Update app.py

app.py

@@ -1,4 +1,4 @@
-import re
+import re, os
 from pathlib import Path
 import gradio as gr
 
@@ -25,6 +25,7 @@ def make_cond_seq(seq_len, msa_file, n_sequences, model_type):
     if model_type == "EvoDiff-MSA":
         checkpoint = MSA_OA_DM_MAXSUB()
         model, collater, tokenizer, scheme = checkpoint
+        print(f"MSA File Path: {msa_file.name}")
         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')
 
     return generated_sequence
@@ -49,6 +50,7 @@ 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 = ''
+        print("Current Scaffold Directory:", os.getcwd())
         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')
@@ -67,9 +69,7 @@ usg_app = gr.Interface(
                 gr.Slider(10, 250, step=1, label = "Sequence Length"),
                 gr.Dropdown(["EvoDiff-Seq-OADM 38M", "EvoDiff-D3PM-Uniform 38M"], value="EvoDiff-Seq-OADM 38M", type="value", label = "Model")
                 ],
-            outputs=[
-                "text"
-            ],
+            outputs=["text"],
             title = "Unconditional sequence generation",
             description="Generate a sequence with `EvoDiff-Seq-OADM 38M` (smaller/faster) or `EvoDiff-D3PM-Uniform 38M` (larger/slower) models."
             )
@@ -82,9 +82,7 @@ csg_app = gr.Interface(
                 gr.Number(value=64, placeholder=64, precision=0, label = "Number of Sequences to Sample"),
                 gr.Dropdown(["EvoDiff-MSA"], value="EvoDiff-MSA", type="value", label = "Model")
                 ],
-            outputs=[
-                "text"
-            ],
+            outputs=["text"],
             # examples=[["https://github.com/microsoft/evodiff/raw/main/examples/example_files/bfd_uniclust_hits.a3m"]], 
             title = "Conditional sequence generation",
             description="Evolutionary guided sequence generation with the `EvoDiff-MSA` model."
@@ -93,14 +91,14 @@ csg_app = gr.Interface(
 idr_app = gr.Interface(
             fn=make_inpainted_idrs,
             inputs=[
-                gr.Textbox(placeholder="DQTERTVRSFEGRRTAPYLDSRNVLTIGYGHLLNRPGANKSWEGRLTSALPREFKQRLTELAASQLHETDVRLATARAQALYGSGAYFESVPVSLNDLWFDSVFNLGERKLLNWSGLRTKLESRDWGAAAKDLGRHTFGREPVSRRMAESMRMRRGIDLNHYNI", label = "Sequence"),
+                gr.Textbox(value = "DQTERTVRSFEGRRTAPYLDSRNVLTIGYGHLLNRPGANKSWEGRLTSALPREFKQRLTELAASQLHETDVRLATARAQALYGSGAYFESVPVSLNDLWFDSVFNLGERKLLNWSGLRTKLESRDWGAAAKDLGRHTFGREPVSRRMAESMRMRRGIDLNHYNI",
+                           placeholder="DQTERTVRSFEGRRTAPYLDSRNVLTIGYGHLLNRPGANKSWEGRLTSALPREFKQRLTELAASQLHETDVRLATARAQALYGSGAYFESVPVSLNDLWFDSVFNLGERKLLNWSGLRTKLESRDWGAAAKDLGRHTFGREPVSRRMAESMRMRRGIDLNHYNI",
+                           label = "Sequence"),
                 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")
                 ],
-            outputs=[
-                "text"
-            ],
+            outputs=["text"],
             title = "Inpainting IDRs",
             description="Inpaining a new region inside a given sequence using the `EvoDiff-Seq` model."
             )
@@ -108,15 +106,13 @@ idr_app = gr.Interface(
 scaffold_app = gr.Interface(
             fn=make_scaffold_motifs,
             inputs=[
-                gr.Textbox(placeholder="1prw", label = "PDB Code"),
+                gr.Textbox(value="1prw", 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, precision=0, label = "Scaffold Length"),
                 gr.Dropdown(["EvoDiff-Seq", "EvoDiff-MSA"], value="EvoDiff-Seq", type="value", label = "Model")
                 ],
-            outputs=[
-                "text"
-            ],
+            outputs=["text"],
             title = "Scaffolding functional motifs",
             description="Scaffolding a new functional motif inside a given PDB structure using the `EvoDiff-Seq` model."
             )