Add omit aa

app.py

@@ -403,6 +403,7 @@ def update(
     sampling_temp,
     model_name,
     backbone_noise,
+    omit_AAs,
     atomsel,
 ):
     from protein_mpnn_utils import (
@@ -455,7 +456,9 @@ def update(
 
     out_folder = "."  # Path to a folder to output sequences, e.g. /home/out/
     jsonl_path = ""  # Path to a folder with parsed pdb into jsonl
-    omit_AAs = "X"  # Specify which amino acids should be omitted in the generated sequence, e.g. 'AC' would omit alanine and cystine.
+    
+    if omit_AAs == "":
+        omit_AAs = "X"  # Specify which amino acids should be omitted in the generated sequence, e.g. 'AC' would omit alanine and cystine.
 
     pssm_multi = 0.0  # A value between [0.0, 1.0], 0.0 means do not use pssm, 1.0 ignore MPNN predictions
     pssm_threshold = 0.0  # A value between -inf + inf to restric per position AAs
@@ -1277,6 +1280,10 @@ with proteinMPNN:
                 gr.Markdown(
                     "for correct symmetric tying lenghts of homomer chains should be the same"
                 )
+            with gr.Row():
+            	omit_AAs = gr.Textbox(
+                	placeholder="Specify omitted amino acids ", label="Omitted amino acids"
+                )
             gr.Markdown("## Fixed positions")
             gr.Markdown(
                 """You can fix important positions in the protein. Resid should be specified with the same numbering as in the input pdb file. The fixed residues will be highlighted in the output. 
@@ -1429,6 +1436,7 @@ with proteinMPNN:
             sampling_temp,
             model_name,
             backbone_noise,
+            omit_AAs,
             atomsel,
         ],
         outputs=[