smiles):
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"""Process a single SMILES string."""
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mol = Chem.MolFromSmiles(smiles)
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if mol is None:
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print(f"Error: Failed to parse SMILES: {smiles}")
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return None
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props = calculate_properties(mol)
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return props
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def process_file(input_file, output_file=None):
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"""Process molecules from a file."""
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input_path = Path(input_file)
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if not input_path.exists():
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print(f"Error: File not found: {input_file}")
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return
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# Determine file type
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if input_path.suffix.lower() in ['.sdf', '.mol']:
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suppl = Chem.SDMolSupplier(str(input_path))
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elif input_path.suffix.lower() in ['.smi', '.smiles', '.txt']:
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suppl = Chem.SmilesMolSupplier(str(input_path), titleLine=False)
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else:
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print(f"Error: Unsupported file format: {input_path.suffix}")
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return
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results = []
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for idx, mol in enumerate(suppl):
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if mol is None:
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print(f"Warning: Failed to parse molecule {idx+1}")
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continue
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props = calculate_properties(mol)
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if props:
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props['Index'] = idx + 1
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results.append(props)
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# Output results
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if output_file:
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write_csv(results, output_file)
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print(f"Results written to: {output_file}")
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else:
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# Print to console
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for props in results:
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print("\n" + "="*60)
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for key, value in props.items():
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print(f"{key:25s}: {value}")
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return results
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def write_csv(results, output_file):
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"""Write results to CSV file."""
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import csv
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if not results:
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print("No results to write")
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return
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with open(output_file, 'w', newline='') as f:
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fieldnames = results[0].keys()
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writer = csv.DictWriter(f, fieldnames=fieldnames)
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writer.writeheader()
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writer.writerows(results)
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def print_properties(props):
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"""Print properties in formatted output."""
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print("\nMolecular Properties:")
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print("="*60)
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# Group related properties
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print("\n[Basic Information]")
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print(f" SMILES: {props['SMILES']}")
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print(f" Formula: {props['Molecular_Formula']}")
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print("\n[Size & Weight]")
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print(f" Molecular Weight: {props['MW']:.2f}")
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print(f" Exact MW: {props['ExactMW']:.4f}")
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print(f" Heavy Atoms: {props['Heavy_Atoms']}")
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print(f" Heteroatoms: {props['Heteroatoms']}")
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print("\n[Lipophilicity]")
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print(f" LogP: {props['LogP']:.2f}")
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print(f" Molar Refractivity: {props['MR']:.2f}")
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print("\n[Polarity]")
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print(f" TPSA: {props['TPSA']:.2f}")
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print(f" Labute ASA: {props['LabuteASA']:.2f}")
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print(f" H-bond Donors: {props['HBD']}")
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print(f" H-bond Acceptors: {props['HBA']}")
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print("\n[Ring Systems]")
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print(f" Total Rings: {props['Rings']}")
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print(f" Aromatic Rings: {props['Aromatic_Rings']}")
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print(f" Saturated Rings: {props['Saturated_Rings']}")
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print(f" Aliphatic Rings: {props['Aliphatic_Rings']}")
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print(f" Aromatic Heterocycles: {props['Aromatic_Heterocycles']}")
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print("\n[Flexibility & Complexity]")
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print(f" Rotatable Bonds: {props['Rotatable_Bonds']}")
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print(f" Fraction Csp3: {props['Fraction_Csp3']:.3f}")
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print(f" Bertz Complexity: {props['BertzCT']:.1f}")
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print("\n[Drug-likeness]")
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print(f" QED Score: {props['QED']:.3f}")
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print(f" Lipinski Pass: {'Yes' if props['Lipinski_Pass'] else 'No'}")
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print(f" Lead-like: {'Yes' if props['Lead-like'] else 'No'}")
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print("="*60)
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def main():
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parser = argparse.ArgumentParser(
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description='Calculate molecular properties for molecules',
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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# Single molecule
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python molecular_properties.py "CCO"
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# From file
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python molecular_properties.py --file molecules.smi
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# Save to CSV
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python molecular_properties.py --file molecules.sdf --output properties.csv
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"""
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)
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parser.add_argument('smiles', nargs='?', help='SMILES string to analyze')
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parser.add_argument('--file', '-f', help='Input file (SDF or SMILES)')
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parser.add_argument('--output', '-o', help='Output CSV file')
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args = parser.parse_args()
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if not args.smiles and not args.file:
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parser.print_help()
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sys.exit(1)
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if args.smiles:
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# Process single molecule
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props = process_single_molecule(args.smiles)
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if props:
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print_properties(props)
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elif args.file:
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# Process file
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process_file(args.file, args.output)
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if __name__ == '__main__':
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main()
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