diff --git a/docs/requirements.txt b/docs/requirements.txt index 6ff7f3c45..61167e156 100644 --- 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 index 24e9a3de6..3cfa5d62a 100644 --- 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 index e6f366ee0..babf6d638 100644 --- 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