Spaces:
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Add py3Dmol
Browse files- app.py +30 -0
- requirements.txt +3 -1
app.py
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@@ -3,6 +3,7 @@ from evodiff.pretrained import OA_DM_38M, D3PM_UNIFORM_38M, MSA_OA_DM_MAXSUB
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from evodiff.generate import generate_oaardm, generate_d3pm
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from evodiff.generate_msa import generate_query_oadm_msa_simple
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import re
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def a3m_file(file):
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@@ -29,6 +30,35 @@ def make_cond_seq(seq_len, msa_file, model_type):
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return generated_sequence
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usg_app = gr.Interface(
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fn=make_uncond_seq,
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inputs=[
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from evodiff.generate import generate_oaardm, generate_d3pm
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from evodiff.generate_msa import generate_query_oadm_msa_simple
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import re
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import py3Dmol
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def a3m_file(file):
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return generated_sequence
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def display_pdb(path_to_pdb):
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'''
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#function to display pdb in py3dmol
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SOURCE: https://huggingface.co/spaces/merle/PROTEIN_GENERATOR/blob/main/app.py
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'''
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pdb = open(path_to_pdb, "r").read()
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view = py3Dmol.view(width=500, height=500)
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view.addModel(pdb, "pdb")
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view.setStyle({'model': -1}, {"cartoon": {'colorscheme':{'prop':'b','gradient':'roygb','min':0,'max':1}}})#'linear', 'min': 0, 'max': 1, 'colors': ["#ff9ef0","#a903fc",]}}})
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view.zoomTo()
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output = view._make_html().replace("'", '"')
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print(view._make_html())
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x = f"""<!DOCTYPE html><html></center> {output} </center></html>""" # do not use ' in this input
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return f"""<iframe height="500px" width="100%" name="result" allow="midi; geolocation; microphone; camera;
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display-capture; encrypted-media;" sandbox="allow-modals allow-forms
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allow-scripts allow-same-origin allow-popups
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allow-top-navigation-by-user-activation allow-downloads" allowfullscreen=""
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allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""
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'''
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return f"""<iframe style="width: 100%; height:700px" name="result" allow="midi; geolocation; microphone; camera;
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display-capture; encrypted-media;" sandbox="allow-modals allow-forms
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allow-scripts allow-same-origin allow-popups
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allow-top-navigation-by-user-activation allow-downloads" allowfullscreen=""
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allowpaymentrequest="" frameborder="0" srcdoc='{x}'></iframe>"""
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'''
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usg_app = gr.Interface(
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fn=make_uncond_seq,
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inputs=[
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requirements.txt
CHANGED
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@@ -21,4 +21,6 @@ evodiff
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torch==2.0.1
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torchvision
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torch_geometric
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torch_scatter
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torch==2.0.1
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torchvision
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torch_geometric
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torch_scatter
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py3Dmol
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colabfold[alphafold-minus-jax]@git+https://github.com/sokrypton/ColabFold
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