Fix script for strings beyond first whitespace

.gitattributes

@@ -58,3 +58,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
 *.smi filter=lfs diff=lfs merge=lfs -text
 *.csv filter=lfs diff=lfs merge=lfs -text
+*.selfies filter=lfs diff=lfs merge=lfs -text

README.md

@@ -57,9 +57,15 @@ find . -name "*.smi" | xargs -I {} -P$(nproc)  sh -c 'python selfies_converter.p
 
 Note: Be cautious when using the command that removes original files. Ensure you have backups before running it.
 
+With gz:
+```bash
+find . -name "*.smi.gz" | xargs -P$(nproc) -I {} sh -c 'f="{}"; g="${f%.gz}"; gzip -dc "$f" > "$g" && python selfies_converter.py "$g" && rm "$g" && rm "$f"'
+```
+
+
 ## Output
 
 Both scripts will create output files in the same directory as the input files:
 
 - The file splitter creates `<original_name>.part01.smi`, `<original_name>.part02.smi`, etc.
-- The SELFIES converter creates `<original_name>.selfies` for the converted file and `<original_name>.alph` for the alphabet file.
+- The SELFIES converter creates `<original_name>.selfies` for the converted file and `<original_name>.alph` for the alphabet file.

selfies_converter.py

@@ -11,6 +11,7 @@ def convert_file(input_file, verbose=False, batch_size=10000):
     alphabet = set()
     total_lines = 0
     processed_lines = 0
+    error_count = 0
 
     # Count total lines if verbose
     if verbose:
@@ -23,9 +24,11 @@ def convert_file(input_file, verbose=False, batch_size=10000):
 
         batch = []
         for line in fin:
-            batch.append(line.strip())
+            # Truncate line at first whitespace
+            smiles = line.split()[0]
+            batch.append(smiles)
             if len(batch) == batch_size:
-                process_batch(batch, fout, alphabet)
+                error_count += process_batch(batch, fout, alphabet)
                 processed_lines += len(batch)
                 if verbose:
                     pbar.update(len(batch))
@@ -33,7 +36,7 @@ def convert_file(input_file, verbose=False, batch_size=10000):
 
         # Process remaining lines
         if batch:
-            process_batch(batch, fout, alphabet)
+            error_count += process_batch(batch, fout, alphabet)
             processed_lines += len(batch)
             if verbose:
                 pbar.update(len(batch))
@@ -47,17 +50,23 @@ def convert_file(input_file, verbose=False, batch_size=10000):
     
     if verbose:
         print(f"Conversion complete. Processed {processed_lines} lines.")
+        print(f"Encountered {error_count} errors during conversion.")
         print(f"SELFIES saved to {selfies_file}")
         print(f"Alphabet saved to {alphabet_file}")
 
 def process_batch(batch, fout, alphabet):
+    error_count = 0
     for smiles in batch:
         try:
-            selfies = sf.encoder(smiles , strict=False)
-            fout.write(f"{selfies}\n")
-            alphabet.update(sf.split_selfies(selfies))
+            selfies = sf.encoder(smiles, strict=False)
+            if selfies:  # Check if the SELFIES string is not empty
+                fout.write(f"{selfies}\n")
+                alphabet.update(sf.split_selfies(selfies))
+            else:
+                error_count += 1
         except sf.EncoderError:
-            continue
+            error_count += 1
+    return error_count
 
 def main():
     parser = argparse.ArgumentParser(description="SELFIES Converter")
@@ -69,4 +78,4 @@ def main():
     convert_file(args.input_file, args.verbose, args.batch_size)
 
 if __name__ == "__main__":
-    main()
+    main()