Merge branch 'main' of https://github.com/aqlaboratory/openfold

.github/workflows/docker-image.yml

+name: Docker Image CI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Build the Docker image
+      run: docker build . --file Dockerfile --tag openfold:$(date +%s)
\ No newline at end of file

.github/workflows/undefined_names.yml

+name: undefined_names
+on: [pull_request, push]
+jobs:
+  undefined_names:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+      - run: pip install --upgrade pip
+      - run: pip install flake8
+      - run: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

.gitignore

+.vscode/
+__pycache__/
+*.egg-info
+build
+dist
+
+# files from script downloads
+data
+openfold/resources/
+tests/test_data/

CITATION.cff

+cff-version: 1.2.0
+preferred-citation:
+    authors:
+    - family-names: "Ahdritz"
+      given-names: "Gustaf"
+      orcid: https://orcid.org/0000-0001-8283-5324
+    - family-names: "Bouatta"
+      given-names: "Nazim"
+      orcid: https://orcid.org/0000-0002-6524-874X
+    - family-names: "Kadyan"
+      given-names: "Sachin"
+      orcid: https://orcid.org/0000-0002-6079-7627
+    - family-names: "Xia"
+      given-names: "Qinghui"
+    - family-names: "Gerecke"
+      given-names: "William"
+      orcid: https://orcid.org/0000-0002-9777-6192
+    - family-names: "O'Donnell"
+      given-names: "Timothy J"
+      orcid: https://orcid.org/0000-0002-9949-069X
+    - family-names: "Berenberg"
+      given-names: "Daniel"
+      orcid: https://orcid.org/0000-0003-4631-0947
+    - family-names: "Fisk"
+      given-names: "Ian"
+    - family-names: "Zanichelli"
+      given-names: "Niccolò"
+      orcid: https://orcid.org/0000-0002-3093-3587
+    - family-names: "Zhang"
+      given-names: "Bo"
+      orcid: https://orcid.org/0000-0002-9714-2827
+    - family-names: "Nowaczynski"
+      given-names: "Arkadiusz"
+      orcid: https://orcid.org/0000-0002-3351-9584
+    - family-names: "Wang"
+      given-names: "Bei"
+      orcid: https://orcid.org/0000-0003-4942-9652
+    - family-names: "Stepniewska-Dziubinska"
+      given-names: "Marta M"
+      orcid: https://orcid.org/0000-0003-4942-9652
+    - family-names: "Zhang"
+      given-names: "Shang"
+      orcid: https://orcid.org/0000-0003-0759-2080
+    - family-names: "Ojewole"
+      given-names: "Adegoke"
+      orcid: https://orcid.org/0000-0003-2661-4388
+    - family-names: "Guney"
+      given-names: "Murat Efe"
+    - family-names: "Biderman"
+      given-names: "Stella"
+      orcid: https://orcid.org/0000-0001-8228-1042
+    - family-names: "Watkins"
+      given-names: "Andrew M"
+      orcid: https://orcid.org/0000-0003-1617-1720
+    - family-names: "Ra"
+      given-names: "Stephen"
+      orcid: https://orcid.org/0000-0002-2820-0050
+    - family-names: "Lorenzo"
+      given-names: "Pablo Ribalta"
+      orcid: https://orcid.org/0000-0002-3657-8053
+    - family-names: "Nivon"
+      given-names: "Lucas"
+    - family-names: "Weitzner"
+      given-names: "Brian"
+      orcid: https://orcid.org/0000-0002-1909-0961
+    - family-names: "Ban"
+      given-names: "Yih-En"
+      orcid: https://orcid.org/0000-0003-3698-3574
+    - family-names: "Ban"
+      given-names: "Yih-En Andrew"
+      orcid: https://orcid.org/0000-0003-3698-3574
+    - family-names: "Sorger"
+      given-names: "Peter K"
+      orcid: https://orcid.org/0000-0002-3364-1838
+    - family-names: "Mostaque"
+      given-names: "Emad"
+    - family-names: "Zhang"
+      given-names: "Zhao"
+      orcid: https://orcid.org/0000-0001-5921-0035
+    - family-names: "Bonneau"
+      given-names: "Richard"
+      orcid: https://orcid.org/0000-0003-4354-7906
+    - family-names: "AlQuraishi"
+      given-names: "Mohammed"
+      orcid: https://orcid.org/0000-0001-6817-1322
+    title: "OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization"
+    type: article
+    doi: 10.1101/2022.11.20.517210
+doi: 10.1101/2022.11.20.517210
+date-released: 2021-11-12
+url: "https://doi.org/10.1101/2022.11.20.517210"

Dockerfile

+FROM nvidia/cuda:11.3.1-cudnn8-runtime-ubuntu18.04
+
+# metainformation
+LABEL org.opencontainers.image.version = "1.0.0"
+LABEL org.opencontainers.image.authors = "Gustaf Ahdritz"
+LABEL org.opencontainers.image.source = "https://github.com/aqlaboratory/openfold"
+LABEL org.opencontainers.image.licenses = "Apache License 2.0"
+LABEL org.opencontainers.image.base.name="docker.io/nvidia/cuda:10.2-cudnn8-runtime-ubuntu18.04"
+
+RUN apt-key del 7fa2af80
+RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
+RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
+
+RUN apt-get update && apt-get install -y wget libxml2 cuda-minimal-build-11-3 libcusparse-dev-11-3 libcublas-dev-11-3 libcusolver-dev-11-3 git
+RUN wget -P /tmp \
+    "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" \
+    && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \
+    && rm /tmp/Miniconda3-latest-Linux-x86_64.sh
+ENV PATH /opt/conda/bin:$PATH
+
+COPY environment.yml /opt/openfold/environment.yml
+
+# installing into the base environment since the docker container wont do anything other than run openfold
+RUN conda env update -n base --file /opt/openfold/environment.yml && conda clean --all
+
+COPY openfold /opt/openfold/openfold
+COPY scripts /opt/openfold/scripts
+COPY run_pretrained_openfold.py /opt/openfold/run_pretrained_openfold.py
+COPY train_openfold.py /opt/openfold/train_openfold.py
+COPY setup.py /opt/openfold/setup.py
+COPY lib/openmm.patch /opt/openfold/lib/openmm.patch
+RUN wget -q -P /opt/openfold/openfold/resources \
+    https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
+RUN patch -p0 -d /opt/conda/lib/python3.7/site-packages/ < /opt/openfold/lib/openmm.patch
+WORKDIR /opt/openfold
+RUN python3 setup.py install

LICENSE

+
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+                           Version 2.0, January 2004
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deepspeed_config.json

+{
+  "fp16": {
+    "enabled": false,
+    "min_loss_scale": 1
+  },
+  "amp": {
+    "enabled": false,
+    "opt_level": "O2"
+  },
+  "bfloat16": {
+    "enabled": true
+  },
+  "zero_optimization": {
+    "stage": 2,
+    "cpu_offload": true,
+    "contiguous_gradients": true
+  },
+  "activation_checkpointing": {
+    "partition_activations": true,
+    "cpu_checkpointing": false,
+    "profile": false
+  },
+  "gradient_clipping": 0.1
+}

environment.yml

+name: openfold_venv
+channels:
+  - conda-forge
+  - bioconda
+  - pytorch
+dependencies:
+  - conda-forge::python=3.7
+  - conda-forge::setuptools=59.5.0
+  - conda-forge::pip
+  - conda-forge::openmm=7.5.1
+  - conda-forge::pdbfixer
+  - conda-forge::cudatoolkit==11.3.*
+  - bioconda::hmmer==3.3.2
+  - bioconda::hhsuite==3.3.0
+  - bioconda::kalign2==2.04
+  - pytorch::pytorch=1.12.*
+  - pip:
+      - biopython==1.79
+      - deepspeed==0.5.10
+      - dm-tree==0.1.6
+      - ml-collections==0.1.0
+      - numpy==1.21.2
+      - PyYAML==5.4.1
+      - requests==2.26.0
+      - scipy==1.7.1
+      - tqdm==4.62.2
+      - typing-extensions==3.10.0.2
+      - pytorch_lightning==1.5.10
+      - wandb==0.12.21
+      - modelcif==0.7
+      - git+https://github.com/NVIDIA/dllogger.git

lib/openmm.patch

+Index: simtk/openmm/app/topology.py
+===================================================================
+--- simtk.orig/openmm/app/topology.py
++++ simtk/openmm/app/topology.py
+@@ -356,19 +356,35 @@
+         def isCyx(res):
+             names = [atom.name for atom in res._atoms]
+             return 'SG' in names and 'HG' not in names
++        # This function is used to prevent multiple di-sulfide bonds from being
++        # assigned to a given atom. This is a DeepMind modification.
++        def isDisulfideBonded(atom):
++            for b in self._bonds:
++                if (atom in b and b[0].name == 'SG' and
++                    b[1].name == 'SG'):
++                    return True
++
++            return False
+ 
+         cyx = [res for res in self.residues() if res.name == 'CYS' and isCyx(res)]
+         atomNames = [[atom.name for atom in res._atoms] for res in cyx]
+         for i in range(len(cyx)):
+             sg1 = cyx[i]._atoms[atomNames[i].index('SG')]
+             pos1 = positions[sg1.index]
++            candidate_distance, candidate_atom = 0.3*nanometers, None
+             for j in range(i):
+                 sg2 = cyx[j]._atoms[atomNames[j].index('SG')]
+                 pos2 = positions[sg2.index]
+                 delta = [x-y for (x,y) in zip(pos1, pos2)]
+                 distance = sqrt(delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2])
+-                if distance < 0.3*nanometers:
+-                    self.addBond(sg1, sg2)
++                if distance < candidate_distance and not isDisulfideBonded(sg2):
++                    candidate_distance = distance
++                    candidate_atom = sg2
++            # Assign bond to closest pair.
++            if candidate_atom:
++                self.addBond(sg1, candidate_atom)
++
++
+ 
+ class Chain(object):
+     """A Chain object represents a chain within a Topology."""

notebooks/environment.yml

+name: openfold_venv
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::openmm=7.5.1
+  - conda-forge::pdbfixer
+  - bioconda::hmmer==3.3.2
+  - bioconda::hhsuite==3.3.0
+  - bioconda::kalign2==2.04
+  - pip:
+      - biopython==1.79
+      - dm-tree==0.1.6
+      - ml-collections==0.1.0
+      - PyYAML==5.4.1
+      - requests==2.26.0
+      - typing-extensions==3.10.0.2

openfold/__init__.py

+from . import model
+from . import utils
+from . import np
+from . import resources
+
+__all__ = ["model", "utils", "np", "data", "resources"]

openfold/data/errors.py

+# Copyright 2021 AlQuraishi Laboratory
+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""General-purpose errors used throughout the data pipeline"""
+class Error(Exception):
+    """Base class for exceptions."""
+
+
+class MultipleChainsError(Error):
+    """An error indicating that multiple chains were found for a given ID."""