From 9db43c047a950031496f91aab86e1c7bba849378 Mon Sep 17 00:00:00 2001
From: Irfan Alibay <IAlibay@users.noreply.github.com>
Date: Fri, 12 Jun 2026 08:35:44 +0100
Subject: [PATCH 1/2] [DNM] Deprecate DBMolecules

Added deprecation warnings for DBMolecules class.
---
 src/lomap/dbmol.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/src/lomap/dbmol.py b/src/lomap/dbmol.py
index 4409545..e56d569 100644
--- a/src/lomap/dbmol.py
+++ b/src/lomap/dbmol.py
@@ -206,6 +206,13 @@ def __init__(
             When using 'threed' option, if to translate the two molecules to superimpose before checking real space
             alignment, default True
         """
+        warnings.warn(
+            "The DBMolecules class and related API is deprecated and will be removed in the next major release. "
+            "Please let us know if keeping this functionality is important to you, "
+            "see https://github.com/OpenFreeEnergy/Lomap/issues/149 for more details.",
+            category=DeprecationWarning,
+        )
+
         # Set the Logging
         if verbose == "off":
             logging.basicConfig(format="%(message)s", level=logging.CRITICAL)
@@ -1154,7 +1161,7 @@ def startup():
     # Emit user-facing warning that the CLI is deprecated and will be removed
     warnings.warn(
         "The dbmol CLI is deprecated and will be removed in the next major release. "
-        "Please let us know if you keeping this CLI entry point is important to you, "
+        "Please let us know if keeping this CLI entry point is important to you, "
         "see https://github.com/OpenFreeEnergy/Lomap/issues/138 for more details.",
         category=DeprecationWarning,
     )

From 1d480219a6acd6c7ead7eb812fb09fa2e5059f25 Mon Sep 17 00:00:00 2001
From: IAlibay <IAlibay@users.noreply.github.com>
Date: Fri, 12 Jun 2026 08:38:51 +0100
Subject: [PATCH 2/2] Add a news item

---
 news/deprecate_dbmolecules.rst | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)
 create mode 100644 news/deprecate_dbmolecules.rst

diff --git a/news/deprecate_dbmolecules.rst b/news/deprecate_dbmolecules.rst
new file mode 100644
index 0000000..61b6c7a
--- /dev/null
+++ b/news/deprecate_dbmolecules.rst
@@ -0,0 +1,24 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* The DBMolecules class is deprecated and will be removed in the next major
+  release. See issue #149 for more details.
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>