as-cle-bert commited on
Commit
7f124ce
Β·
verified Β·
1 Parent(s): 127f385

Update app.py

Browse files
Files changed (1) hide show
  1. app.py +15 -5
app.py CHANGED
@@ -3,7 +3,7 @@ from transformers.models.esm.openfold_utils.protein import to_pdb, Protein as OF
3
  from transformers.models.esm.openfold_utils.feats import atom14_to_atom37
4
  from proteins_viz import *
5
  import gradio as gr
6
- import spaces
7
 
8
  def convert_outputs_to_pdb(outputs):
9
  final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs)
@@ -40,7 +40,7 @@ torch.backends.cuda.matmul.allow_tf32 = True
40
 
41
  model.trunk.set_chunk_size(64)
42
 
43
- @spaces.GPU(duration=120)
44
  def fold_protein(test_protein):
45
  tokenized_input = tokenizer([test_protein], return_tensors="pt", add_special_tokens=False)['input_ids']
46
  tokenized_input = tokenized_input.cuda()
@@ -55,8 +55,18 @@ def fold_protein(test_protein):
55
  iface = gr.Interface(
56
  title="everything-ai-proteinfold",
57
  fn=fold_protein,
58
- inputs="text",
59
- outputs="image",
 
 
 
 
 
 
 
 
 
 
60
  )
61
 
62
- iface.launch(server_name="0.0.0.0", share=False)
 
3
  from transformers.models.esm.openfold_utils.feats import atom14_to_atom37
4
  from proteins_viz import *
5
  import gradio as gr
6
+
7
 
8
  def convert_outputs_to_pdb(outputs):
9
  final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs)
 
40
 
41
  model.trunk.set_chunk_size(64)
42
 
43
+
44
  def fold_protein(test_protein):
45
  tokenized_input = tokenizer([test_protein], return_tensors="pt", add_special_tokens=False)['input_ids']
46
  tokenized_input = tokenized_input.cuda()
 
55
  iface = gr.Interface(
56
  title="everything-ai-proteinfold",
57
  fn=fold_protein,
58
+ inputs=gr.Textbox(
59
+ label="Protein Sequence",
60
+ info="Find sequences examples below, and complete examples with images at: https://github.com/AstraBert/proteinviz/tree/main/examples.md; if you input a sequence, you're gonna get the static image and the HTML file with the 3D model to explore and play with",
61
+ lines=50,
62
+ value=f"Paste or write amino-acidic sequence here",
63
+ ),
64
+ outputs=[gr.Image(label="Protein static image"), gr.File(label="Protein 3D model HTML")],
65
+ examples=[
66
+ {"sequence": "MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH"},
67
+ {"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS"},
68
+ {"sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"},
69
+ ]
70
  )
71
 
72
+ iface.launch(server_name="0.0.0.0", share=False)