From 10644138e7e9ef5fbbb9e41f63fc39a2b8c2b451 Mon Sep 17 00:00:00 2001
From: Lester Hedges <lester.hedges@gmail.com>
Date: Fri, 17 May 2024 11:07:25 +0100
Subject: [PATCH] Pass property map as kwarg and make sure box is reduced.
 [closes #291] [closes openbiosim/sire#197]

---
 nodes/playground/prepareFEP.ipynb | 15 +++++++++++----
 nodes/playground/prepareFEP.py    |  9 ++++++++-
 2 files changed, 19 insertions(+), 5 deletions(-)

diff --git a/nodes/playground/prepareFEP.ipynb b/nodes/playground/prepareFEP.ipynb
index a9929c669..688439b4c 100644
--- a/nodes/playground/prepareFEP.ipynb
+++ b/nodes/playground/prepareFEP.ipynb
@@ -317,7 +317,10 @@
     ")\n",
     "# Create a composite system\n",
     "system1.removeMolecules(lig1)\n",
-    "system1.addMolecules(merged)"
+    "system1.addMolecules(merged)\n",
+    "# Make sure the box vectors are in reduced form.\n",
+    "system1.reduceBoxVectors()\n",
+    "system1.rotateBoxVectors()"
    ]
   },
   {
@@ -336,7 +339,11 @@
     "    \"merged_at_lam0.pdb\",\n",
     "    merged,\n",
     "    \"PDB\",\n",
-    "    {\"coordinates\": \"coordinates0\", \"bond\": \"bond0\", \"element\": \"element0\"},\n",
+    "    property_map={\n",
+    "        \"coordinates\": \"coordinates0\",\n",
+    "        \"bond\": \"bond0\",\n",
+    "        \"element\": \"element0\",\n",
+    "    },\n",
     ")\n",
     "if is_somd2:\n",
     "    BSS.Stream.save(system1, root)\n",
@@ -426,9 +433,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.11"
+   "version": "3.12.2"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }
diff --git a/nodes/playground/prepareFEP.py b/nodes/playground/prepareFEP.py
index 5561f7158..39d57e45d 100644
--- a/nodes/playground/prepareFEP.py
+++ b/nodes/playground/prepareFEP.py
@@ -258,6 +258,9 @@ def loadMapping(mapping_file):
 # Create a composite system
 system1.removeMolecules(lig1)
 system1.addMolecules(merged)
+# Make sure the box vectors are in reduced form.
+system1.reduceBoxVectors()
+system1.rotateBoxVectors()
 
 
 # In[ ]:
@@ -273,7 +276,11 @@ def loadMapping(mapping_file):
     "merged_at_lam0.pdb",
     merged,
     "PDB",
-    {"coordinates": "coordinates0", "bond": "bond0", "element": "element0"},
+    property_map={
+        "coordinates": "coordinates0",
+        "bond": "bond0",
+        "element": "element0",
+    },
 )
 if is_somd2:
     BSS.Stream.save(system1, root)