Ensure all ints are ints

README.md

@@ -1,8 +1,8 @@
 ---
-title: Evodiff
-emoji: 🐠
-colorFrom: pink
-colorTo: pink
+title: EvoDiff
+emoji: 🧬
+colorFrom: blue
+colorTo: orange
 sdk: gradio
 sdk_version: 3.45.2
 app_file: app.py

app.py

@@ -70,12 +70,12 @@ def make_uncond_seq(seq_len, model_type, pred_structure):
     if model_type == "EvoDiff-Seq-OADM 38M":
         checkpoint = OA_DM_38M()
         model, collater, tokenizer, scheme = checkpoint
-        tokeinzed_sample, generated_sequence = generate_oaardm(model, tokenizer, seq_len, batch_size=1, device='cpu')
+        tokeinzed_sample, generated_sequence = generate_oaardm(model, tokenizer, int(seq_len), batch_size=1, device='cpu')
     
     if model_type == "EvoDiff-D3PM-Uniform 38M":
         checkpoint = D3PM_UNIFORM_38M(return_all=True)
         model, collater, tokenizer, scheme, timestep, Q_bar, Q = checkpoint
-        tokeinzed_sample, generated_sequence = generate_d3pm(model, tokenizer, Q, Q_bar, timestep, seq_len, batch_size=1, device='cpu')
+        tokeinzed_sample, generated_sequence = generate_d3pm(model, tokenizer, Q, Q_bar, timestep, int(seq_len), batch_size=1, device='cpu')
 
     if pred_structure:
         path_to_pdb = predict_protein(generated_sequence)
@@ -85,11 +85,11 @@ def make_uncond_seq(seq_len, model_type, pred_structure):
     else:
         return generated_sequence, None
 
-def make_cond_seq(seq_len, msa_file, model_type, pred_structure):
+def make_cond_seq(seq_len, msa_file, n_sequences, model_type, pred_structure):
     if model_type == "EvoDiff-MSA":
         checkpoint = MSA_OA_DM_MAXSUB()
         model, collater, tokenizer, scheme = checkpoint
-        tokeinzed_sample, generated_sequence  = generate_query_oadm_msa_simple(msa_file.name, model, tokenizer, n_sequences=64, seq_length=seq_len, device='cpu', selection_type='random')
+        tokeinzed_sample, generated_sequence  = generate_query_oadm_msa_simple(msa_file.name, model, tokenizer, int(n_sequences), seq_length=int(seq_len), device='cpu', selection_type='random')
 
     if pred_structure:
         path_to_pdb = predict_protein(generated_sequence)
@@ -103,7 +103,7 @@ def make_inpainted_idrs(sequence, start_idx, end_idx, model_type, pred_structure
     if model_type == "EvoDiff-Seq":
         checkpoint = OA_DM_38M()
         model, collater, tokenizer, scheme = checkpoint
-        sample, entire_sequence, generated_idr = inpaint_simple(model, sequence, start_idx, end_idx, tokenizer=tokenizer, device='cpu')
+        sample, entire_sequence, generated_idr = inpaint_simple(model, sequence, int(start_idx), int(end_idx), tokenizer=tokenizer, device='cpu')
 
         generated_idr_output = {
             "original_sequence": sequence,
@@ -125,6 +125,8 @@ def make_scaffold_motifs(pdb_code, start_idx, end_idx, scaffold_length, model_ty
         checkpoint = OA_DM_38M()
         model, collater, tokenizer, scheme = checkpoint
         data_top_dir = './'
+        start_idx = list(map(int, start_idx.strip('][').split(', ')))
+        end_idx = list(map(int, end_idx.strip('][').split(', ')))
         generated_sequence, new_start_idx, new_end_idx = generate_scaffold(model, pdb_code, start_idx, end_idx, scaffold_length, data_top_dir, tokenizer, device='cpu')
 
         generated_scaffold_output = {
@@ -162,6 +164,7 @@ csg_app = gr.Interface(
             inputs=[
                 gr.Slider(10, 100, label = "Sequence Length"),
                 gr.File(file_types=["a3m"], label = "MSA File"),
+                gr.Number(value=1, placeholder=1, precision=0, label = "Number of Sequences")
                 gr.Dropdown(["EvoDiff-MSA"], value="EvoDiff-MSA", type="value", label = "Model"),
                 gr.Checkbox(value=False, label = "Predict Structure?", visible=False)
                 ],
@@ -178,8 +181,8 @@ idr_app = gr.Interface(
             fn=make_inpainted_idrs,
             inputs=[
                 gr.Textbox(placeholder="DQTERTVRSFEGRRTAPYLDSRNVLTIGYGHLLNRPGANKSWEGRLTSALPREFKQRLTELAASQLHETDVRLATARAQALYGSGAYFESVPVSLNDLWFDSVFNLGERKLLNWSGLRTKLESRDWGAAAKDLGRHTFGREPVSRRMAESMRMRRGIDLNHYNI", label = "Sequence"),
-                gr.Number(value=20, placeholder=20, label = "Start Index"),
-                gr.Number(value=50, placeholder=50, label = "End Index"),
+                gr.Number(value=20, placeholder=20, precision=0, label = "Start Index"),
+                gr.Number(value=50, placeholder=50, precision=0, label = "End Index"),
                 gr.Dropdown(["EvoDiff-Seq"], value="EvoDiff-Seq", type="value", label = "Model"),
                 gr.Checkbox(value=False, label = "Predict Structure?", visible=False)
                 ],
@@ -197,7 +200,7 @@ scaffold_app = gr.Interface(
                 gr.Textbox(placeholder="1prw", label = "PDB Code"),
                 gr.Textbox(value="[15, 51]", placeholder="[15, 51]", label = "Start Index (as list)"),
                 gr.Textbox(value="[34, 70]", placeholder="[34, 70]", label = "End Index (as list)"),
-                gr.Number(value=75, placeholder=75, label = "Scaffold Length"),
+                gr.Number(value=75, placeholder=75, precision=0, label = "Scaffold Length"),
                 gr.Dropdown(["EvoDiff-Seq", "EvoDiff-MSA"], value="EvoDiff-Seq", type="value", label = "Model"),
                 gr.Checkbox(value=False, label = "Predict Structure?", visible=False)
                 ],