Fix various environment installation issues

Author: amorehead

.gitignore

@@ -165,9 +165,10 @@ configs/local/default.yaml
 # Forks
 /workdir/
 /forks/alphafold3/*prediction_outputs/
-/forks/chai-lab/chai-lab/
-/forks/chai-lab/prediction_inputs/
-/forks/chai-lab/prediction_outputs/
+/forks/chai-lab-orig/
+/forks/chai-lab*/chai-lab/
+/forks/chai-lab*/prediction_inputs/
+/forks/chai-lab*/prediction_outputs/
 /forks/DiffDock1.0/
 /forks/DiffDock/DiffDock/
 /forks/DynamicBind/*.npy

README.md

@@ -55,9 +55,9 @@ To reproduce, customize, or extend the `PoseBench` benchmark, we recommend fully
 First, install `mamba` for dependency management (as a fast alternative to Anaconda)
 
 ```bash
-wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
-bash Mambaforge-$(uname)-$(uname -m).sh  # accept all terms and install to the default location
-rm Mambaforge-$(uname)-$(uname -m).sh  # (optionally) remove installer after using it
+wget "https://github.com/conda-forge/miniforge/releases/download/24.11.3-0/Miniforge3-$(uname)-$(uname -m).sh"
+bash Miniforge3-$(uname)-$(uname -m).sh  # accept all terms and install to the default location
+rm Miniforge3-$(uname)-$(uname -m).sh  # (optionally) remove installer after using it
 source ~/.bashrc  # alternatively, one can restart their shell session to achieve the same result
 ```
 
@@ -84,7 +84,7 @@ pip install -e . --no-deps
 # - casp15_ligand_scoring environment (~3 GB)
 mamba env create -f environments/casp15_ligand_scoring_environment.yaml
 conda activate casp15_ligand_scoring  # NOTE: one still needs to use `conda` to (de)activate environments
-pip3 install -e .
+pip3 install -e .  # NOTE: must comment out `posecheck` requirement in `pyproject.toml` beforehand and restore it thereafter
 # - DiffDock environment (~13 GB)
 mamba env create -f environments/diffdock_environment.yaml --prefix forks/DiffDock/DiffDock/
 conda activate forks/DiffDock/DiffDock/  # NOTE: one still needs to use `conda` to (de)activate environments

environments/casp15_ligand_scoring_environment.yaml

@@ -104,5 +104,5 @@ dependencies:
       - scipy==1.7.3
       - six==1.16.0
       - spyrmsd==0.6.0
-      - tqdm-4.67.1
+      - tqdm==4.67.1
       - zipp==3.15.0

environments/posebench_environment.yaml

@@ -196,7 +196,7 @@ dependencies:
   - mkl=2022.1.0=h84fe81f_915
   - mkl-devel=2022.1.0=ha770c72_916
   - mkl-include=2022.1.0=h84fe81f_915
-  - mmseqs2=17.b804f=hd6d6fdc_1
+  # - mmseqs2=17.b804f=hd6d6fdc_1  # NOTE: This package is only required for failure mode analyses
   - mpc=1.3.1=hfe3b2da_0
   - mpfr=4.2.1=h9458935_1
   - munkres=1.1.4=pyh9f0ad1d_0

notebooks/failure_modes_analysis_plotting.ipynb

@@ -36,6 +36,26 @@
     "from posebench.utils.data_utils import parse_fasta"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "#### Install MMseqs2"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "vscode": {
+     "languageId": "shellscript"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "!mamba install -c bioconda mmseqs2=17.b804f=hd6d6fdc_1"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

pyproject.toml

@@ -70,7 +70,7 @@ dependencies = [
     "seaborn",         # for plotting
     "setuptools",      # for packaging
     "spyrmsd",         # for RMSD calculations
-    "wrapt_timeout_decorator>=1.5.1", # for preventing certain functions from executing indefinitely
+    "wrapt_timeout_decorator", # for preventing certain functions from executing indefinitely
     "tqdm",            # progress bars
     "loguru",          # for cleaner logging
 ]