Merge pull request #117 from adaptyvbio/more_metrics

Add more metrics

.conda/arm64/meta.yaml

@@ -41,6 +41,8 @@ requirements:
     - awscli==1.25.60
     - bs4
     - rcsbsearch
+    - tmtools
+    - fair-esm
 
 about:
   home: https://github.com/adaptyvbio/ProteinFlow

.conda/default/meta.yaml

@@ -41,6 +41,8 @@ requirements:
     - awscli==1.25.60
     - bs4
     - rcsbsearch
+    - tmtools
+    - fair-esm
     - mmseqs2
     - foldseek
 

.github/workflows/pre-commit.yml

@@ -11,5 +11,5 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
-    - uses: actions/setup-python@v3
+    - uses: actions/setup-python@v4
     - uses: pre-commit/[email protected]

.gitignore

@@ -10,9 +10,13 @@ rcsbsearch/
 *ipynb
 ./*zip
 tmp/
+esmfold_output/
+igfold_output/
+igfold_refine_output/
+immunebuilder_output/
 all_structures/
 all_structures.zip
+run_metrics.py
+*.csv
 esmfold_output/
 igfold_output/
-*.csv
-run_metrics.py

install_optional.sh

@@ -0,0 +1,14 @@
+conda install -y -c conda-forge openmm==7.7.0 pdbfixer
+conda install -y -c bioconda anarci
+
+python -m pip install torch==1.13.1+cu117 torchvision==0.14.1+cu117 torchaudio==0.13.1 --extra-index-url https://download.pytorch.org/whl/cu117
+# choose the CUDA version that matches your system (check with `nvcc --version` and get the right command at https://pytorch.org/get-started/previous-versions/)
+
+python -m pip install "fair-esm[esmfold]"
+python -m pip install 'dllogger @ git+https://github.com/NVIDIA/dllogger.git'
+python -m pip install 'openfold @ git+https://github.com/aqlaboratory/openfold.git@4b41059694619831a7db195b7e0988fc4ff3a307'
+
+python -m pip install ablang igfold immunebuilder
+
+python -m pip install -e .
+python -m pip install ipykernel

proteinflow/constants.py

@@ -245,4 +245,5 @@ def _PMAP(x):
     ]
 
 
-COLORS = ["#62B9DC", "#EAB1C5", "#0C9094", "#8090E6", "#96E396", "#FCAC97", "#740E66"]
+COLORS = ["#8DCBF7", "#9CBBFF", "#8EDBEB", "#8090E6", "#96E396", "#FCAC97", "#740E66"]
+ACCENT_COLOR = "#D96181"