ColabDesign onboarded (#637)

Co-authored-by: Niklas Rindtorff <NiklasTR@users.noreply.github.com>

tools/colabdesign/Dockerfile

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+FROM us-docker.pkg.dev/colab-images/public/runtime
+RUN apt update -y \
+    && apt install -y wget nano
+RUN pip3 install hydra-core --upgrade
+RUN mkdir /app
+# installation
+COPY install.py /app
+RUN cd app && python3 install.py
+COPY . /app
+# entrypoint
+WORKDIR /app
+ENTRYPOINT []
+CMD ["bash"]

tools/colabdesign/_colabdesign-dev.json

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+{
+    "class": "CommandLineTool",
+    "name": "colabdesign-dev",
+    "description": "one-pot design of protein backbones and sequences",
+    "author": "",
+    "baseCommand": ["/bin/bash", "-c"],
+    "arguments": [
+        "wget https://raw.githubusercontent.com/labdao/plex/add_colabdesign_frfr/tools/colabdesign/install.py;",
+        "wget https://raw.githubusercontent.com/labdao/plex/add_colabdesign_frfr/tools/colabdesign/main.py;",
+        "mv /inputs/*.pdb /inputs/target_protein.pdb && mv /inputs/*.yaml /inputs/config.yaml;",
+        "python install.py;",
+        "echo 'Install complete!';",
+        "echo 'Attempting main.py...';",
+        "python main.py;",
+        "echo 'main.py complete!';"
+      ],
+    "dockerPull": "docker.io/niklastr/dev@sha256:01dd6d1eb418d67e97e7517de220e76f9403517502efa411f68c2eeb88977d0f",
+    "gpuBool": true,
+    "networkBool": true,
+    "inputs": {
+      "protein": {
+        "type": "File",
+        "item": "",
+        "glob": ["*.pdb"]
+      },
+      "config": {
+        "type": "File",
+        "item": "",
+        "glob": ["*.yaml"]
+      }
+    },
+    "outputs": {
+      "compressed_designs": {
+        "type": "Array",
+        "item": "File",
+        "glob": ["*.zip"]
+      }
+    }
+  }

tools/colabdesign/colabdesign.json

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+{
+  "class": "CommandLineTool",
+  "name": "colabdesign-dev",
+  "description": "one-pot design of protein backbones and sequences",
+  "author": "",
+  "baseCommand": ["/bin/bash", "-c"],
+  "arguments": [
+      "mv /inputs/*.pdb /inputs/target_protein.pdb && mv /inputs/*.yaml /inputs/config.yaml;",
+      "python main.py;"
+    ],
+  "dockerPull": "quay.io/labdao/colabdesign@sha256:800f4532138afa9664278d6af4769a6f2c3e30fa554cb53e4a0e9491c10bb48a",
+  "gpuBool": true,
+  "networkBool": true,
+  "inputs": {
+    "protein": {
+      "type": "File",
+      "item": "",
+      "glob": ["*.pdb"]
+    },
+    "config": {
+      "type": "File",
+      "item": "",
+      "glob": ["*.yaml"]
+    }
+  },
+  "outputs": {
+    "best_design": {
+      "type": "File",
+      "item": "",
+      "glob": ["best.pdb"]
+    },
+    "design_scores": {
+      "type": "File",
+      "item": "",
+      "glob": ["mpnn_results.csv"]
+    },
+    "design_sequences": {
+      "type": "File",
+      "item": "",
+      "glob": ["design.fasta"]
+    },
+    "compressed_designs": {
+      "type": "Array",
+      "item": "File",
+      "glob": ["*.zip"]
+    }
+  }
+}

tools/colabdesign/config.yaml

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+basic_settings:
+  experiment_name: default
+  binder_length: 50
+  pdb: /inputs/target_protein.pdb
+  pdb_chain: D
+  num_designs: 2
+advanced_settings:
+  pdb_start_residue: 50
+  pdb_end_residue: 200
+  hotspot: ''
+  min_binder_length: null
+  max_binder_length: null
+  use_beta_model: false
+expert_settings:
+  RFDiffusion_Binder:
+    contigs_override: ''
+    # the contigs_override completely overrules all other contig related settings. Make sure it is '' if you do not want to overwrite settings.
+    iterations: 50
+    visual: none
+  RFDiffusion_Symmetry:
+    symmetry: none
+    order: 1
+    chains: ''
+    add_potential: true
+  ProteinMPNN:
+    num_seqs: 8
+    rm_aa: C
+    mpnn_sampling_temp: 0.1
+    use_solubleMPNN: true
+    initial_guess: true
+  Alphafold:
+    use_multimer: false
+    num_recycles: 3

tools/colabdesign/dev

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+FROM us-docker.pkg.dev/colab-images/public/runtime
+RUN apt update -y \
+    && apt install -y wget nano
+RUN pip3 install hydra-core --upgrade
+RUN mkdir /app
+#entrypoint
+WORKDIR /app
+ENTRYPOINT []
+CMD ["bash"]

tools/colabdesign/install.py

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+import os, time, signal
+import sys, random, string, re
+
+print("Starting install.py...")
+
+if not os.path.isdir("params"):
+  os.system("apt-get install aria2")
+  os.system("mkdir params")
+  # send param download into background
+  os.system("(\
+  aria2c -q -x 16 https://files.ipd.uw.edu/krypton/schedules.zip; \
+  aria2c -q -x 16 http://files.ipd.uw.edu/pub/RFdiffusion/6f5902ac237024bdd0c176cb93063dc4/Base_ckpt.pt; \
+  aria2c -q -x 16 http://files.ipd.uw.edu/pub/RFdiffusion/e29311f6f1bf1af907f9ef9f44b8328b/Complex_base_ckpt.pt; \
+  aria2c -q -x 16 http://files.ipd.uw.edu/pub/RFdiffusion/f572d396fae9206628714fb2ce00f72e/Complex_beta_ckpt.pt; \
+  aria2c -q -x 16 https://storage.googleapis.com/alphafold/alphafold_params_2022-12-06.tar; \
+  tar -xf alphafold_params_2022-12-06.tar -C params; \
+  touch params/done.txt) &")
+
+if not os.path.isdir("RFdiffusion"):
+  print("installing RFdiffusion...")
+  os.system("git clone https://github.com/sokrypton/RFdiffusion.git")
+  os.system("pip -q install jedi omegaconf hydra-core icecream pyrsistent")
+  os.system("pip install dgl==1.0.2+cu116 -f https://data.dgl.ai/wheels/cu116/repo.html")
+  os.system("cd RFdiffusion/env/SE3Transformer; pip -q install --no-cache-dir -r requirements.txt; pip -q install .")
+  os.system("wget -qnc https://files.ipd.uw.edu/krypton/ananas")
+  os.system("chmod +x ananas")
+
+if not os.path.isdir("colabdesign"):
+  print("installing ColabDesign...")
+  os.system("pip -q install git+https://github.com/sokrypton/ColabDesign.git")
+  os.system("ln -s /usr/local/lib/python3.*/dist-packages/colabdesign colabdesign")
+
+if not os.path.isdir("RFdiffusion/models"):
+  print("downloading RFdiffusion params...")
+  os.system("mkdir RFdiffusion/models")
+  models = ["Base_ckpt.pt","Complex_base_ckpt.pt","Complex_beta_ckpt.pt"]
+  for m in models:
+    while os.path.isfile(f"{m}.aria2"):
+      time.sleep(5)
+  os.system(f"mv {' '.join(models)} RFdiffusion/models")
+  os.system("unzip schedules.zip; rm schedules.zip")
+
+if 'RFdiffusion' not in sys.path:
+  os.environ["DGLBACKEND"] = "pytorch"
+  sys.path.append('RFdiffusion')
+
+print("Completed install.py...")