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Simon Duerr commited on
Commit
0fc2f31
•
1 Parent(s): 334e3a1

fix:zip file path, memory consumption, feat: surface toggle, 6moa example

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Files changed (3) hide show
  1. app.py +25 -3
  2. examples/6moa_ligand.sdf +71 -0
  3. examples/6moa_protein_processed.pdb +0 -0
app.py CHANGED
@@ -156,6 +156,7 @@ def molecule(input_pdb, ligand_pdb, original_ligand):
156
  </head>
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  <body>
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  <button id="startanimation">Replay diffusion process</button>
 
159
  <div>
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  <span class="green"></span> Uploaded ligand position
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  <span class="magenta"></span> Predicted ligand position
@@ -174,7 +175,8 @@ def molecule(input_pdb, ligand_pdb, original_ligand):
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  + """
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  let viewer = null;
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-
 
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  $(document).ready(function () {
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  let element = $("#container");
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  let config = { backgroundColor: "white" };
@@ -197,6 +199,15 @@ def molecule(input_pdb, ligand_pdb, original_ligand):
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  $("#startanimation").click(function() {
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  viewer.animate({loop: "forward",reps: 1});
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  });
 
 
 
 
 
 
 
 
 
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  </script>
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  </body></html>"""
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  )
@@ -212,7 +223,7 @@ import sys
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213
 
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  def esm(protein_path, out_file):
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- print("runingn esm")
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  esm_embedding_prep(out_file, protein_path)
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  # create args object with defaults
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  os.environ["HOME"] = "esm/model_weights"
@@ -449,11 +460,15 @@ def update(inp, file, ligand_inp, ligand_file, n_it):
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  failures += 1
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  return None
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  # zip outputs
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- zippath = shutil.make_archive(pdb_path, "zip", write_dir)
 
 
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  print("Zipped outputs to", zippath)
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  labels = [
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  f"rank {i+1}, confidence {confidences[i]:.2f}" for i in range(len(filenames))
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  ]
 
 
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  return (
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  molecule(pdb_path, filenames[0], ligand_file),
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  gr.Dropdown.update(choices=labels, value=labels[0]),
@@ -515,6 +530,13 @@ with demo:
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  "examples/6w70_ligand.sdf",
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  10,
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  ],
 
 
 
 
 
 
 
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  [
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  "",
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  "examples/6o5u_protein_processed.pdb",
 
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  </head>
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  <body>
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  <button id="startanimation">Replay diffusion process</button>
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+ <button id="Toggle surface">Toggle surface representation</button>
160
  <div>
161
  <span class="green"></span> Uploaded ligand position
162
  <span class="magenta"></span> Predicted ligand position
 
175
  + """
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  let viewer = null;
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+ let surface = false;
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+ let surf = null;
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  $(document).ready(function () {
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  let element = $("#container");
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  let config = { backgroundColor: "white" };
 
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  $("#startanimation").click(function() {
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  viewer.animate({loop: "forward",reps: 1});
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  });
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+ $("#togglesurface").click(function() {
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+ if (surface!=true){
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+ surf = viewer.addSurface(py3Dmol.VDW,{"opacity":0.9,"color":"white"});
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+ surface = true;
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+ }else{
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+ removeSurface(surf)
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+ surface = false;
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+ }
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+ });
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  </script>
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  </body></html>"""
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  )
 
223
 
224
 
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  def esm(protein_path, out_file):
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+ print("running esm")
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  esm_embedding_prep(out_file, protein_path)
228
  # create args object with defaults
229
  os.environ["HOME"] = "esm/model_weights"
 
460
  failures += 1
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  return None
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  # zip outputs
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+ zippath = shutil.make_archive(
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+ os.path.join("results", os.path.basename(pdb_path)), "zip", write_dir
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+ )
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  print("Zipped outputs to", zippath)
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  labels = [
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  f"rank {i+1}, confidence {confidences[i]:.2f}" for i in range(len(filenames))
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  ]
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+
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+ torch.cuda.empty_cache()
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  return (
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  molecule(pdb_path, filenames[0], ligand_file),
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  gr.Dropdown.update(choices=labels, value=labels[0]),
 
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  "examples/6w70_ligand.sdf",
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  10,
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  ],
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+ [
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+ "6moa",
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+ "examples/6moa_protein_processed.pdb",
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+ "",
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+ "examples/6moa_ligand.sdf",
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+ 10,
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+ ],
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  [
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  "",
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  "examples/6o5u_protein_processed.pdb",
examples/6moa_ligand.sdf ADDED
@@ -0,0 +1,71 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+
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+ RDKit 3D
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+
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+ 30 35 0 0 0 0 0 0 0 0999 V2000
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+ 7.0027 58.4275 -3.0563 N 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.0581 59.0122 -2.5200 N 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.7347 63.8265 -5.1605 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 10.2222 64.5824 -6.1570 N 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.4349 62.8237 -7.1167 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 9.6965 64.0557 -3.7051 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 4.4459 61.3389 -3.5948 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 3.3642 61.9433 -2.9935 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 2.0968 61.5645 -3.3844 C 0 0 0 0 0 0 0 0 0 0 0 0
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+ 1.8948 60.6282 -4.3295 N 0 0 0 0 0 0 0 0 0 0 0 0
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+ 1 2 1 0
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+ 2 3 2 0
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+ 4 5 2 0
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+ 16 12 1 0
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+ 24 20 2 0
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+ M END
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+ $$$$
examples/6moa_protein_processed.pdb ADDED
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