Clarify output dir, use tempdir for chain processing

README.md

@@ -91,21 +91,25 @@ unzip models.zip
 
 # Now select one of multiple options:
 
+# Now select one of multiple options:
+
 # 1. Predict single PDB (solved)
 python discotope3/main.py --pdb_or_zip_file data/example_pdbs_solved/7c4s.pdb
 
 # 2. Predict AlphaFold structure
 python discotope3/main.py --pdb_or_zip_file data/example_pdbs_alphafold/7tdm_B.pdb --struc_type alphafold
 
 # 3. Predict a folder of PDBs
-python discotope3/main.py --pdb_dir data/example_pdbs_solved
+python discotope3/main.py --pdb_dir data/example_pdbs_solved --out_dir output/example_pdbs_solved
 
 # 4. Predict a ZIP file of PDBs
-python discotope3/main.py --pdb_or_zip_file pdbs_in_zipfile.zip
+python discotope3/main.py --pdb_or_zip_file pdbs_in_zipfile.zip --out_dir output/pdbs_in_zipfile
+
+# 5. Fetch PDBs from RCSB
+python discotope3/main.py --list_file pdb_list_solved.txt --struc_type solved --out_dir output/pdb_list_solved
 
-# 5. Fetch PDB IDs from file and predict
-# Nb: Fetches from RCSB if struc_type is solved and AlphaFolddb if alphafold
-python discotope3/main.py --list_file pdb_list_solved.txt --struc_type solved
+# 6. Fetch PDBs from Alphafolddb
+python discotope3/main.py --list_file pdb_list_af2.txt --struc_type alphafold --out_dir output/pdb_list_af2
 ```
 
 # DiscoTope-3.0 output

discotope3/esm/data.py

@@ -12,6 +12,7 @@
 from typing import List, Sequence, Tuple, Union
 
 import torch
+
 from discotope3.esm.constants import proteinseq_toks
 
 RawMSA = Sequence[Tuple[str, str]]

discotope3/esm/pretrained.py

@@ -9,9 +9,10 @@
 from argparse import Namespace
 from pathlib import Path
 
-import discotope3.esm
 import torch
 
+import discotope3.esm
+
 
 def _has_regression_weights(model_name):
  """Return whether we expect / require regression weights;

discotope3/esm_util_custom.py

@@ -13,6 +13,7 @@
 from biotite.structure import filter_backbone, get_chains
 from biotite.structure.io import pdb, pdbx
 from biotite.structure.residues import get_residues
+
 from discotope3.esm.data import BatchConverter