Selfies_converter added

selfies_converter.py

@@ -0,0 +1,46 @@
+import argparse
+import os
+import selfies as sf
+from tqdm import tqdm
+
+def convert_file(input_file, verbose=False):
+    base_name = os.path.splitext(input_file)[0]
+    selfies_file = f"{base_name}.selfies"
+    alphabet_file = f"{base_name}.alph"
+    
+    alphabet = set()
+    
+    with open(input_file, 'r') as fin, open(selfies_file, 'w') as fout:
+        lines = fin.readlines()
+        if verbose:
+            lines = tqdm(lines, desc=f"Converting {input_file}")
+        
+        for line in lines:
+            smiles = line.strip()
+            try:
+                selfies = sf.encoder(smiles, strict=False)
+                fout.write(f"{selfies}\n")
+                alphabet.update(sf.split_selfies(selfies))
+            except sf.EncoderError as e:
+                if verbose:
+                    print(f"Failed to encode: {smiles}, {e}")
+                continue
+    
+    with open(alphabet_file, 'w') as f:
+        for symbol in sorted(alphabet):
+            f.write(f"{symbol}\n")
+    
+    if verbose:
+        print(f"Conversion complete. SELFIES saved to {selfies_file}")
+        print(f"Alphabet saved to {alphabet_file}")
+
+def main():
+    parser = argparse.ArgumentParser(description="SELFIES Converter")
+    parser.add_argument("input_file", help="Input SMILES file (.smi)")
+    parser.add_argument("-v", "--verbose", action="store_true", help="Increase output verbosity")
+    args = parser.parse_args()
+
+    convert_file(args.input_file, args.verbose)
+
+if __name__ == "__main__":
+    main()