From 11454194f5210d45197a834777fd50660bfcb4d5 Mon Sep 17 00:00:00 2001
From: Thomas Kemmer <thomas@binaryden.de>
Date: Wed, 11 Mar 2026 09:47:44 +0100
Subject: [PATCH 1/2] FragmentDB: add DOD fragment

Signed-off-by: Thomas Kemmer <thomas@binaryden.de>
---
 data/fragmentdb/FragmentDB.json       |  1 +
 data/fragmentdb/fragments/DOD.json    | 56 +++++++++++++++++++++++++++
 test/preprocessing/test_fragmentdb.jl |  4 +-
 3 files changed, 59 insertions(+), 2 deletions(-)
 create mode 100644 data/fragmentdb/fragments/DOD.json

diff --git a/data/fragmentdb/FragmentDB.json b/data/fragmentdb/FragmentDB.json
index 0d15a82c..9a438f66 100644
--- a/data/fragmentdb/FragmentDB.json
+++ b/data/fragmentdb/FragmentDB.json
@@ -28,6 +28,7 @@
     "MG": "fragments/MG.json",
     "ZN": "fragments/ZN.json",
     "HOH": "fragments/HOH.json",
+    "DOD": "fragments/DOD.json",
     "A": "fragments/A.json",
     "C": "fragments/C.json",
     "G": "fragments/G.json",
diff --git a/data/fragmentdb/fragments/DOD.json b/data/fragmentdb/fragments/DOD.json
new file mode 100644
index 00000000..c6b3966d
--- /dev/null
+++ b/data/fragmentdb/fragments/DOD.json
@@ -0,0 +1,56 @@
+{
+  "name": "DOD",
+  "names": [
+    "Deuterated water"
+  ],
+  "type": "None",
+  "atoms": [
+    {
+      "name": "O",
+      "element": "O",
+      "r": [
+        42.646,
+        44.869,
+        64.255
+      ]
+    },
+    {
+      "name": "D1",
+      "element": "H",
+      "r": [
+        43.596,
+        44.869,
+        64.255
+      ]
+    },
+    {
+      "name": "D2",
+      "element": "H",
+      "r": [
+        42.408,
+        44.869,
+        65.175
+      ]
+    }
+  ],
+  "bonds": [
+    {
+      "number": 1,
+      "a1": "O",
+      "a2": "D1",
+      "order": "Single"
+    },
+    {
+      "number": 2,
+      "a1": "O",
+      "a2": "D2",
+      "order": "Single"
+    }
+  ],
+  "connections": [],
+  "variants": [
+    {
+      "name": "DOD"
+    }
+  ]
+}
diff --git a/test/preprocessing/test_fragmentdb.jl b/test/preprocessing/test_fragmentdb.jl
index 748233f0..d0825f08 100644
--- a/test/preprocessing/test_fragmentdb.jl
+++ b/test/preprocessing/test_fragmentdb.jl
@@ -2,7 +2,7 @@
     using BiochemicalAlgorithms: get_reference_fragment
 
     for fdb in (default_fragmentdb(), FragmentDB(), FragmentDB{Float32}(), FragmentDB{Float64}())
-        @test length(fdb.fragments) == 33
+        @test length(fdb.fragments) == 34
         @test length(fdb.name_mappings) == 6
         @test length(fdb.defaults) == 1
         @test fdb.defaults["Naming"] == "PDB"
@@ -52,7 +52,7 @@
         end
 
         # show method
-        @test contains(repr(fdb), "33 fragments")
+        @test contains(repr(fdb), "34 fragments")
     end
 end
 

From 300e763c81a91e4dcc8ba604139c3d96e1a6c524 Mon Sep 17 00:00:00 2001
From: Thomas Kemmer <thomas@binaryden.de>
Date: Wed, 11 Mar 2026 09:48:26 +0100
Subject: [PATCH 2/2] FragmentDB: add PO4 fragment

Signed-off-by: Thomas Kemmer <thomas@binaryden.de>
---
 data/fragmentdb/FragmentDB.json       |  1 +
 data/fragmentdb/fragments/PO4.json    | 86 +++++++++++++++++++++++++++
 test/preprocessing/test_fragmentdb.jl |  4 +-
 3 files changed, 89 insertions(+), 2 deletions(-)
 create mode 100644 data/fragmentdb/fragments/PO4.json

diff --git a/data/fragmentdb/FragmentDB.json b/data/fragmentdb/FragmentDB.json
index 9a438f66..0ecc583e 100644
--- a/data/fragmentdb/FragmentDB.json
+++ b/data/fragmentdb/FragmentDB.json
@@ -26,6 +26,7 @@
     "NME": "fragments/NME.json",
     "CA": "fragments/CA.json",
     "MG": "fragments/MG.json",
+    "PO4": "fragments/PO4.json",
     "ZN": "fragments/ZN.json",
     "HOH": "fragments/HOH.json",
     "DOD": "fragments/DOD.json",
diff --git a/data/fragmentdb/fragments/PO4.json b/data/fragmentdb/fragments/PO4.json
new file mode 100644
index 00000000..6201a525
--- /dev/null
+++ b/data/fragmentdb/fragments/PO4.json
@@ -0,0 +1,86 @@
+{
+  "name": "PO4",
+  "names": [
+    "Phosphate ion"
+  ],
+  "type": "None",
+  "atoms": [
+    {
+      "name": "P",
+      "element": "P",
+      "r": [
+        0.0,
+        0.0,
+        0.0
+      ]
+    },
+    {
+      "name": "O1",
+      "element": "O",
+      "r": [
+        0.0,
+        -1.288,
+        -0.911
+      ]
+    },
+    {
+      "name": "O2",
+      "element": "O",
+      "r": [
+        0.0,
+        1.288,
+        -0.911
+      ]
+    },
+    {
+      "name": "O3",
+      "element": "O",
+      "r": [
+        -1.288,
+        0.0,
+        0.911
+      ]
+    },
+    {
+      "name": "O4",
+      "element": "O",
+      "r": [
+        1.288,
+        0.0,
+        0.911
+      ]
+    }
+  ],
+  "bonds": [
+    {
+      "number": 1,
+      "a1": "P",
+      "a2": "O1",
+      "order": "Double"
+    },
+    {
+      "number": 1,
+      "a1": "P",
+      "a2": "O2",
+      "order": "Single"
+    },
+    {
+      "number": 1,
+      "a1": "P",
+      "a2": "O3",
+      "order": "Single"
+    },
+    {
+      "number": 1,
+      "a1": "P",
+      "a2": "O4",
+      "order": "Single"
+    }
+  ],
+  "connections": [],
+  "variants": [
+    {
+      "name": "PO4"
+    }
+  ]
+}
diff --git a/test/preprocessing/test_fragmentdb.jl b/test/preprocessing/test_fragmentdb.jl
index d0825f08..2e943e52 100644
--- a/test/preprocessing/test_fragmentdb.jl
+++ b/test/preprocessing/test_fragmentdb.jl
@@ -2,7 +2,7 @@
     using BiochemicalAlgorithms: get_reference_fragment
 
     for fdb in (default_fragmentdb(), FragmentDB(), FragmentDB{Float32}(), FragmentDB{Float64}())
-        @test length(fdb.fragments) == 34
+        @test length(fdb.fragments) == 35
         @test length(fdb.name_mappings) == 6
         @test length(fdb.defaults) == 1
         @test fdb.defaults["Naming"] == "PDB"
@@ -52,7 +52,7 @@
         end
 
         # show method
-        @test contains(repr(fdb), "34 fragments")
+        @test contains(repr(fdb), "35 fragments")
     end
 end