First commit

KmerTokenizer,py

@@ -0,0 +1,32 @@
+def atomwise_tokenizer(smi, exclusive_tokens = None):
+    """
+    Tokenize a SMILES molecule at atom-level:
+        (1) 'Br' and 'Cl' are two-character tokens
+        (2) Symbols with bracket are considered as tokens
+
+    exclusive_tokens: A list of specifical symbols with bracket you want to keep. e.g., ['[C@@H]', '[nH]'].
+    Other symbols with bracket will be replaced by '[UNK]'. default is `None`.
+    """
+    import re
+    pattern =  "(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\\\|\/|:|~|@|\?|>|\*|\$|\%[0-9]{2}|[0-9])"
+    regex = re.compile(pattern)
+    tokens = [token for token in regex.findall(smi)]
+
+    if exclusive_tokens:
+        for i, tok in enumerate(tokens):
+            if tok.startswith('['):
+                if tok not in exclusive_tokens:
+                    tokens[i] = '[UNK]'
+    return tokens
+    
+def kmer_tokenizer(smiles, ngram=4, stride=1, remove_last = False, exclusive_tokens = None):
+    units = atomwise_tokenizer(smiles, exclusive_tokens = exclusive_tokens) #collect all the atom-wise tokens from the SMILES
+    if ngram == 1:
+        tokens = units
+    else:
+        tokens = [tokens_to_mer(units[i:i+ngram]) for i in range(0, len(units), stride) if len(units[i:i+ngram]) == ngram]
+
+    if remove_last:
+        if len(tokens[-1]) < ngram: #truncate last whole k-mer if the length of the last k-mers is less than ngram.
+            tokens = tokens[:-1]
+    return tokens

app.py

@@ -1,7 +1,9 @@
 import gradio as gr
+from KmerTokenizer import kmer_tokenizer
 
-def greet(name):
-    return "Hello " + name + "!!"
+def fn(name, num =3):
+    return name*num
 
-iface = gr.Interface(fn=greet, inputs="text", outputs="text")
+
+iface = gr.Interface(fn=kmer_tokenizer, inputs=["text", "Dropdown" ], outputs="text")
 iface.launch()