Add requirements & minor edits

requirements.txt

+absl-py==0.13.0
+bio==0.8.9
+biopython==1.79
+biothings-client==0.2.6
+certifi==2021.5.30
+charset-normalizer==2.0.5
+contextlib2==21.6.0
+deepspeed==0.5.3
+dm-tree==0.1.6
+idna==3.2
+ml-collections==0.1.0
+mygene==3.2.2
+ninja==1.10.2
+numpy==1.21.2
+packaging==21.0
+plac==1.3.3
+protobuf==3.18.0
+psutil==5.8.0
+pyparsing==2.4.7
+PyYAML==5.4.1
+requests==2.26.0
+scipy==1.7.1
+six==1.16.0
+tensorboardX==1.8
+torch==1.9.0
+tqdm==4.62.2
+triton==1.0.0
+typing-extensions==3.10.0.2
+urllib3==1.26.6

run_pretrained_alphafold.py

@@ -98,7 +98,9 @@ amber_relaxer = relax.AmberRelaxation(
 )
 
 # Relax the prediction.
+t = time.time()
 relaxed_pdb_str, _, _ = amber_relaxer.process(prot=unrelaxed_protein)
+print(f"Relaxation time: {time.time() - t}")
 
 # Save the relaxed PDB.
 output_dir = '.'

scripts/install_third_party_dependencies.sh

@@ -2,7 +2,7 @@
 
 # Install Miniconda locally
 rm -rf lib/conda
-rm /tmp/Miniconda3-latest-Linux-x86_64.sh
+rm -f /tmp/Miniconda3-latest-Linux-x86_64.sh
 wget -q -P /tmp \
     https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \
     && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p lib/conda \