For tests, use Python 3.10 stk,stko.

lab-cosmo · Sep 27, 2024 · a32eedc · a32eedc
1 parent 3e72ec1
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Showing 3 changed files with 13 additions and 11 deletions.
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -8,9 +8,9 @@ numpy
 ipywidgets
 matplotlib
 ase==3.22.1
-rdkit==2023.9.5
-stk==2024.9.23.1
-stko==v2024.8.29.1
+rdkit==2023.9.4
+stk==2022.6.17.0
+stko==0.0.40
 
 # required for the examples of chemiscope.explore
 mace-torch

diff --git a/python/examples/8-showing_custom_bonds.py b/python/examples/8-showing_custom_bonds.py
@@ -134,10 +134,12 @@
 # https://stko-docs.readthedocs.io/en/latest/
 
 energy = stko.UFFEnergy()
-analyser = stko.molecule_analysis.GeometryAnalyser()
+shape_calc = stko.ShapeCalculator()
 properties = {
-    "e": [energy.get_energy(molecule) for molecule in structures],
-    "rg": [analyser.get_radius_gyration(molecule) for molecule in structures],
+    "uffenergy": [energy.get_energy(molecule) for molecule in structures],
+    "aspheriticty": [
+        shape_calc.get_results(molecule).get_asphericity() for molecule in structures
+    ],
 }
 
 
@@ -175,7 +177,7 @@
     frames=structures,
     properties=properties,
     meta=dict(name="Missing bonds by automation."),
-    settings=chemiscope.quick_settings(x="rg", y="e", color=""),
+    settings=chemiscope.quick_settings(x="aspheriticty", y="uffenergy", color=""),
 )
 
 
@@ -198,8 +200,8 @@
     properties=properties,
     meta=dict(name="Added all stk bonds."),
     settings=chemiscope.quick_settings(
-        x="rg",
-        y="e",
+        x="aspheriticty",
+        y="uffenergy",
         color="",
         structure_settings={
             "shape": shape_string,

diff --git a/python/examples/data/stk_3.mol b/python/examples/data/stk_3.mol
@@ -173,8 +173,8 @@ M  V30 165 H 5.7344 4.0818 -6.8141 0
 M  V30 166 H 7.2407 5.2573 -4.4052 0
 M  V30 167 H 5.6374 5.9354 -4.8815 0
 M  V30 168 H 6.0976 3.7143 -3.1964 0
-M  V30 169 Br 1.1870 0.0000 0.0000 0
-M  V30 170 Br -1.1870 0.0000 0.0000 0
+M  V30 169 Br 2.1870 0.0000 0.0000 0
+M  V30 170 Br -0.1870 0.0000 0.0000 0
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2