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Update app.py
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app.py
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@@ -3,7 +3,7 @@ from transformers.models.esm.openfold_utils.protein import to_pdb, Protein as OF
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from transformers.models.esm.openfold_utils.feats import atom14_to_atom37
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from proteins_viz import *
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import gradio as gr
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-
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def convert_outputs_to_pdb(outputs):
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final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs)
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@@ -40,7 +40,7 @@ torch.backends.cuda.matmul.allow_tf32 = True
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model.trunk.set_chunk_size(64)
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-
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def fold_protein(test_protein):
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tokenized_input = tokenizer([test_protein], return_tensors="pt", add_special_tokens=False)['input_ids']
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tokenized_input = tokenized_input.cuda()
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@@ -55,8 +55,18 @@ def fold_protein(test_protein):
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iface = gr.Interface(
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title="everything-ai-proteinfold",
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fn=fold_protein,
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inputs=
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)
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iface.launch(server_name="0.0.0.0", share=False)
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from transformers.models.esm.openfold_utils.feats import atom14_to_atom37
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from proteins_viz import *
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import gradio as gr
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+
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def convert_outputs_to_pdb(outputs):
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final_atom_positions = atom14_to_atom37(outputs["positions"][-1], outputs)
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model.trunk.set_chunk_size(64)
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+
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def fold_protein(test_protein):
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tokenized_input = tokenizer([test_protein], return_tensors="pt", add_special_tokens=False)['input_ids']
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tokenized_input = tokenized_input.cuda()
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iface = gr.Interface(
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title="everything-ai-proteinfold",
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fn=fold_protein,
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inputs=gr.Textbox(
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label="Protein Sequence",
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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",
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lines=50,
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value=f"Paste or write amino-acidic sequence here",
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),
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outputs=[gr.Image(label="Protein static image"), gr.File(label="Protein 3D model HTML")],
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examples=[
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{"sequence": "MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH"},
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{"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCMSCKCVLS"},
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{"sequence": "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"},
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]
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)
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iface.launch(server_name="0.0.0.0", share=False)
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