diff --git a/bin/pdb_to_residues_esm.py b/bin/pdb_to_residues_esm.py
index 109fc4b..9b2a7af 100644
--- a/bin/pdb_to_residues_esm.py
+++ b/bin/pdb_to_residues_esm.py
@@ -13,8 +13,14 @@ pip install git+https://github.com/facebookresearch/esm.git
 
 # uses the following notebook as a reference:
 # https://colab.research.google.com/github/facebookresearch/esm/blob/main/examples/inverse_folding/notebook.ipynb
+import os
+import glob
+import functools
 import logging
 import argparse
+from typing import List, Optional
+
+from tqdm.auto import tqdm
 
 # Verfies that the environment is set up correctly
 import torch
@@ -28,6 +34,7 @@ import esm.inverse_folding
 
 def write_fa(fname: str, seq: str):
     """Write a fasta file"""
+    assert fname.endswith(".fasta")
     with open(fname, "w") as f:
         f.write(">sampled\n")
         for chunk in [seq[i : i + 80] for i in range(0, len(seq), 80)]:
@@ -35,14 +42,49 @@ def write_fa(fname: str, seq: str):
     return fname
 
 
+def generate_residues(
+    fpath: str, model, chain_id: str = "A", n: int = 10, temperature: float = 1.0
+) -> List[str]:
+    """Generate residues for the structure contained in the PDB file"""
+    structure = esm.inverse_folding.util.load_structure(fpath, chain_id)
+    # Coords have shape (seq_len, 3, 3)
+    coords, native_seq = esm.inverse_folding.util.extract_coords_from_structure(
+        structure
+    )
+    logging.debug(f"Native sequence: {native_seq}")
+    retval = []
+    for _ in range(n):
+        sampled_seq = model.sample(coords, temperature=temperature)
+        logging.debug(f"Sampled sequence: {sampled_seq}")
+        retval.append(sampled_seq)
+    return retval
+
+
+def update_fname(fname: str, i: int, new_dir: str = "") -> str:
+    """
+    Update the pdb filename to include a numeric index and a .fasta extension.
+    If new_dir is given then we move the output filename to that directory.
+    """
+    assert os.path.isfile(fname)
+    parent, child = os.path.split(fname)
+    assert child
+    child_base, _child_ext = os.path.splitext(child)
+    assert child_base
+    if new_dir:
+        assert os.path.isdir(new_dir), f"Expected {new_dir} to be a directory"
+        parent = new_dir
+    return os.path.join(parent, f"{child_base}_esm_generated_{i}.fasta")
+
+
 def build_parser() -> argparse.ArgumentParser:
     """Build a basic CLI"""
     parser = argparse.ArgumentParser(
         description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter
     )
-    parser.add_argument("fname", type=str, help="PDB file to generate residues for")
     parser.add_argument(
-        "-c", "--chain", type=str, default="A", help="Chain to use within PDB file"
+        "fname",
+        type=str,
+        help="PDB file to generate residues for, or a folder containing these",
     )
     parser.add_argument(
         "-t",
@@ -52,11 +94,7 @@ def build_parser() -> argparse.ArgumentParser:
         help="Temperature to sample at. Lower values result in lower diversity but higher sequence recovery",
     )
     parser.add_argument(
-        "-o",
-        "--output",
-        type=str,
-        default="",
-        help="Output file (fasta format) to write to. If not provided, default to input + .fasta",
+        "-n", type=int, default=10, help="Number of sequences to generate per structure"
     )
     parser.add_argument(
         "-s",
@@ -72,31 +110,38 @@ def main():
     parser = build_parser()
     args = parser.parse_args()
 
-    # Load in the file
-    fpath = args.fname
-    chain_id = args.chain
-    structure = esm.inverse_folding.util.load_structure(fpath, chain_id)
-    # Coords have shape (seq_len, 3, 3)
-    coords, native_seq = esm.inverse_folding.util.extract_coords_from_structure(
-        structure
-    )
-    logging.info(f"Native sequence: {native_seq}")
-
     # Load the model
     model, alphabet = esm.pretrained.esm_if1_gvp4_t16_142M_UR50()
     model = model.eval()
-
-    # Sample the residues
     torch.manual_seed(args.seed)
-    sampled_seq = model.sample(coords, temperature=1.0)
-    logging.info(f"Sampled sequence: {sampled_seq}")
 
-    # If output file is given, write it
-    out = args.output
-    if out == "":
-        out = fpath.replace(".pdb", ".fasta")
-    if args.output:
-        write_fa(out, sampled_seq)
+    pfunc = functools.partial(
+        generate_residues, model=model, n=args.n, temperature=args.temperature
+    )
+
+    # Load in the file
+    if os.path.isfile(args.fname):
+        # If output file is given, write it
+        sequences = pfunc(args.fname)
+        for i, seq in enumerate(sequences):
+            out_fname = update_fname(args.fname, i)
+            write_fa(out_fname, seq)
+    elif os.path.isdir(args.fname):
+        # create a subdirecotry to store the fastas
+        outdir = os.path.join(args.fname, "esm_generated_fastas")
+        os.makedirs(outdir, exist_ok=True)
+        logging.info(f"Writing output to {outdir}")
+        # Query for inputs and process them
+        inputs = glob.glob(os.path.join(args.fname, "*.pdb"))
+        logging.info(f"Found {len(inputs)} PDB files to process in {args.fname}")
+        generated = [pfunc(f) for f in tqdm(inputs)]
+        # Write outputs
+        for orig_fname, seqs in zip(inputs, generated):
+            for i, seq in enumerate(seqs):
+                out_fname = update_fname(orig_fname, i, new_dir=outdir)
+                write_fa(out_fname, seq)
+    else:
+        raise RuntimeError(f"Expected {args.fname} to be a file or directory")
 
 
 if __name__ == "__main__":