Merge pull request #230 from SCM-NV/DavidOrmrodMorley/mol-formats-exa…

…mple-fix Molecule Formats Example Fixes
SCM-NV · Feb 25, 2025 · 6515567 · 6515567
2 parents 1d2b7ae + 617fd9b
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diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats.ipynb.rst b/doc/source/examples/MoleculeFormats/MoleculeFormats.ipynb.rst
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_15_2.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_15_2.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_21_0.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_21_0.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_26_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_26_1.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_29_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_29_1.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_31_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_31_1.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_36_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_36_1.png
diff --git a/...uleFormats_files/MoleculeFormats_38_1.png → ...uleFormats_files/MoleculeFormats_38_0.png b/...uleFormats_files/MoleculeFormats_38_1.png → ...uleFormats_files/MoleculeFormats_38_0.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_40_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_40_1.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_46_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_46_1.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_49_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_49_1.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_4_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_4_1.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_57_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_57_1.png
diff --git a/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_9_1.png b/doc/source/examples/MoleculeFormats/MoleculeFormats_files/MoleculeFormats_9_1.png
diff --git a/examples/MoleculeFormats/MoleculeFormats.ipynb b/examples/MoleculeFormats/MoleculeFormats.ipynb
diff --git a/examples/MoleculeFormats/MoleculeFormats.py b/examples/MoleculeFormats/MoleculeFormats.py
@@ -140,6 +140,7 @@ def head(filename, n: int = 4):
 from scm.plams import toASE
 from ase import Atoms
 from ase.visualize.plot import plot_atoms
+import matplotlib.pyplot as plt
 
 print(f"{type(mol)=}")
 print(f"{mol.get_formula()=}")
@@ -148,7 +149,8 @@ def head(filename, n: int = 4):
 print(f"{type(ase_atoms)=}")
 print(f"{ase_atoms.get_chemical_formula()=}")
 
-plot_atoms(ase_atoms, rotation="-85x,5y,0z")
+_, ax = plt.subplots(figsize=(2, 2))
+plot_atoms(ase_atoms, rotation="-85x,5y,0z", ax=ax)
 
 
 # #### Convert ASE Atoms to PLAMS Molecule
@@ -240,6 +242,9 @@ def head(filename, n: int = 4):
 
 # ### pymatgen Structure and Molecule Python classes
 
+# Note that for this part of the example, the `pymatgen` package needs to be installed. This can be done via `amspackages`.
+
+
 # #### Convert PLAMS Molecule to pymatgen Structure (periodic)
 #
 # There is no builtin converter between PLAMS Molecule and pymatgen Structure (periodic crystal). Instead, you need to go through the ASE interface to both packages: