From 7b3085bbaba97d3639e6c1620eb3af24d063bf3e Mon Sep 17 00:00:00 2001
From: Maxx Tessmer <mhtessmer@gmail.com>
Date: Wed, 22 Apr 2026 20:20:13 -0700
Subject: [PATCH] Fix bug sometimes skipping peptide bond when using bio ccd to
 infer bonds.

---
 src/chilife/Topology.py | 12 +++++++-----
 src/chilife/__init__.py |  2 +-
 tests/test_MolSys.py    |  2 +-
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/chilife/Topology.py b/src/chilife/Topology.py
index 2853fc0..900cc32 100644
--- a/src/chilife/Topology.py
+++ b/src/chilife/Topology.py
@@ -422,10 +422,8 @@ def bonds_from_ccd_data(molsys, ccd_data):
 
         if "chem_comp" in ccd_data[res.resname]:
             res_ccd_data = ccd_data[res.resname]["chem_comp"]
-            if (
-                pres := res.previous_residue()
-            ) is not None and "link type" in res_ccd_data:
-                link_type = res_ccd_data["link type"]
+            if (pres := res.previous_residue()) is not None and "type" in res_ccd_data:
+                link_type = res_ccd_data["type"].lower()
                 if link_type in POLYMER_LINKAGE_TYPES:
                     a1, a2, btype, bchiral = POLYMER_LINKAGE_TYPES[link_type]
                     i1 = pres.ix[pres.names == a1].flat[0]
@@ -477,4 +475,8 @@ def numpyify_ccd(ccd_data):
 
 
 # Linkage data is atom name of the previous residue followed by atom name of the current residue followed by bond type
-POLYMER_LINKAGE_TYPES = {"L-peptide linking": ["C", "N", BondType.SINGLE, "N"]}
+POLYMER_LINKAGE_TYPES = {
+    "l-peptide linking": ["C", "N", BondType.SINGLE, "N"],
+    "peptide linking": ["C", "N", BondType.SINGLE, "N"],
+    "d-peptide linking": ["C", "N", BondType.SINGLE, "N"],
+}
diff --git a/src/chilife/__init__.py b/src/chilife/__init__.py
index 63fe186..a0a5aba 100644
--- a/src/chilife/__init__.py
+++ b/src/chilife/__init__.py
@@ -44,4 +44,4 @@
 # SpinLabel = SpinLabel.SpinLabel
 # dSpinLabel = dSpinLabel.dSpinLabel
 
-__version__ = "1.2.1"
+__version__ = "1.2.2"
diff --git a/tests/test_MolSys.py b/tests/test_MolSys.py
index 390c4f7..6acaf43 100644
--- a/tests/test_MolSys.py
+++ b/tests/test_MolSys.py
@@ -707,5 +707,5 @@ def test_write_sdf():
 
 def test_use_ccd():
     mol = MolSys.from_pdb("test_data/7o1o.pdb", use_ccd=chilife.bio_ccd)
-    assert len(mol.bonds) == 5508
+    assert len(mol.bonds) == 5863
     assert chilife.BondType.DOUBLE in mol.bond_types