Advance required python version from 3.7 to 3.9

Dockerfile

@@ -1,5 +1,6 @@
 FROM nvidia/cuda:11.3.1-cudnn8-runtime-ubuntu18.04
 
+# ADDED THIS LINE TO PROVOKE A NEW DOCKER BUILD TO TEST THAT IS STILL WORKS
 # metainformation
 LABEL org.opencontainers.image.version = "1.0.0"
 LABEL org.opencontainers.image.authors = "Gustaf Ahdritz"
@@ -31,6 +32,6 @@ 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
+RUN patch -p0 -d /opt/conda/lib/python3.9/site-packages/ < /opt/openfold/lib/openmm.patch
 WORKDIR /opt/openfold
 RUN python3 setup.py install

environment.yml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - pytorch
 dependencies:
-  - conda-forge::python=3.7
+  - conda-forge::python=3.9
   - conda-forge::setuptools=59.5.0
   - conda-forge::pip
   - conda-forge::openmm=7.5.1

notebooks/OpenFold.ipynb

@@ -97,13 +97,16 @@
         "#@markdown **Note**: This installs the software on the Colab \n",
         "#@markdown notebook in the cloud and not on your computer.\n",
         "\n",
+        "import sys\n",
         "from IPython.utils import io\n",
         "import os\n",
         "import subprocess\n",
         "import tqdm.notebook\n",
         "\n",
         "TQDM_BAR_FORMAT = '{l_bar}{bar}| {n_fmt}/{total_fmt} [elapsed: {elapsed} remaining: {remaining}]'\n",
         "\n",
+        "python_version = '.'.join(sys.version.split('.')[:2]) # get string like \"3.9\"\n",
+        "\n",
         "try:\n",
         "  with io.capture_output() as captured:\n",
         "    %shell sudo apt install --quiet --yes hmmer\n",
@@ -125,12 +128,13 @@
         "    %shell conda install -y -q -c conda-forge -c bioconda \\\n",
         "      kalign2=2.04 \\\n",
         "      hhsuite=3.3.0 \\\n",
-        "      python=3.8 \\\n",
+        "      python={python_version} \\\n",
         "      2>&1 1>/dev/null\n",
         "    %shell pip install -q \\\n",
         "      ml-collections==0.1.0 \\\n",
         "      PyYAML==5.4.1 \\\n",
-        "      biopython==1.79\n",
+        "      biopython==1.79 \\\n",
+        "      modelcif==0.7\n",
         "\n",
         "    # Create a ramdisk to store a database chunk to make Jackhmmer run fast.\n",
         "    %shell sudo mkdir -m 777 --parents /tmp/ramdisk\n",
@@ -183,7 +187,7 @@
         "\n",
         "    %shell conda install -y -q -c conda-forge openmm=7.5.1\n",
         "    # Apply OpenMM patch.\n",
-        "    %shell pushd /opt/conda/lib/python3.8/site-packages/ && \\\n",
+        "    %shell pushd /opt/conda/lib/python{python_version}/site-packages/ && \\\n",
         "        patch -p0 < /content/openfold/lib/openmm.patch && \\\n",
         "        popd\n",
         "    %shell conda install -y -q -c conda-forge pdbfixer=1.7\n",
@@ -220,8 +224,8 @@
         "import unittest.mock\n",
         "import sys\n",
         "\n",
-        "sys.path.insert(0, '/usr/local/lib/python3.8/site-packages/')\n",
-        "sys.path.append('/opt/conda/lib/python3.8/site-packages')\n",
+        "sys.path.insert(0, f'/usr/local/lib/python{python_version}/site-packages/')\n",
+        "sys.path.append(f'/opt/conda/lib/python{python_version}/site-packages')\n",
         "\n",
         "# Allows us to skip installing these packages\n",
         "unnecessary_modules = [\n",

openfold/np/relax/relax.py

@@ -57,7 +57,7 @@ def __init__(
         self._use_gpu = use_gpu
 
     def process(
-        self, *, prot: protein.Protein, cif_output: bool
+        self, *, prot: protein.Protein, cif_output: bool = False
     ) -> Tuple[str, Dict[str, Any], np.ndarray]:
         """Runs Amber relax on a prediction, adds hydrogens, returns PDB string."""
         out = amber_minimize.run_pipeline(

openfold/utils/script_utils.py

@@ -228,7 +228,7 @@ def prep_output(out, batch, feature_dict, feature_processor, config_preset, mult
     return unrelaxed_protein
 
 
-def relax_protein(config, model_device, unrelaxed_protein, output_directory, output_name, cif_output):
+def relax_protein(config, model_device, unrelaxed_protein, output_directory, output_name, cif_output=False):
     amber_relaxer = relax.AmberRelaxation(
         use_gpu=(model_device != "cpu"),
         **config.relax,
@@ -257,4 +257,4 @@ def relax_protein(config, model_device, unrelaxed_protein, output_directory, out
     with open(relaxed_output_path, 'w') as fp:
         fp.write(struct_str)
 
-    logger.info(f"Relaxed output written to {relaxed_output_path}...")
+    logger.info(f"Relaxed output written to {relaxed_output_path}...")

scripts/install_third_party_dependencies.sh

@@ -27,7 +27,7 @@ cd $CUR_DIR
 
 # Install DeepMind's OpenMM patch
 OPENFOLD_DIR=$PWD
-pushd lib/conda/envs/$ENV_NAME/lib/python3.7/site-packages/ \
+pushd lib/conda/envs/$ENV_NAME/lib/python3.9/site-packages/ \
     && patch -p0 < $OPENFOLD_DIR/lib/openmm.patch \
     && popd
 

setup.py

@@ -128,7 +128,7 @@ def get_cuda_bare_metal_version(cuda_dir):
     classifiers=[
         'License :: OSI Approved :: Apache Software License',
         'Operating System :: POSIX :: Linux',
-        'Programming Language :: Python :: 3.7,'
+        'Programming Language :: Python :: 3.9,'
         'Topic :: Scientific/Engineering :: Artificial Intelligence',
     ],
 )