From 466273494290b3dff842b8a78bdc861c2a642d6f Mon Sep 17 00:00:00 2001
From: Omar-A-hassan <quickyomar@gmail.com>
Date: Thu, 6 Aug 2026 17:05:07 +0300
Subject: [PATCH] fix(utils): assign unique chain IDs when parsing multi-record
 FASTAs

---
 src/simplefold/utils/fasta_utils.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/simplefold/utils/fasta_utils.py b/src/simplefold/utils/fasta_utils.py
index a64612a..d2598de 100644
--- a/src/simplefold/utils/fasta_utils.py
+++ b/src/simplefold/utils/fasta_utils.py
@@ -64,11 +64,12 @@ def parse_fasta(path: Path, ccd: Mapping[str, Mol]) -> Target:  # noqa: C901
         records = list(SeqIO.parse(f, "fasta"))
 
     sequences = []
-    for seq_record in records:
+    for i, seq_record in enumerate(records):
         seq = str(seq_record.seq)
+        chain_id = chr(ord("A") + i) if i < 26 else f"A{i}"
         molecule = {
             "protein": {
-                "id": "A", # Set a default chain ID
+                "id": chain_id,
                 "sequence": seq,
                 "modifications": [],
                 "msa": None,