Merge pull request #202 from timodonnell/setup-tweaks

Minor fixes in setup scripts

README.md

@@ -141,8 +141,8 @@ python3 run_pretrained_openfold.py \
     --jackhmmer_binary_path lib/conda/envs/openfold_venv/bin/jackhmmer \
     --hhblits_binary_path lib/conda/envs/openfold_venv/bin/hhblits \
     --hhsearch_binary_path lib/conda/envs/openfold_venv/bin/hhsearch \
-    --kalign_binary_path lib/conda/envs/openfold_venv/bin/kalign
-    --config_preset "model_1_ptm"
+    --kalign_binary_path lib/conda/envs/openfold_venv/bin/kalign \
+    --config_preset "model_1_ptm" \
     --openfold_checkpoint_path openfold/resources/openfold_params/finetuning_ptm_2.pt
 ```
 

openfold/np/residue_constants.py

@@ -1121,10 +1121,10 @@ def _make_rigid_transformation_4x4(ex, ey, translation):
 # and an array with (restype, atomtype, coord) for the atom positions
 # and compute affine transformation matrices (4,4) from one rigid group to the
 # previous group
-restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=np.int)
+restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=int)
 restype_atom37_mask = np.zeros([21, 37], dtype=np.float32)
 restype_atom37_rigid_group_positions = np.zeros([21, 37, 3], dtype=np.float32)
-restype_atom14_to_rigid_group = np.zeros([21, 14], dtype=np.int)
+restype_atom14_to_rigid_group = np.zeros([21, 14], dtype=int)
 restype_atom14_mask = np.zeros([21, 14], dtype=np.float32)
 restype_atom14_rigid_group_positions = np.zeros([21, 14, 3], dtype=np.float32)
 restype_rigid_group_default_frame = np.zeros([21, 8, 4, 4], dtype=np.float32)
@@ -1280,7 +1280,7 @@ def make_atom14_dists_bounds(
 
 restype_atom14_ambiguous_atoms = np.zeros((21, 14), dtype=np.float32)
 restype_atom14_ambiguous_atoms_swap_idx = np.tile(
-    np.arange(14, dtype=np.int), (21, 1)
+    np.arange(14, dtype=int), (21, 1)
 )
 
 

scripts/download_colabfold_envdb.sh

@@ -35,4 +35,4 @@ SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/colabfold/colabfold_envdb_202108.ta
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}" -x 4
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}" -x 4 --check-certificate=false

scripts/download_pdb70.sh

@@ -35,7 +35,7 @@ SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}" --check-certificate=false
 tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
   --directory="${ROOT_DIR}"
 rm "${ROOT_DIR}/${BASENAME}"

scripts/download_uniref30.sh

@@ -35,4 +35,5 @@ SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/colabfold/uniref30_2103.tar.gz"
 BASENAME=$(basename "${SOURCE_URL}")
 
 mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}" -x 4
+aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}" -x 4 --check-certificate=false
+gunzip "${ROOT_DIR}/${BASENAME}"

scripts/install_third_party_dependencies.sh

@@ -27,7 +27,7 @@ pushd lib/conda/envs/$ENV_NAME/lib/python3.7/site-packages/ \
     && popd
 
 # Download folding resources
-wget -q -P openfold/resources \
+wget --no-check-certificate -P openfold/resources \
     https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt
 
 # Certain tests need access to this file

scripts/utils.py

@@ -82,13 +82,16 @@ def get_nvidia_cc():
     result = cuda.cuInit(0)
     if result != CUDA_SUCCESS:
         cuda.cuGetErrorString(result, ctypes.byref(error_str))
-        return None, error_str.value.decode()
+        if error_str.value:
+            return None, error_str.value.decode()
+        else:
+            return None, "Unknown error: cuInit returned %d" % result
     result = cuda.cuDeviceGetCount(ctypes.byref(nGpus))
     if result != CUDA_SUCCESS:
         cuda.cuGetErrorString(result, ctypes.byref(error_str))
         return None, error_str.value.decode()
 
-    if(nGpus.value < 1):
+    if nGpus.value < 1:
         return None, "No GPUs detected"
 
     result = cuda.cuDeviceGet(ctypes.byref(device), 0)