File size: 2,261 Bytes
27dc10f | 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 | import os
import sys
from rdkit import Chem
# --- Configuration ---
input_cxsmiles_file = "2024.07_Enamine_REAL_HAC_25_1B_CXSMILES.cxsmiles" # <-- CHANGE THIS to your input filename
output_smiles_file = "enamine_smiles_1B.txt" # <-- CHANGE THIS to your desired output filename
# --- End Configuration ---
# --- Script Start ---
# Check if input file exists
if not os.path.isfile(input_cxsmiles_file):
print(f"ERROR: Input file not found: {input_cxsmiles_file}")
sys.exit(1)
print(f"Reading CXSMILES from: {input_cxsmiles_file}")
print(f"Writing standard SMILES to: {output_smiles_file}")
print("-" * 30)
count_success = 0
count_error = 0
# Open input and output files safely
try:
with open(input_cxsmiles_file, 'r') as infile, open(output_smiles_file, 'w') as outfile:
# Process each line in the input file
for i, line in enumerate(infile):
cxsmiles_line = line.strip() # Remove leading/trailing whitespace
if not cxsmiles_line: # Skip empty lines
continue
try:
# RDKit's MolFromSmiles often ignores CXSMILES extensions
# It reads the core structure.
mol = Chem.MolFromSmiles(cxsmiles_line)
if mol is not None:
# Convert the RDKit molecule back to a standard, canonical SMILES
standard_smiles = Chem.MolToSmiles(mol)
outfile.write(standard_smiles + '\n')
count_success += 1
else:
# RDKit couldn't parse this line
print(f"Warning: Could not parse line {i+1}. Input: '{cxsmiles_line}'")
count_error += 1
except Exception as e:
# Catch any other unexpected errors during RDKit processing
print(f"Error processing line {i+1}: '{cxsmiles_line}'. Details: {e}")
count_error += 1
except IOError as e:
print(f"ERROR: Could not open or write file. Details: {e}")
sys.exit(1)
print("-" * 30)
print(f"Processing finished.")
print(f"Successfully converted: {count_success} lines.")
print(f"Failed/Skipped: {count_error} lines.")
print(f"Output written to: {output_smiles_file}") |