make chains_to_design and parse_these_chains_only consistent

README.md

@@ -257,24 +257,24 @@ python run.py \
 ```
 
 ### 17 --chains_to_design
-Specify which chains (e.g. "ABC") need to be redesigned, other chains will be kept fixed. Outputs in seqs/backbones will still have atoms/sequences for the whole input PDB.
+Specify which chains (e.g. "A,B,C") need to be redesigned, other chains will be kept fixed. Outputs in seqs/backbones will still have atoms/sequences for the whole input PDB.
 ```
 python run.py \
         --model_type "ligand_mpnn" \
         --seed 111 \
         --pdb_path "./inputs/4GYT.pdb" \
         --out_folder "./outputs/chains_to_design" \
-        --chains_to_design "B"
+        --chains_to_design "A,B"
 ```
 ### 18 --parse_these_chains_only
-Parse and design only specified chains (e.g. "ABC"). Outputs will have only specified chains.
+Parse and design only specified chains (e.g. "A,B,C"). Outputs will have only specified chains.
 ```
 python run.py \
         --model_type "ligand_mpnn" \
         --seed 111 \
         --pdb_path "./inputs/4GYT.pdb" \
         --out_folder "./outputs/parse_these_chains_only" \
-        --parse_these_chains_only "B"
+        --parse_these_chains_only "A,B"
 ```
 
 ### 19 --model_type "ligand_mpnn"

run.py

@@ -180,6 +180,12 @@ def main(args) -> None:
         device=device,
     )
 
+    if len(args.parse_these_chains_only) != 0:
+        parse_these_chains_only_list = args.parse_these_chains_only.split(",")
+    else:
+        parse_these_chains_only_list = []
+
+
     # loop over PDB paths
     for pdb in pdb_paths:
         if args.verbose:
@@ -192,7 +198,7 @@ def main(args) -> None:
         protein_dict, backbone, other_atoms, icodes, _ = parse_PDB(
             pdb,
             device=device,
-            chains=args.parse_these_chains_only,
+            chains=parse_these_chains_only_list,
             parse_all_atoms=parse_all_atoms_flag,
             parse_atoms_with_zero_occupancy=args.parse_atoms_with_zero_occupancy,
         )
@@ -269,10 +275,11 @@ def main(args) -> None:
             protein_dict["membrane_per_residue_labels"] = (
                 args.global_transmembrane_label + 0 * fixed_positions
             )
-        if type(args.chains_to_design) == str:
+        if len(args.chains_to_design) != 0:
             chains_to_design_list = args.chains_to_design.split(",")
         else:
             chains_to_design_list = protein_dict["chain_letters"]
+
         chain_mask = torch.tensor(
             np.array(
                 [
@@ -876,15 +883,15 @@ def main(args) -> None:
     argparser.add_argument(
         "--chains_to_design",
         type=str,
-        default=None,
-        help="Specify which chains to redesign, all others will be kept fixed.",
+        default="",
+        help="Specify which chains to redesign, all others will be kept fixed, 'A,B,C,F'",
     )
 
     argparser.add_argument(
         "--parse_these_chains_only",
         type=str,
         default="",
-        help="Provide chains letters for parsing backbones, 'ABCF'",
+        help="Provide chains letters for parsing backbones, 'A,B,C,F'",
     )
 
     argparser.add_argument(

run_examples.sh

@@ -121,15 +121,15 @@ python run.py \
         --seed 111 \
         --pdb_path "./inputs/4GYT.pdb" \
         --out_folder "./outputs/chains_to_design" \
-        --chains_to_design "B"
+        --chains_to_design "A,B"
 
 #18
 python run.py \
         --model_type "ligand_mpnn" \
         --seed 111 \
         --pdb_path "./inputs/4GYT.pdb" \
         --out_folder "./outputs/parse_these_chains_only" \
-        --parse_these_chains_only "B"
+        --parse_these_chains_only "A,B"
 
 #19
 python run.py \