initial alphafold2

3972a903 · zhuwenwen · 3972a903 · 3972a903 · 3972a903 · 3972a903
Commit 3972a903 authored Apr 10, 2023 by zhuwenwen
20 changed files
--- a/alphafold/relax/cleanup_test.py
+++ b/alphafold/relax/cleanup_test.py
--- a/alphafold/relax/relax.py
+++ b/alphafold/relax/relax.py
--- a/alphafold/relax/relax_test.py
+++ b/alphafold/relax/relax_test.py
--- a/alphafold/relax/testdata/model_output.pdb
+++ b/alphafold/relax/testdata/model_output.pdb
--- a/alphafold/relax/testdata/multiple_disulfides_target.pdb
+++ b/alphafold/relax/testdata/multiple_disulfides_target.pdb
--- a/alphafold/relax/testdata/with_violations.pdb
+++ b/alphafold/relax/testdata/with_violations.pdb
--- a/alphafold/relax/testdata/with_violations_casp14.pdb
+++ b/alphafold/relax/testdata/with_violations_casp14.pdb
--- a/alphafold/relax/utils.py
+++ b/alphafold/relax/utils.py
--- a/alphafold/relax/utils_test.py
+++ b/alphafold/relax/utils_test.py
--- a/docker/__init__.py
+++ b/docker/__init__.py
--- a/docker/jax_0.3.14_ROCM.patch
+++ b/docker/jax_0.3.14_ROCM.patch
--- a/docker/openmm.patch
+++ b/docker/openmm.patch
--- a/docker/openmm.patch.orig
+++ b/docker/openmm.patch.orig
--- a/docker/openmm.patch.rej
+++ b/docker/openmm.patch.rej
--- a/docker/run_patch.sh
+++ b/docker/run_patch.sh
+cd ../
+work_path="$PWD"
+a="$(which python)"
+cd "$(dirname "$(dirname "$a")")/lib/python3.8/site-packages" 
+patch -p0 < "$work_path/docker/openmm.patch"
+patch -p1 < "$work_path/docker/jax_0.3.14_ROCM.patch"
--- a/exp/run_docker.sh
+++ b/exp/run_docker.sh
--- a/exp/run_local.sh
+++ b/exp/run_local.sh
--- a/icon.jpg
+++ b/icon.jpg
--- a/imgs/casp14_predictions.gif
+++ b/imgs/casp14_predictions.gif
--- a/imgs/header.jpg
+++ b/imgs/header.jpg