fix failing tests

Author: a-r-j

biopandas/mmcif/pandas_mmcif.py

@@ -430,7 +430,11 @@ def amino3to1(
         indices = []
 
         residue_number_insertion = (
-            tmp[residue_number_col].astype(str) + tmp["pdbx_PDB_ins_code"]
+            tmp[chain_col].astype(str)
+            + "_"
+            + tmp[residue_number_col].astype(str)
+            + "_"
+            + tmp["pdbx_PDB_ins_code"].fillna("")
         )
 
         for num, ind in zip(residue_number_insertion, np.arange(tmp.shape[0])):

biopandas/mmtf/pandas_mmtf.py

@@ -236,7 +236,11 @@ def amino3to1(self, record="ATOM", residue_col="residue_name", fillna="?"):
         indices = []
 
         residue_number_insertion = (
-            tmp["residue_number"].astype(str) + tmp["insertion"]
+            tmp["chain_id"].astype(str)
+            + "_"
+            + tmp["residue_number"].astype(str)
+            + "_"
+            + tmp["insertion"].fillna("")
         )
 
         for num, ind in zip(residue_number_insertion, np.arange(tmp.shape[0])):

biopandas/pdb/pandas_pdb.py

@@ -606,7 +606,13 @@ def amino3to1(self, record="ATOM", residue_col="residue_name", fillna="?"):
         cmp = "placeholder"
         indices = []
 
-        residue_number_insertion = tmp["residue_number"].astype(str) + tmp["insertion"]
+        residue_number_insertion = (
+            tmp["chain_id"].astype(str)
+            + "_"
+            + tmp["residue_number"].astype(str)
+            + "_"
+            + tmp["insertion"].fillna("")
+        )
 
         for num, ind in zip(residue_number_insertion, np.arange(tmp.shape[0])):
             if num != cmp:

docs/CHANGELOG.md

@@ -1,5 +1,6 @@
 # Release Notes ![](img/logos/3eiy_120.png)
 
+- Fix: improves robustness of `amino3to1` residue identification by handling `NaN` insertion codes (NumPy 2.4+ compatibility) and including chain IDs and separators to avoid collisions.
 - Supports `mol` files that have empty lines between blocks, (Via [Ruibin Liu](https://github.com/Ruibin-Liu) PR #[140](https://github.com/BioPandas/biopandas/pull/140#))
 
 The CHANGELOG for the current development version is available at