added AF2 dependencies to SE3-nvidia.yml

remove amber relax option from af2_metrics.py, since this isn't used normally and requires additional dependency config
RosettaCommons · Nov 10, 2022 · c882ab0 · c882ab0
1 parent 0d7cf3c
commit c882ab0
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Showing 2 changed files with 50 additions and 21 deletions.
diff --git a/envs/SE3-nvidia.yml b/envs/SE3-nvidia.yml
@@ -9,6 +9,7 @@ channels:
 dependencies:
   - _libgcc_mutex=0.1=conda_forge
   - _openmp_mutex=4.5=1_gnu
+  - absl-py=1.3.0=py39h06a4308_0
   - anyio=3.3.0=py39hf3d152e_0
   - argon2-cffi=20.1.0=py39h3811e60_2
   - async_generator=1.10=py_0
@@ -18,12 +19,13 @@ dependencies:
   - backports=1.0=py_2
   - backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
   - beautifulsoup4=4.11.1=py39h06a4308_0
+  - biopython=1.78=py39h7f8727e_0
   - blas=1.0=mkl
   - bleach=4.1.0=pyhd8ed1ab_0
   - brotlipy=0.7.0=py39h3811e60_1001
   - bzip2=1.0.8=h7f98852_4
-  - ca-certificates=2022.4.26=h06a4308_0
-  - certifi=2022.5.18.1=py39h06a4308_0
+  - ca-certificates=2022.9.24=ha878542_0
+  - certifi=2022.9.24=pyhd8ed1ab_0
   - cffi=1.14.6=py39he32792d_0
   - chardet=4.0.0=py39hf3d152e_1
   - charset-normalizer=2.0.0=pyhd8ed1ab_0
@@ -36,9 +38,11 @@ dependencies:
   - decorator=5.0.9=pyhd8ed1ab_0
   - defusedxml=0.7.1=pyhd8ed1ab_0
   - dgl-cuda11.1=0.8.2=py39_0
+  - dm-tree=0.1.5=py39h51133e4_0
   - entrypoints=0.3=pyhd8ed1ab_1003
   - expat=2.4.1=h9c3ff4c_0
   - ffmpeg=4.3=hf484d3e_0
+  - fftw=3.3.9=h27cfd23_1
   - fontconfig=2.13.1=he4413a7_1000
   - freetype=2.10.4=h0708190_1
   - gettext=0.19.8.1=h0b5b191_1005
@@ -91,7 +95,6 @@ dependencies:
   - libxml2=2.9.9=h13577e0_2
   - llvmlite=0.37.0=py39h1bbdace_0
   - lz4-c=1.9.3=h9c3ff4c_1
-  - markupsafe=2.0.1=py39h3811e60_0
   - matplotlib=3.4.3=py39hf3d152e_1
   - matplotlib-base=3.4.3=py39h2fa2bec_1
   - matplotlib-inline=0.1.3=pyhd8ed1ab_0
@@ -113,17 +116,21 @@ dependencies:
   - numba=0.54.0=py39h56b8d98_0
   - numpy=1.20.3=py39hf144106_0
   - numpy-base=1.20.3=py39h74d4b33_0
+  - ocl-icd=2.3.1=h7f98852_0
+  - ocl-icd-system=1.0.0=1
   - olefile=0.46=pyh9f0ad1d_1
   - openh264=2.1.1=h780b84a_0
   - openjpeg=2.4.0=hb52868f_1
-  - openssl=1.1.1o=h7f8727e_0
+  - openmm=7.6.0=py39h33ab577_0
+  - openssl=1.1.1l=h7f98852_0
   - packaging=21.0=pyhd8ed1ab_0
   - pandas=1.3.2=py39hde0f152_0
   - pandoc=2.14.2=h7f98852_0
   - pandocfilters=1.5.0=pyhd8ed1ab_0
   - parso=0.8.2=pyhd8ed1ab_0
   - patsy=0.5.2=pyhd8ed1ab_0
   - pcre=8.45=h9c3ff4c_0
+  - pdbfixer=1.8.1=pyh6c4a22f_0
   - pexpect=4.8.0=pyh9f0ad1d_2
   - pickleshare=0.7.5=py_1003
   - pillow=8.3.1=py39h2c7a002_0
@@ -192,13 +199,48 @@ dependencies:
   - zlib=1.2.11=h516909a_1010
   - zstd=1.4.9=ha95c52a_0
   - pip:
-    - asttokens==2.0.5
+    - astunparse==1.6.3
+    - cachetools==5.2.0
+    - contextlib2==21.6.0
+    - dm-haiku==0.0.8
     - e3nn==0.3.4
-    - lie-learn==0.0.1.post1
-    - executing==0.8.2
+    - flatbuffers==22.10.26
+    - gast==0.4.0
     - gemmi==0.4.8
-    - icecream==2.1.1
+    - google-auth==2.14.1
+    - google-auth-oauthlib==0.4.6
+    - google-pasta==0.2.0
+    - grpcio==1.50.0
+    - h5py==3.7.0
+    - jax==0.3.24
+    - jaxlib==0.3.24
+    - jmp==0.0.2
+    - keras==2.10.0
+    - keras-preprocessing==1.1.2
+    - libclang==14.0.6
+    - lie-learn==0.0.1.post1
+    - markdown==3.4.1
+    - markupsafe==2.1.1
+    - ml-collections==0.1.1
     - mpmath==1.2.1
+    - oauthlib==3.2.2
     - opt-einsum==3.3.0
     - opt-einsum-fx==0.1.2
+    - protobuf==3.19.6
+    - pyasn1==0.4.8
+    - pyasn1-modules==0.2.8
+    - pyyaml==6.0
+    - requests-oauthlib==1.3.1
+    - rsa==4.9
     - sympy==1.8
+    - tabulate==0.9.0
+    - tensorboard==2.10.1
+    - tensorboard-data-server==0.6.1
+    - tensorboard-plugin-wit==1.8.1
+    - tensorflow==2.10.0
+    - tensorflow-estimator==2.10.0
+    - tensorflow-io-gcs-filesystem==0.27.0
+    - termcolor==2.1.0
+    - werkzeug==2.2.2
+    - wrapt==1.14.1
+prefix: /home/jue/.conda/envs/SE3test
diff --git a/scripts/af2_metrics.py b/scripts/af2_metrics.py
@@ -37,7 +37,6 @@
 from alphafold.model import data
 from alphafold.model import config
 from alphafold.model import model
-from alphafold.relax import relax
 
 from jax.lib import xla_bridge
 from alphafold.model.tf import shape_placeholders                                                        
@@ -69,7 +68,6 @@ def get_args(argv=None):
     p.add_argument('--model_num', default=4, type=int, choices=[1,2,3,4,5], help='AlphaFold model to use')
     p.add_argument('--use_ptm', default=False, action="store_true", help='Use ptm model variant')
     p.add_argument('--num_recycle', default=3, type=int, help='Number of recycles for AlphaFold prediction')
-    p.add_argument('--amber_relax', action="store_true", help='Do AMBER relax after AF2 prediction.')
 
 
     if argv is not None:
@@ -323,17 +321,6 @@ def main():
             )
             pdb_lines = protein.to_pdb(unrelaxed_protein)
 
-            # relax, if wanted
-            if args.amber_relax:
-                amber_relaxer = relax.AmberRelaxation(
-                    max_iterations=0,
-                    tolerance=2.39,
-                    stiffness=10.0,
-                    exclude_residues=[],
-                    max_outer_iterations=20
-                )
-                pdb_lines, _, _ = amber_relaxer.process(prot=unrelaxed_protein)
-
             # save AF2 pdb
             with open(os.path.join(args.outdir,name+'.pdb'), 'w') as f:
                 f.write(pdb_lines)