From 7868faac62d76434867a746c5da5266d27c13f7e Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Fri, 20 Sep 2024 19:22:59 +0200
Subject: [PATCH 01/35] Write example script.

---
 python/examples/8-showing_custom_bonds.py | 230 ++++++++++++++++++++++
 1 file changed, 230 insertions(+)
 create mode 100644 python/examples/8-showing_custom_bonds.py

diff --git a/python/examples/8-showing_custom_bonds.py b/python/examples/8-showing_custom_bonds.py
new file mode 100644
index 000000000..19f2b3e70
--- /dev/null
+++ b/python/examples/8-showing_custom_bonds.py
@@ -0,0 +1,230 @@
+"""
+Showing custom bonds
+====================
+
+This example demonstrates how to add shapes into the chemiscope output such
+that custom bonds that would not normally be assigned by ASE can be rendered.
+
+"""
+
+# %%
+#
+import stk
+import stko
+import ase.io
+import pathlib
+import chemiscope
+
+working_path = pathlib.Path(__file__).resolve().parent
+data_path = working_path / "data"
+
+########################################################################
+# This is just for development, where I build the library of structures.
+energy = stko.UFFEnergy()
+analyser = stko.molecule_analysis.GeometryAnalyser()
+xyz_path = data_path / "stkbuilt.xyz"
+string = ""
+
+host = stk.ConstructedMolecule(
+    topology_graph=stk.cage.FourPlusSix(
+        building_blocks=(
+            stk.BuildingBlock(
+                smiles="NC1CCCCC1N",
+                functional_groups=[
+                    stk.PrimaryAminoFactory(),
+                ],
+            ),
+            stk.BuildingBlock(
+                smiles="O=Cc1cc(C=O)cc(C=O)c1",
+                functional_groups=[stk.AldehydeFactory()],
+            ),
+        ),
+        optimizer=stk.MCHammer(),
+    ),
+)
+molecule = stk.ConstructedMolecule(
+    topology_graph=stk.host_guest.Complex(
+        host=stk.BuildingBlock.init_from_molecule(host),
+        guests=stk.host_guest.Guest(
+            building_block=stk.BuildingBlock("[Br][Br]"),
+        ),
+    ),
+)
+teststring = stk.XyzWriter().to_string(molecule)
+teststring = teststring.split("\n")
+teststring[1] = (
+    f"e='{energy.get_energy(molecule)}' "
+    f"rg='{analyser.get_radius_gyration(molecule)}'"
+)
+string += "\n".join(teststring)
+
+bb1 = stk.BuildingBlock(
+    smiles="NCCN",
+    functional_groups=[stk.PrimaryAminoFactory()],
+)
+bb2 = stk.BuildingBlock(
+    smiles="O=CC(C=O)C=O",
+    functional_groups=[stk.AldehydeFactory()],
+)
+molecule = stk.ConstructedMolecule(
+    topology_graph=stk.cage.FourPlusSix((bb1, bb2)),
+)
+molecule.write(data_path / "unoptcage.mol")
+teststring = stk.XyzWriter().to_string(molecule)
+teststring = teststring.split("\n")
+teststring[1] = (
+    f"e='{energy.get_energy(molecule)}' "
+    f"rg='{analyser.get_radius_gyration(molecule)}'"
+)
+string += "\n".join(teststring)
+
+molecule = stk.ConstructedMolecule(
+    topology_graph=stk.cage.FourPlusSix(
+        building_blocks=(bb1, bb2),
+        optimizer=stk.MCHammer(),
+    )
+)
+teststring = stk.XyzWriter().to_string(molecule)
+teststring = teststring.split("\n")
+teststring[1] = (
+    f"e='{energy.get_energy(molecule)}' "
+    f"rg='{analyser.get_radius_gyration(molecule)}'"
+)
+string += "\n".join(teststring)
+
+
+palladium_atom = stk.BuildingBlock(
+    smiles="[Pd+2]",
+    functional_groups=(stk.SingleAtom(stk.Pd(0, charge=2)) for i in range(4)),
+    position_matrix=[[0.0, 0.0, 0.0]],
+)
+bb1 = stk.BuildingBlock(
+    smiles=("C1=NC=CC(C2=CC=CC(C3=C" "C=NC=C3)=C2)=C1"),
+    functional_groups=[
+        stk.SmartsFunctionalGroupFactory(
+            smarts="[#6]~[#7X2]~[#6]",
+            bonders=(1,),
+            deleters=(),
+        ),
+    ],
+)
+molecule = stk.ConstructedMolecule(
+    stk.cage.M2L4Lantern(
+        building_blocks=(palladium_atom, bb1),
+        # Ensure that bonds between the
+        # GenericFunctionalGroups of the ligand and the
+        # SingleAtom functional groups of the metal are
+        # dative.
+        reaction_factory=stk.DativeReactionFactory(
+            stk.GenericReactionFactory(
+                bond_orders={
+                    frozenset(
+                        {
+                            stk.GenericFunctionalGroup,
+                            stk.SingleAtom,
+                        }
+                    ): 9,
+                },
+            ),
+        ),
+    ),
+)
+molecule.write(data_path / "metalcage.mol")
+teststring = stk.XyzWriter().to_string(molecule)
+teststring = teststring.split("\n")
+teststring[1] = (
+    f"e='{energy.get_energy(molecule)}' "
+    f"rg='{analyser.get_radius_gyration(molecule)}'"
+)
+string += "\n".join(teststring)
+
+
+with xyz_path.open("w") as f:
+    f.write(string)
+
+########################################################################
+
+
+print(
+    "one change I am interested in, is if you want to use the standard "
+    "load xyz > chemiscope workflow, like here. "
+    "or, if I use rdkit/stk to provide the graph automatically? "
+    "I would not want to add any dependancies in doing so"
+)
+
+
+# %%
+#
+# Load structures from an extended xyz file.
+frames = ase.io.read(xyz_path, ":")
+
+
+# %%
+#
+# Write to json file without added shapes and note that the XX-XX bonds are
+# missing.
+
+chemiscope.write_input(
+    "noshape_example.json.gz",
+    frames=frames,
+    properties=chemiscope.extract_properties(frames, only=["e", "rg"]),
+    meta=dict(name="Missing bonds by automation."),
+    settings=chemiscope.quick_settings(x="rg", y="e", color=""),
+)
+
+
+# %%
+#
+# Compute the shape dicionary from the structures based on XX.
+mol1 = stk.BuildingBlock.init_from_file(data_path / "unoptcage.mol")
+mol1_bonds = tuple(
+    (bond.get_atom1().get_id(), bond.get_atom2().get_id()) for bond in mol1.get_bonds()
+)
+
+mol3 = stk.BuildingBlock.init_from_file(data_path / "metalcage.mol")
+mol3_bonds = tuple(
+    (bond.get_atom1().get_id(), bond.get_atom2().get_id()) for bond in mol3.get_bonds()
+)
+bonds_per_frames = {
+    # Here, we do it by hand to fill in some issues.
+    0: ((0, 60), (22, 132), (30, 85), (34, 150), (4, 96), (46, 169)),
+    2: ((3, 48), (11, 56), (19, 72)),
+    # In these two examples, we are using "fake", unoptimised models and show
+    # how to generate these from a mol file.
+    # Although these examples currently require a new dependancy, so I can
+    # alter them as needed?
+    1: mol1_bonds,
+    3: mol3_bonds,
+}
+
+shape_dict = chemiscope.convert_bonds_as_shapes(
+    frames=frames,
+    bonds_per_frames=bonds_per_frames,
+)
+# Write the shape string for settings to turn them on automatically.
+shape_string = ",".join(shape_dict.keys())
+
+# %%
+#
+# Write to json file with added shapes and note that the XX-XX bonds are
+# present.
+chemiscope.write_input(
+    "shape_example.json.gz",
+    frames=frames,
+    properties=chemiscope.extract_properties(frames, only=["e", "rg"]),
+    meta=dict(name="Added some bonds."),
+    settings=chemiscope.quick_settings(
+        x="rg",
+        y="e",
+        color="",
+        structure_settings={
+            "shape": shape_string,
+            "atoms": True,
+            "bonds": True,
+            "spaceFilling": False,
+        },
+    ),
+    shapes=shape_dict,
+)
+
+raise SystemExit

From f37c99e6a4324df47729c533dc9cd1a0322547fd Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Fri, 20 Sep 2024 19:23:25 +0200
Subject: [PATCH 02/35] Write bonds to shape function, add to init.

---
 python/chemiscope/__init__.py            |  1 +
 python/chemiscope/structures/__init__.py |  6 +-
 python/chemiscope/structures/_bonding.py | 88 ++++++++++++++++++++++++
 3 files changed, 94 insertions(+), 1 deletion(-)
 create mode 100644 python/chemiscope/structures/_bonding.py

diff --git a/python/chemiscope/__init__.py b/python/chemiscope/__init__.py
index 9723959c1..4a137f8d5 100644
--- a/python/chemiscope/__init__.py
+++ b/python/chemiscope/__init__.py
@@ -10,6 +10,7 @@
     ellipsoid_from_tensor,
     extract_properties,
     librascal_atomic_environments,
+    convert_bonds_as_shapes,
 )
 from .explore import explore, metatensor_featurizer  # noqa: F401
 from .version import __version__  # noqa: F401
diff --git a/python/chemiscope/structures/__init__.py b/python/chemiscope/structures/__init__.py
index 3f6fa9991..165b594ac 100644
--- a/python/chemiscope/structures/__init__.py
+++ b/python/chemiscope/structures/__init__.py
@@ -14,13 +14,17 @@
     center_shape,
     ellipsoid_from_tensor,
 )
-
+from ._bonding import convert_bonds_as_shapes  # noqa: F401
 from ._ase import (  # noqa: F401
     ase_merge_pi_frames,
     ase_tensors_to_ellipsoids,
     ase_vectors_to_arrows,
 )
 
+__all__ = [
+    "convert_bonds_as_shapes",
+]
+
 
 def _guess_adapter(frames):
     """
diff --git a/python/chemiscope/structures/_bonding.py b/python/chemiscope/structures/_bonding.py
new file mode 100644
index 000000000..cbe2cd33d
--- /dev/null
+++ b/python/chemiscope/structures/_bonding.py
@@ -0,0 +1,88 @@
+"""Module for handling bonding in chemiscope."""
+
+try:
+    import ase
+
+    HAVE_ASE = True
+except ImportError:
+    HAVE_ASE = False
+
+
+def convert_bonds_as_shapes(
+    frames: list[ase.Atoms],
+    bonds_per_frames: dict[int, list[tuple[int, int]]],
+) -> dict[str, dict]:
+    """Convert connections between atom ids in each structure to shapes.
+
+    Parameters:
+
+        frames:
+            List of ase.Atoms object, which each are an molecule in chemiscope.
+
+        bonds_per_frames:
+            The bonds you want to add between atoms with the given ids. The key
+            to the dictionary should align with the id of the molecule in
+            frames.
+
+    """
+    shape_dict: dict[str, dict] = {}
+    max_length = 0
+    for fid, molecule in enumerate(frames):
+        bonds_to_add = bonds_per_frames[fid]
+
+        for bid, bond_info in enumerate(bonds_to_add):
+            bname = f"bond_{bid}"
+
+            # Compute the bond vector.
+            position_matrix = molecule.get_positions()
+            bond_geometry = {
+                "vector": (
+                    position_matrix[bond_info[1]] - position_matrix[bond_info[0]]
+                ).tolist(),
+                "position": (position_matrix[bond_info[0]]).tolist(),
+            }
+
+            # Add the bond name to the dictionary to be iterated through.
+            if bname not in shape_dict:
+                if bname == "bond_0":
+                    shape_dict[bname] = {
+                        "kind": "cylinder",
+                        "parameters": {
+                            "global": {"radius": 0.12, "color": "#fc5500"},
+                            "structure": [],
+                        },
+                    }
+
+                else:
+                    num_to_add = len(shape_dict["bond_0"]["parameters"]["structure"])
+                    shape_dict[bname] = {
+                        "kind": "cylinder",
+                        "parameters": {
+                            "global": {"radius": 0.12, "color": "#fc5500"},
+                            # Add zero placements for previously non-existant
+                            # bond shapes up to the length of bond_0 -1,
+                            # because that should already be at the current
+                            # length that the new one should be.
+                            "structure": [
+                                {"vector": [0, 0, 0], "position": [0, 0, 0]}
+                                for i in range(num_to_add - 1)
+                            ],
+                        },
+                    }
+
+            # Add vector to the shape dictionary.
+            shape_dict[bname]["parameters"]["structure"].append(bond_geometry)
+            max_length = max(
+                (max_length, len(shape_dict[bname]["parameters"]["structure"]))
+            )
+
+        # Fill in bond shapes that are not the same length as the max length.
+        for bname in shape_dict.keys():
+            missing = max_length - len(shape_dict[bname]["parameters"]["structure"])
+            if missing == 0:
+                continue
+            for i in range(missing):
+                fake_bond = {"vector": [0, 0, 0], "position": [0, 0, 0]}
+                shape_dict[bname]["parameters"]["structure"].append(fake_bond)
+
+    return shape_dict

From d81dd4fa8520e07a97e6bc758c0f25daf7ad5658 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Fri, 20 Sep 2024 19:23:36 +0200
Subject: [PATCH 03/35] Save outputs.

---
 python/examples/data/metalcage.mol | 272 +++++++++++++++++
 python/examples/data/stkbuilt.xyz  | 460 +++++++++++++++++++++++++++++
 python/examples/data/unoptcage.mol | 176 +++++++++++
 3 files changed, 908 insertions(+)
 create mode 100644 python/examples/data/metalcage.mol
 create mode 100644 python/examples/data/stkbuilt.xyz
 create mode 100644 python/examples/data/unoptcage.mol

diff --git a/python/examples/data/metalcage.mol b/python/examples/data/metalcage.mol
new file mode 100644
index 000000000..f0dfe7c02
--- /dev/null
+++ b/python/examples/data/metalcage.mol
@@ -0,0 +1,272 @@
+
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 122 136 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 Pd 0.0000 6.7061 0.0000 0 CHG=2
+M  V30 2 Pd 0.0000 -6.7061 0.0000 0 CHG=2
+M  V30 3 C 14.6172 4.7881 -0.6066 0
+M  V30 4 N 13.4123 4.8933 -0.0000 0
+M  V30 5 C 12.9018 3.7993 0.5932 0
+M  V30 6 C 13.5659 2.5874 0.5996 0
+M  V30 7 C 14.7939 2.4749 -0.0171 0
+M  V30 8 C 15.4939 1.1926 -0.0090 0
+M  V30 9 C 16.8711 1.1292 -0.0077 0
+M  V30 10 C 17.5565 -0.0840 0.0004 0
+M  V30 11 C 16.8578 -1.2740 0.0075 0
+M  V30 12 C 15.4780 -1.2425 0.0064 0
+M  V30 13 C 14.7497 -2.4936 0.0146 0
+M  V30 14 C 13.5220 -2.5919 0.6235 0
+M  V30 15 C 12.8806 -3.8096 0.5967 0
+M  V30 16 N 13.4123 -4.8933 0.0000 0
+M  V30 17 C 14.6118 -4.8155 -0.6003 0
+M  V30 18 C 15.2647 -3.6219 -0.5866 0
+M  V30 19 C 14.8141 -0.0144 -0.0018 0
+M  V30 20 C 15.3148 3.5984 -0.6246 0
+M  V30 21 H 14.9944 5.6977 -1.0750 0
+M  V30 22 H 11.9249 3.8319 1.1009 0
+M  V30 23 H 13.1630 1.6997 1.0741 0
+M  V30 24 H 17.4342 2.0590 -0.0132 0
+M  V30 25 H 18.6349 -0.1061 0.0012 0
+M  V30 26 H 17.3723 -2.2363 0.0139 0
+M  V30 27 H 13.0431 -1.7455 1.1225 0
+M  V30 28 H 11.9020 -3.9029 1.0772 0
+M  V30 29 H 15.0316 -5.7081 -1.0820 0
+M  V30 30 H 16.2391 -3.5986 -1.0858 0
+M  V30 31 H 13.7460 0.0126 -0.0026 0
+M  V30 32 H 16.2634 3.5747 -1.1195 0
+M  V30 33 C 0.6066 4.7881 14.6172 0
+M  V30 34 N 0.0000 4.8933 13.4123 0
+M  V30 35 C -0.5932 3.7993 12.9018 0
+M  V30 36 C -0.5996 2.5874 13.5659 0
+M  V30 37 C 0.0171 2.4749 14.7939 0
+M  V30 38 C 0.0090 1.1926 15.4939 0
+M  V30 39 C 0.0077 1.1292 16.8711 0
+M  V30 40 C -0.0004 -0.0840 17.5565 0
+M  V30 41 C -0.0075 -1.2740 16.8578 0
+M  V30 42 C -0.0064 -1.2425 15.4780 0
+M  V30 43 C -0.0146 -2.4936 14.7497 0
+M  V30 44 C -0.6235 -2.5919 13.5220 0
+M  V30 45 C -0.5967 -3.8096 12.8806 0
+M  V30 46 N 0.0000 -4.8933 13.4123 0
+M  V30 47 C 0.6003 -4.8155 14.6118 0
+M  V30 48 C 0.5866 -3.6219 15.2647 0
+M  V30 49 C 0.0018 -0.0144 14.8141 0
+M  V30 50 C 0.6246 3.5984 15.3148 0
+M  V30 51 H 1.0750 5.6977 14.9944 0
+M  V30 52 H -1.1009 3.8319 11.9249 0
+M  V30 53 H -1.0741 1.6997 13.1630 0
+M  V30 54 H 0.0132 2.0590 17.4342 0
+M  V30 55 H -0.0012 -0.1061 18.6349 0
+M  V30 56 H -0.0139 -2.2363 17.3723 0
+M  V30 57 H -1.1225 -1.7455 13.0431 0
+M  V30 58 H -1.0772 -3.9029 11.9020 0
+M  V30 59 H 1.0820 -5.7081 15.0316 0
+M  V30 60 H 1.0858 -3.5986 16.2391 0
+M  V30 61 H 0.0026 0.0126 13.7460 0
+M  V30 62 H 1.1195 3.5747 16.2634 0
+M  V30 63 C -14.6172 4.7881 0.6066 0
+M  V30 64 N -13.4123 4.8933 0.0000 0
+M  V30 65 C -12.9018 3.7993 -0.5932 0
+M  V30 66 C -13.5659 2.5874 -0.5996 0
+M  V30 67 C -14.7939 2.4749 0.0171 0
+M  V30 68 C -15.4939 1.1926 0.0090 0
+M  V30 69 C -16.8711 1.1292 0.0077 0
+M  V30 70 C -17.5565 -0.0840 -0.0004 0
+M  V30 71 C -16.8578 -1.2740 -0.0075 0
+M  V30 72 C -15.4780 -1.2425 -0.0064 0
+M  V30 73 C -14.7497 -2.4936 -0.0146 0
+M  V30 74 C -13.5220 -2.5919 -0.6235 0
+M  V30 75 C -12.8806 -3.8096 -0.5967 0
+M  V30 76 N -13.4123 -4.8933 -0.0000 0
+M  V30 77 C -14.6118 -4.8155 0.6003 0
+M  V30 78 C -15.2647 -3.6219 0.5866 0
+M  V30 79 C -14.8141 -0.0144 0.0018 0
+M  V30 80 C -15.3148 3.5984 0.6246 0
+M  V30 81 H -14.9944 5.6977 1.0750 0
+M  V30 82 H -11.9249 3.8319 -1.1009 0
+M  V30 83 H -13.1630 1.6997 -1.0741 0
+M  V30 84 H -17.4342 2.0590 0.0132 0
+M  V30 85 H -18.6349 -0.1061 -0.0012 0
+M  V30 86 H -17.3723 -2.2363 -0.0139 0
+M  V30 87 H -13.0431 -1.7455 -1.1225 0
+M  V30 88 H -11.9020 -3.9029 -1.0772 0
+M  V30 89 H -15.0316 -5.7081 1.0820 0
+M  V30 90 H -16.2391 -3.5986 1.0858 0
+M  V30 91 H -13.7460 0.0126 0.0026 0
+M  V30 92 H -16.2634 3.5747 1.1195 0
+M  V30 93 C -0.6066 4.7881 -14.6172 0
+M  V30 94 N -0.0000 4.8933 -13.4123 0
+M  V30 95 C 0.5932 3.7993 -12.9018 0
+M  V30 96 C 0.5996 2.5874 -13.5659 0
+M  V30 97 C -0.0171 2.4749 -14.7939 0
+M  V30 98 C -0.0090 1.1926 -15.4939 0
+M  V30 99 C -0.0077 1.1292 -16.8711 0
+M  V30 100 C 0.0004 -0.0840 -17.5565 0
+M  V30 101 C 0.0075 -1.2740 -16.8578 0
+M  V30 102 C 0.0064 -1.2425 -15.4780 0
+M  V30 103 C 0.0146 -2.4936 -14.7497 0
+M  V30 104 C 0.6235 -2.5919 -13.5220 0
+M  V30 105 C 0.5967 -3.8096 -12.8806 0
+M  V30 106 N -0.0000 -4.8933 -13.4123 0
+M  V30 107 C -0.6003 -4.8155 -14.6118 0
+M  V30 108 C -0.5866 -3.6219 -15.2647 0
+M  V30 109 C -0.0018 -0.0144 -14.8141 0
+M  V30 110 C -0.6246 3.5984 -15.3148 0
+M  V30 111 H -1.0750 5.6977 -14.9944 0
+M  V30 112 H 1.1009 3.8319 -11.9249 0
+M  V30 113 H 1.0741 1.6997 -13.1630 0
+M  V30 114 H -0.0132 2.0590 -17.4342 0
+M  V30 115 H 0.0012 -0.1061 -18.6349 0
+M  V30 116 H 0.0139 -2.2363 -17.3723 0
+M  V30 117 H 1.1225 -1.7455 -13.0431 0
+M  V30 118 H 1.0772 -3.9029 -11.9020 0
+M  V30 119 H -1.0820 -5.7081 -15.0316 0
+M  V30 120 H -1.0858 -3.5986 -16.2391 0
+M  V30 121 H -0.0026 0.0126 -13.7460 0
+M  V30 122 H -1.1195 3.5747 -16.2634 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 3 4
+M  V30 2 1 4 5
+M  V30 3 2 5 6
+M  V30 4 1 6 7
+M  V30 5 1 7 8
+M  V30 6 2 8 9
+M  V30 7 1 9 10
+M  V30 8 2 10 11
+M  V30 9 1 11 12
+M  V30 10 1 12 13
+M  V30 11 2 13 14
+M  V30 12 1 14 15
+M  V30 13 2 15 16
+M  V30 14 1 16 17
+M  V30 15 2 17 18
+M  V30 16 2 12 19
+M  V30 17 2 7 20
+M  V30 18 1 20 3
+M  V30 19 1 19 8
+M  V30 20 1 18 13
+M  V30 21 1 3 21
+M  V30 22 1 5 22
+M  V30 23 1 6 23
+M  V30 24 1 9 24
+M  V30 25 1 10 25
+M  V30 26 1 11 26
+M  V30 27 1 14 27
+M  V30 28 1 15 28
+M  V30 29 1 17 29
+M  V30 30 1 18 30
+M  V30 31 1 19 31
+M  V30 32 1 20 32
+M  V30 33 2 33 34
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+M  V30 END BOND
+M  V30 END CTAB
+M  END
+
+$$$$
diff --git a/python/examples/data/stkbuilt.xyz b/python/examples/data/stkbuilt.xyz
new file mode 100644
index 000000000..a2b2b77c1
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+H 11.924946 3.831871 1.100866
+H 13.163007 1.699657 1.074149
+H 17.434224 2.059040 -0.013178
+H 18.634873 -0.106053 0.001236
+H 17.372346 -2.236272 0.013913
+H 13.043071 -1.745509 1.122496
+H 11.901981 -3.902911 1.077175
+H 15.031603 -5.708122 -1.081966
+H 16.239128 -3.598600 -1.085790
+H 13.746032 0.012568 -0.002636
+H 16.263366 3.574652 -1.119470
+C 0.606619 4.788114 14.617151
+N 0.000000 4.893306 13.412279
+C -0.593223 3.799282 12.901820
+C -0.599618 2.587447 13.565877
+C 0.017105 2.474878 14.793916
+C 0.008968 1.192641 15.493884
+C 0.007671 1.129187 16.871077
+C -0.000424 -0.083989 17.556534
+C -0.007511 -1.274026 16.857801
+C -0.006411 -1.242464 15.478020
+C -0.014614 -2.493615 14.749705
+C -0.623452 -2.591883 13.522003
+C -0.596673 -3.809551 12.880642
+N 0.000000 -4.893306 13.412279
+C 0.600290 -4.815506 14.611776
+C 0.586634 -3.621907 15.264750
+C 0.001813 -0.014410 14.814107
+C 0.624584 3.598395 15.314784
+H 1.075037 5.697699 14.994387
+H -1.100866 3.831871 11.924946
+H -1.074149 1.699657 13.163007
+H 0.013178 2.059040 17.434224
+H -0.001236 -0.106053 18.634873
+H -0.013913 -2.236272 17.372346
+H -1.122496 -1.745509 13.043071
+H -1.077175 -3.902911 11.901981
+H 1.081966 -5.708122 15.031603
+H 1.085790 -3.598600 16.239128
+H 0.002636 0.012568 13.746032
+H 1.119470 3.574652 16.263366
+C -14.617151 4.788114 0.606619
+N -13.412279 4.893306 0.000000
+C -12.901820 3.799282 -0.593223
+C -13.565877 2.587447 -0.599618
+C -14.793916 2.474878 0.017105
+C -15.493884 1.192641 0.008968
+C -16.871077 1.129187 0.007671
+C -17.556534 -0.083989 -0.000424
+C -16.857801 -1.274026 -0.007511
+C -15.478020 -1.242464 -0.006411
+C -14.749705 -2.493615 -0.014614
+C -13.522003 -2.591883 -0.623452
+C -12.880642 -3.809551 -0.596673
+N -13.412279 -4.893306 -0.000000
+C -14.611776 -4.815506 0.600290
+C -15.264750 -3.621907 0.586634
+C -14.814107 -0.014410 0.001813
+C -15.314784 3.598395 0.624584
+H -14.994387 5.697699 1.075037
+H -11.924946 3.831871 -1.100866
+H -13.163007 1.699657 -1.074149
+H -17.434224 2.059040 0.013178
+H -18.634873 -0.106053 -0.001236
+H -17.372346 -2.236272 -0.013913
+H -13.043071 -1.745509 -1.122496
+H -11.901981 -3.902911 -1.077175
+H -15.031603 -5.708122 1.081966
+H -16.239128 -3.598600 1.085790
+H -13.746032 0.012568 0.002636
+H -16.263366 3.574652 1.119470
+C -0.606619 4.788114 -14.617151
+N -0.000000 4.893306 -13.412279
+C 0.593223 3.799282 -12.901820
+C 0.599618 2.587447 -13.565877
+C -0.017105 2.474878 -14.793916
+C -0.008968 1.192641 -15.493884
+C -0.007671 1.129187 -16.871077
+C 0.000424 -0.083989 -17.556534
+C 0.007511 -1.274026 -16.857801
+C 0.006411 -1.242464 -15.478020
+C 0.014614 -2.493615 -14.749705
+C 0.623452 -2.591883 -13.522003
+C 0.596673 -3.809551 -12.880642
+N -0.000000 -4.893306 -13.412279
+C -0.600290 -4.815506 -14.611776
+C -0.586634 -3.621907 -15.264750
+C -0.001813 -0.014410 -14.814107
+C -0.624584 3.598395 -15.314784
+H -1.075037 5.697699 -14.994387
+H 1.100866 3.831871 -11.924946
+H 1.074149 1.699657 -13.163007
+H -0.013178 2.059040 -17.434224
+H 0.001236 -0.106053 -18.634873
+H 0.013913 -2.236272 -17.372346
+H 1.122496 -1.745509 -13.043071
+H 1.077175 -3.902911 -11.901981
+H -1.081966 -5.708122 -15.031603
+H -1.085790 -3.598600 -16.239128
+H -0.002636 0.012568 -13.746032
+H -1.119470 3.574652 -16.263366
diff --git a/python/examples/data/unoptcage.mol b/python/examples/data/unoptcage.mol
new file mode 100644
index 000000000..d61446e47
--- /dev/null
+++ b/python/examples/data/unoptcage.mol
@@ -0,0 +1,176 @@
+
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 80 82 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -1.2134 -0.7006 7.6921 0
+M  V30 2 C 0.0024 0.0195 8.1532 0
+M  V30 3 C 1.2289 -0.7128 7.6921 0
+M  V30 4 C -0.0155 1.4134 7.6921 0
+M  V30 5 H -1.4106 -0.8660 6.6467 0
+M  V30 6 H 0.0228 0.0328 9.2640 0
+M  V30 7 H 1.3779 -0.8508 6.6158 0
+M  V30 8 H 0.7696 2.1271 7.9093 0
+M  V30 9 C -6.6851 -3.8596 -1.2430 0
+M  V30 10 C -6.6459 -3.8550 -2.7289 0
+M  V30 11 C -6.6921 -2.4414 -3.2314 0
+M  V30 12 C -5.4646 -4.5773 -3.2177 0
+M  V30 13 H -5.9270 -3.3704 -0.6555 0
+M  V30 14 H -7.5451 -4.3758 -3.1221 0
+M  V30 15 H -5.8930 -1.7560 -2.9293 0
+M  V30 16 H -5.2299 -4.7022 -4.2675 0
+M  V30 17 C 6.6851 -3.8596 -1.2430 0
+M  V30 18 C 6.6615 -3.8280 -2.7289 0
+M  V30 19 C 5.4604 -4.5748 -3.2314 0
+M  V30 20 C 6.6963 -2.4438 -3.2177 0
+M  V30 21 H 5.8824 -3.4478 -0.6555 0
+M  V30 22 H 7.5621 -4.3463 -3.1221 0
+M  V30 23 H 4.4673 -4.2255 -2.9293 0
+M  V30 24 H 6.6872 -2.1781 -4.2675 0
+M  V30 25 C -0.0000 7.7193 -1.2430 0
+M  V30 26 C -0.0156 7.6830 -2.7289 0
+M  V30 27 C 1.2317 7.0162 -3.2314 0
+M  V30 28 C -1.2317 7.0211 -3.2177 0
+M  V30 29 H 0.0447 6.8181 -0.6555 0
+M  V30 30 H -0.0170 8.7221 -3.1221 0
+M  V30 31 H 1.4257 5.9815 -2.9293 0
+M  V30 32 H -1.4573 6.8803 -4.2675 0
+M  V30 33 N -3.2178 -1.8578 4.4191 0
+M  V30 34 C -4.6051 -2.2313 4.4421 0
+M  V30 35 C -4.9290 -3.2079 3.3152 0
+M  V30 36 N -4.6808 -2.7024 2.0300 0
+M  V30 37 H -5.2477 -1.3300 4.3651 0
+M  V30 38 H -4.7784 -2.7831 5.3911 0
+M  V30 39 H -4.2388 -4.0831 3.4884 0
+M  V30 40 H -5.9702 -3.5517 3.4212 0
+M  V30 41 N 3.2255 -1.8639 4.4191 0
+M  V30 42 C 4.2425 -2.8787 4.4421 0
+M  V30 43 C 5.2503 -2.6710 3.3153 0
+M  V30 44 N 4.6885 -2.7085 2.0300 0
+M  V30 45 H 3.7830 -3.8858 4.3649 0
+M  V30 46 H 4.8069 -2.7532 5.3911 0
+M  V30 47 H 5.6634 -1.6358 3.4886 0
+M  V30 48 H 6.0684 -3.4011 3.4212 0
+M  V30 49 N -0.0077 3.7216 4.4191 0
+M  V30 50 C 0.3608 5.1103 4.4424 0
+M  V30 51 C -0.3230 5.8783 3.3150 0
+M  V30 52 N -0.0077 5.4110 2.0300 0
+M  V30 53 H 1.4626 5.2174 4.3663 0
+M  V30 54 H -0.0316 5.5358 5.3911 0
+M  V30 55 H -1.4260 5.7170 3.4873 0
+M  V30 56 H -0.1013 6.9522 3.4211 0
+M  V30 57 N -1.4651 -4.5761 -3.2246 0
+M  V30 58 C -0.6824 -5.3003 -4.1877 0
+M  V30 59 C 0.6815 -5.6755 -3.6155 0
+M  V30 60 N 1.4609 -4.5761 -3.2246 0
+M  V30 61 H -0.5584 -4.6999 -5.1126 0
+M  V30 62 H -1.2113 -6.2578 -4.3839 0
+M  V30 63 H 0.4477 -6.2857 -2.6961 0
+M  V30 64 H 1.2149 -6.3136 -4.3380 0
+M  V30 65 N -4.6934 1.0229 -3.2246 0
+M  V30 66 C -5.2985 2.2760 -3.5825 0
+M  V30 67 C -4.2593 3.2509 -4.1283 0
+M  V30 68 N -3.2304 3.5569 -3.2246 0
+M  V30 69 H -5.8160 2.7179 -2.7060 0
+M  V30 70 H -6.0020 2.0714 -4.4183 0
+M  V30 71 H -3.8042 2.7182 -5.0123 0
+M  V30 72 H -4.7677 4.1603 -4.4863 0
+M  V30 73 N 4.6955 1.0192 -3.2246 0
+M  V30 74 C 4.9314 2.0591 -4.1877 0
+M  V30 75 C 4.5743 3.4280 -3.6155 0
+M  V30 76 N 3.2325 3.5532 -3.2246 0
+M  V30 77 H 4.3495 1.8663 -5.1126 0
+M  V30 78 H 6.0251 2.0799 -4.3839 0
+M  V30 79 H 5.2197 3.5306 -2.6961 0
+M  V30 80 H 4.8603 4.2089 -4.3380 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 2 4
+M  V30 4 1 1 5
+M  V30 5 1 2 6
+M  V30 6 1 3 7
+M  V30 7 1 4 8
+M  V30 8 1 9 10
+M  V30 9 1 10 11
+M  V30 10 1 10 12
+M  V30 11 1 9 13
+M  V30 12 1 10 14
+M  V30 13 1 11 15
+M  V30 14 1 12 16
+M  V30 15 1 17 18
+M  V30 16 1 18 19
+M  V30 17 1 18 20
+M  V30 18 1 17 21
+M  V30 19 1 18 22
+M  V30 20 1 19 23
+M  V30 21 1 20 24
+M  V30 22 1 25 26
+M  V30 23 1 26 27
+M  V30 24 1 26 28
+M  V30 25 1 25 29
+M  V30 26 1 26 30
+M  V30 27 1 27 31
+M  V30 28 1 28 32
+M  V30 29 1 33 34
+M  V30 30 1 34 35
+M  V30 31 1 35 36
+M  V30 32 1 34 37
+M  V30 33 1 34 38
+M  V30 34 1 35 39
+M  V30 35 1 35 40
+M  V30 36 1 41 42
+M  V30 37 1 42 43
+M  V30 38 1 43 44
+M  V30 39 1 42 45
+M  V30 40 1 42 46
+M  V30 41 1 43 47
+M  V30 42 1 43 48
+M  V30 43 1 49 50
+M  V30 44 1 50 51
+M  V30 45 1 51 52
+M  V30 46 1 50 53
+M  V30 47 1 50 54
+M  V30 48 1 51 55
+M  V30 49 1 51 56
+M  V30 50 1 57 58
+M  V30 51 1 58 59
+M  V30 52 1 59 60
+M  V30 53 1 58 61
+M  V30 54 1 58 62
+M  V30 55 1 59 63
+M  V30 56 1 59 64
+M  V30 57 1 65 66
+M  V30 58 1 66 67
+M  V30 59 1 67 68
+M  V30 60 1 66 69
+M  V30 61 1 66 70
+M  V30 62 1 67 71
+M  V30 63 1 67 72
+M  V30 64 1 73 74
+M  V30 65 1 74 75
+M  V30 66 1 75 76
+M  V30 67 1 74 77
+M  V30 68 1 74 78
+M  V30 69 1 75 79
+M  V30 70 1 75 80
+M  V30 71 2 1 33
+M  V30 72 2 9 36
+M  V30 73 2 3 41
+M  V30 74 2 17 44
+M  V30 75 2 4 49
+M  V30 76 2 25 52
+M  V30 77 2 12 57
+M  V30 78 2 19 60
+M  V30 79 2 11 65
+M  V30 80 2 28 68
+M  V30 81 2 20 73
+M  V30 82 2 27 76
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+
+$$$$

From 0f572e9f428049a68a23e57e0e7b12e3ee150350 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:22:11 +0200
Subject: [PATCH 04/35] Add dependancy for tests.

---
 tox.ini | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tox.ini b/tox.ini
index 86749e9e1..a3099cbfb 100644
--- a/tox.ini
+++ b/tox.ini
@@ -27,6 +27,8 @@ commands =
 description = Run Python unit tests
 deps =
     ase==3.22.1
+    rdkit==2024.3.4
+    stk
 
 commands =
     pip install chemiscope[explore]

From bb7eb925f053d41f379177892ef50ad4579c9a44 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:23:35 +0200
Subject: [PATCH 05/35] Add example to README.

---
 python/README.md | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/python/README.md b/python/README.md
index 7a7fd5d58..ddd6ae200 100644
--- a/python/README.md
+++ b/python/README.md
@@ -53,3 +53,35 @@ properties = {
 
 chemiscope.show(frames=frames, properties=properties)
 ```
+
+To create a new chemiscope input file using `stk`_:
+
+.. _`stk`: https://github.com/lukasturcani/stk
+
+`stk` is an optional dependancy:
+
+```bash
+pip install stk
+```
+
+```python
+import chemiscope
+import stk
+
+# read frames using ase
+frames = [stk.BuildingBlock(smiles="NCCN")]
+
+# add additional properties to display
+properties = {
+    "<property name>": {
+        target: "atom",
+        values: [3, 4, 2, 8, 9, 10],
+    }
+}
+
+chemiscope.write_input(
+    "my-input.json.gz",
+    frames=frames,
+    properties=properties,
+)
+```
\ No newline at end of file

From 52ceea155ab6df1cf1ff8411e01c400fb15707ba Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:25:14 +0200
Subject: [PATCH 06/35] Move function.

---
 python/chemiscope/__init__.py                 |  2 +-
 python/chemiscope/structures/__init__.py      |  4 +-
 .../structures/{_bonding.py => _stk.py}       | 43 +++++++++++--------
 3 files changed, 28 insertions(+), 21 deletions(-)
 rename python/chemiscope/structures/{_bonding.py => _stk.py} (74%)

diff --git a/python/chemiscope/__init__.py b/python/chemiscope/__init__.py
index 4a137f8d5..c275c6bcd 100644
--- a/python/chemiscope/__init__.py
+++ b/python/chemiscope/__init__.py
@@ -10,7 +10,7 @@
     ellipsoid_from_tensor,
     extract_properties,
     librascal_atomic_environments,
-    convert_bonds_as_shapes,
+    convert_stk_bonds_as_shapes,
 )
 from .explore import explore, metatensor_featurizer  # noqa: F401
 from .version import __version__  # noqa: F401
diff --git a/python/chemiscope/structures/__init__.py b/python/chemiscope/structures/__init__.py
index 165b594ac..ca8041ee9 100644
--- a/python/chemiscope/structures/__init__.py
+++ b/python/chemiscope/structures/__init__.py
@@ -14,7 +14,7 @@
     center_shape,
     ellipsoid_from_tensor,
 )
-from ._bonding import convert_bonds_as_shapes  # noqa: F401
+
 from ._ase import (  # noqa: F401
     ase_merge_pi_frames,
     ase_tensors_to_ellipsoids,
@@ -22,7 +22,7 @@
 )
 
 __all__ = [
-    "convert_bonds_as_shapes",
+    "convert_stk_bonds_as_shapes",
 ]
 
 
diff --git a/python/chemiscope/structures/_bonding.py b/python/chemiscope/structures/_stk.py
similarity index 74%
rename from python/chemiscope/structures/_bonding.py
rename to python/chemiscope/structures/_stk.py
index cbe2cd33d..a406dd537 100644
--- a/python/chemiscope/structures/_bonding.py
+++ b/python/chemiscope/structures/_stk.py
@@ -1,40 +1,47 @@
-"""Module for handling bonding in chemiscope."""
 
 try:
-    import ase
+    import stk
 
-    HAVE_ASE = True
+    HAVE_STK = True
 except ImportError:
-    HAVE_ASE = False
+    HAVE_STK = False
 
 
-def convert_bonds_as_shapes(
-    frames: list[ase.Atoms],
-    bonds_per_frames: dict[int, list[tuple[int, int]]],
+def convert_stk_bonds_as_shapes(
+    frames: list[stk.Molecule],
+    bond_color: str,
+    bond_radius: float,
 ) -> dict[str, dict]:
     """Convert connections between atom ids in each structure to shapes.
 
     Parameters:
 
         frames:
-            List of ase.Atoms object, which each are an molecule in chemiscope.
+            List of stk.Molecule objects, which each are structures in
+            chemiscope.
+
+        bond_colour:
+            How to colour the bonds added.
+
+        bond_radius:
+            Radius of bonds to add.
 
-        bonds_per_frames:
-            The bonds you want to add between atoms with the given ids. The key
-            to the dictionary should align with the id of the molecule in
-            frames.
 
     """
+
     shape_dict: dict[str, dict] = {}
     max_length = 0
-    for fid, molecule in enumerate(frames):
-        bonds_to_add = bonds_per_frames[fid]
+    for molecule in frames:
+        bonds_to_add = tuple(
+            (bond.get_atom1().get_id(), bond.get_atom2().get_id())
+            for bond in molecule.get_bonds()
+        )
 
         for bid, bond_info in enumerate(bonds_to_add):
             bname = f"bond_{bid}"
 
             # Compute the bond vector.
-            position_matrix = molecule.get_positions()
+            position_matrix = molecule.get_position_matrix()
             bond_geometry = {
                 "vector": (
                     position_matrix[bond_info[1]] - position_matrix[bond_info[0]]
@@ -48,7 +55,7 @@ def convert_bonds_as_shapes(
                     shape_dict[bname] = {
                         "kind": "cylinder",
                         "parameters": {
-                            "global": {"radius": 0.12, "color": "#fc5500"},
+                            "global": {"radius": bond_radius, "color": bond_color},
                             "structure": [],
                         },
                     }
@@ -58,7 +65,7 @@ def convert_bonds_as_shapes(
                     shape_dict[bname] = {
                         "kind": "cylinder",
                         "parameters": {
-                            "global": {"radius": 0.12, "color": "#fc5500"},
+                            "global": {"radius": bond_radius, "color": bond_color},
                             # Add zero placements for previously non-existant
                             # bond shapes up to the length of bond_0 -1,
                             # because that should already be at the current
@@ -81,7 +88,7 @@ def convert_bonds_as_shapes(
             missing = max_length - len(shape_dict[bname]["parameters"]["structure"])
             if missing == 0:
                 continue
-            for i in range(missing):
+            for _ in range(missing):
                 fake_bond = {"vector": [0, 0, 0], "position": [0, 0, 0]}
                 shape_dict[bname]["parameters"]["structure"].append(fake_bond)
 

From cb1ef9154c6999f3122d9e3175c1c5bef2e20c2d Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:26:00 +0200
Subject: [PATCH 07/35] Update example function.

---
 python/examples/8-showing_custom_bonds.py | 316 +++++++--------
 python/examples/data/metalcage.mol        | 272 -------------
 python/examples/data/stkbuilt.xyz         | 460 ----------------------
 python/examples/data/unoptcage.mol        | 176 ---------
 4 files changed, 151 insertions(+), 1073 deletions(-)
 delete mode 100644 python/examples/data/metalcage.mol
 delete mode 100644 python/examples/data/stkbuilt.xyz
 delete mode 100644 python/examples/data/unoptcage.mol

diff --git a/python/examples/8-showing_custom_bonds.py b/python/examples/8-showing_custom_bonds.py
index 19f2b3e70..c806d9e7a 100644
--- a/python/examples/8-showing_custom_bonds.py
+++ b/python/examples/8-showing_custom_bonds.py
@@ -1,173 +1,180 @@
 """
-Showing custom bonds
-====================
+Showing custom bonds using stk
+==============================
 
 This example demonstrates how to add shapes into the chemiscope output such
 that custom bonds that would not normally be assigned by ASE can be rendered.
 
+This is done by using stk to generate and analyse molecules, which comes with
+topology/bonding information by default (using the cheminformatic software
+rdkit).
+
 """
 
-# %%
-#
+import pathlib
+
 import stk
 import stko
-import ase.io
-import pathlib
+from rdkit.Chem import AllChem as rdkit
+
 import chemiscope
 
 working_path = pathlib.Path(__file__).resolve().parent
 data_path = working_path / "data"
 
-########################################################################
-# This is just for development, where I build the library of structures.
-energy = stko.UFFEnergy()
-analyser = stko.molecule_analysis.GeometryAnalyser()
-xyz_path = data_path / "stkbuilt.xyz"
-string = ""
-
-host = stk.ConstructedMolecule(
-    topology_graph=stk.cage.FourPlusSix(
-        building_blocks=(
-            stk.BuildingBlock(
-                smiles="NC1CCCCC1N",
-                functional_groups=[
-                    stk.PrimaryAminoFactory(),
-                ],
-            ),
-            stk.BuildingBlock(
-                smiles="O=Cc1cc(C=O)cc(C=O)c1",
-                functional_groups=[stk.AldehydeFactory()],
+# %%
+#
+# Generate a list of stk BuildingBlocks (representation of a molecule) with
+# properties. This also includes working with rdkit, which comes installed
+# with stk.
+
+rdkitmol = rdkit.MolFromSmiles("Cc1ccccc1")
+rdkitmol = rdkit.AddHs(rdkitmol)
+rdkit.Kekulize(rdkitmol)
+params = rdkit.ETKDGv3()
+params.randomSeed = 0xF00D
+rdkit.EmbedMolecule(rdkitmol, params)
+
+structures = [
+    # A building block.
+    stk.BuildingBlock(smiles="NCCN"),
+    # A mostly optimised cage molecule.
+    stk.ConstructedMolecule(
+        topology_graph=stk.cage.FourPlusSix(
+            building_blocks=(
+                stk.BuildingBlock(
+                    smiles="NCCN",
+                    functional_groups=[stk.PrimaryAminoFactory()],
+                ),
+                stk.BuildingBlock(
+                    smiles="O=CC(C=O)C=O",
+                    functional_groups=[stk.AldehydeFactory()],
+                ),
             ),
+            optimizer=stk.MCHammer(),
         ),
-        optimizer=stk.MCHammer(),
     ),
-)
-molecule = stk.ConstructedMolecule(
-    topology_graph=stk.host_guest.Complex(
-        host=stk.BuildingBlock.init_from_molecule(host),
-        guests=stk.host_guest.Guest(
-            building_block=stk.BuildingBlock("[Br][Br]"),
+    # A metal-organic cage.
+    stk.ConstructedMolecule(
+        stk.cage.M2L4Lantern(
+            building_blocks=(
+                stk.BuildingBlock(
+                    smiles="[Pd+2]",
+                    functional_groups=(
+                        stk.SingleAtom(stk.Pd(0, charge=2)) for i in range(4)
+                    ),
+                    position_matrix=[[0.0, 0.0, 0.0]],
+                ),
+                stk.BuildingBlock(
+                    smiles=("C1=NC=CC(C2=CC=CC(C3=C" "C=NC=C3)=C2)=C1"),
+                    functional_groups=[
+                        stk.SmartsFunctionalGroupFactory(
+                            smarts="[#6]~[#7X2]~[#6]",
+                            bonders=(1,),
+                            deleters=(),
+                        ),
+                    ],
+                ),
+            ),
+            # Ensure that bonds between the
+            # GenericFunctionalGroups of the ligand and the
+            # SingleAtom functional groups of the metal are
+            # dative.
+            reaction_factory=stk.DativeReactionFactory(
+                stk.GenericReactionFactory(
+                    bond_orders={
+                        frozenset(
+                            {
+                                stk.GenericFunctionalGroup,
+                                stk.SingleAtom,
+                            }
+                        ): 9,
+                    },
+                ),
+            ),
         ),
     ),
-)
-teststring = stk.XyzWriter().to_string(molecule)
-teststring = teststring.split("\n")
-teststring[1] = (
-    f"e='{energy.get_energy(molecule)}' "
-    f"rg='{analyser.get_radius_gyration(molecule)}'"
-)
-string += "\n".join(teststring)
-
-bb1 = stk.BuildingBlock(
-    smiles="NCCN",
-    functional_groups=[stk.PrimaryAminoFactory()],
-)
-bb2 = stk.BuildingBlock(
-    smiles="O=CC(C=O)C=O",
-    functional_groups=[stk.AldehydeFactory()],
-)
-molecule = stk.ConstructedMolecule(
-    topology_graph=stk.cage.FourPlusSix((bb1, bb2)),
-)
-molecule.write(data_path / "unoptcage.mol")
-teststring = stk.XyzWriter().to_string(molecule)
-teststring = teststring.split("\n")
-teststring[1] = (
-    f"e='{energy.get_energy(molecule)}' "
-    f"rg='{analyser.get_radius_gyration(molecule)}'"
-)
-string += "\n".join(teststring)
-
-molecule = stk.ConstructedMolecule(
-    topology_graph=stk.cage.FourPlusSix(
-        building_blocks=(bb1, bb2),
-        optimizer=stk.MCHammer(),
-    )
-)
-teststring = stk.XyzWriter().to_string(molecule)
-teststring = teststring.split("\n")
-teststring[1] = (
-    f"e='{energy.get_energy(molecule)}' "
-    f"rg='{analyser.get_radius_gyration(molecule)}'"
-)
-string += "\n".join(teststring)
-
-
-palladium_atom = stk.BuildingBlock(
-    smiles="[Pd+2]",
-    functional_groups=(stk.SingleAtom(stk.Pd(0, charge=2)) for i in range(4)),
-    position_matrix=[[0.0, 0.0, 0.0]],
-)
-bb1 = stk.BuildingBlock(
-    smiles=("C1=NC=CC(C2=CC=CC(C3=C" "C=NC=C3)=C2)=C1"),
-    functional_groups=[
-        stk.SmartsFunctionalGroupFactory(
-            smarts="[#6]~[#7X2]~[#6]",
-            bonders=(1,),
-            deleters=(),
-        ),
-    ],
-)
-molecule = stk.ConstructedMolecule(
-    stk.cage.M2L4Lantern(
-        building_blocks=(palladium_atom, bb1),
-        # Ensure that bonds between the
-        # GenericFunctionalGroups of the ligand and the
-        # SingleAtom functional groups of the metal are
-        # dative.
-        reaction_factory=stk.DativeReactionFactory(
-            stk.GenericReactionFactory(
-                bond_orders={
-                    frozenset(
-                        {
-                            stk.GenericFunctionalGroup,
-                            stk.SingleAtom,
-                        }
-                    ): 9,
-                },
+    # A host guest molecule.
+    stk.ConstructedMolecule(
+        topology_graph=stk.host_guest.Complex(
+            host=stk.BuildingBlock.init_from_molecule(
+                stk.ConstructedMolecule(
+                    topology_graph=stk.cage.FourPlusSix(
+                        building_blocks=(
+                            stk.BuildingBlock(
+                                smiles="NC1CCCCC1N",
+                                functional_groups=[
+                                    stk.PrimaryAminoFactory(),
+                                ],
+                            ),
+                            stk.BuildingBlock(
+                                smiles="O=Cc1cc(C=O)cc(C=O)c1",
+                                functional_groups=[stk.AldehydeFactory()],
+                            ),
+                        ),
+                        optimizer=stk.MCHammer(),
+                    ),
+                )
+            ),
+            guests=stk.host_guest.Guest(
+                building_block=stk.BuildingBlock("[Br][Br]"),
             ),
         ),
     ),
-)
-molecule.write(data_path / "metalcage.mol")
-teststring = stk.XyzWriter().to_string(molecule)
-teststring = teststring.split("\n")
-teststring[1] = (
-    f"e='{energy.get_energy(molecule)}' "
-    f"rg='{analyser.get_radius_gyration(molecule)}'"
-)
-string += "\n".join(teststring)
+    # From rdkit.
+    stk.BuildingBlock.init_from_rdkit_mol(rdkitmol),
+]
 
+# Write to file for sanity checks.
+for i, struct in enumerate(structures):
+    struct.write(data_path / f"stk_{i}.mol")
 
-with xyz_path.open("w") as f:
-    f.write(string)
+# %%
+#
+# Write their properties using any method, here we show using stko:
+# https://stko-docs.readthedocs.io/en/latest/
 
-########################################################################
+energy = stko.UFFEnergy()
+analyser = stko.molecule_analysis.GeometryAnalyser()
+properties = {
+    "e": [energy.get_energy(molecule) for molecule in structures],
+    "rg": [analyser.get_radius_gyration(molecule) for molecule in structures],
+}
 
 
-print(
-    "one change I am interested in, is if you want to use the standard "
-    "load xyz > chemiscope workflow, like here. "
-    "or, if I use rdkit/stk to provide the graph automatically? "
-    "I would not want to add any dependancies in doing so"
+# %%
+#
+# Get the stk bonding information and convert them into shapes.
+shape_dict = chemiscope.convert_stk_bonds_as_shapes(
+    frames=structures,
+    bond_color="#fc5500",
+    bond_radius=0.12,
 )
 
+# Write the shape string for settings to turn them on automatically.
+shape_string = ",".join(shape_dict.keys())
+
 
 # %%
 #
-# Load structures from an extended xyz file.
-frames = ase.io.read(xyz_path, ":")
+# A chemiscope widget can be used to visualize structures and properties.
+# This generates a Chemiscope object that is rendered to an interactive
+# widget when executed in a Jupyter notebook.
+
+chemiscope.show(frames=structures, properties=properties)
 
 
 # %%
 #
-# Write to json file without added shapes and note that the XX-XX bonds are
-# missing.
+# For sharing with collaborators, or when one does not want to use an interactive
+# notebook, one can also write a JSON (or compressed JSON) file that contains all
+# information about structures and properties, and can be viewed at chemiscope.org
+# Save as a file that can be viewed at chemiscope.org
 
 chemiscope.write_input(
-    "noshape_example.json.gz",
-    frames=frames,
-    properties=chemiscope.extract_properties(frames, only=["e", "rg"]),
+    path="noshape_example.json.gz",
+    frames=structures,
+    properties=properties,
     meta=dict(name="Missing bonds by automation."),
     settings=chemiscope.quick_settings(x="rg", y="e", color=""),
 )
@@ -175,44 +182,22 @@
 
 # %%
 #
-# Compute the shape dicionary from the structures based on XX.
-mol1 = stk.BuildingBlock.init_from_file(data_path / "unoptcage.mol")
-mol1_bonds = tuple(
-    (bond.get_atom1().get_id(), bond.get_atom2().get_id()) for bond in mol1.get_bonds()
-)
+# Now with added bonding information.
 
-mol3 = stk.BuildingBlock.init_from_file(data_path / "metalcage.mol")
-mol3_bonds = tuple(
-    (bond.get_atom1().get_id(), bond.get_atom2().get_id()) for bond in mol3.get_bonds()
-)
-bonds_per_frames = {
-    # Here, we do it by hand to fill in some issues.
-    0: ((0, 60), (22, 132), (30, 85), (34, 150), (4, 96), (46, 169)),
-    2: ((3, 48), (11, 56), (19, 72)),
-    # In these two examples, we are using "fake", unoptimised models and show
-    # how to generate these from a mol file.
-    # Although these examples currently require a new dependancy, so I can
-    # alter them as needed?
-    1: mol1_bonds,
-    3: mol3_bonds,
-}
-
-shape_dict = chemiscope.convert_bonds_as_shapes(
-    frames=frames,
-    bonds_per_frames=bonds_per_frames,
+chemiscope.show(
+    frames=structures,
+    properties=properties,
+    shapes=shape_dict,
 )
-# Write the shape string for settings to turn them on automatically.
-shape_string = ",".join(shape_dict.keys())
 
 # %%
 #
-# Write to json file with added shapes and note that the XX-XX bonds are
-# present.
+# Write to json file with added shapes and note are present.
 chemiscope.write_input(
-    "shape_example.json.gz",
-    frames=frames,
-    properties=chemiscope.extract_properties(frames, only=["e", "rg"]),
-    meta=dict(name="Added some bonds."),
+    path="shape_example.json.gz",
+    frames=structures,
+    properties=properties,
+    meta=dict(name="Added all stk bonds."),
     settings=chemiscope.quick_settings(
         x="rg",
         y="e",
@@ -220,11 +205,12 @@
         structure_settings={
             "shape": shape_string,
             "atoms": True,
-            "bonds": True,
+            "bonds": False,
             "spaceFilling": False,
         },
     ),
     shapes=shape_dict,
 )
 
+
 raise SystemExit
diff --git a/python/examples/data/metalcage.mol b/python/examples/data/metalcage.mol
deleted file mode 100644
index f0dfe7c02..000000000
--- a/python/examples/data/metalcage.mol
+++ /dev/null
@@ -1,272 +0,0 @@
-
-     RDKit          3D
-
-  0  0  0  0  0  0  0  0  0  0999 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 122 136 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 Pd 0.0000 6.7061 0.0000 0 CHG=2
-M  V30 2 Pd 0.0000 -6.7061 0.0000 0 CHG=2
-M  V30 3 C 14.6172 4.7881 -0.6066 0
-M  V30 4 N 13.4123 4.8933 -0.0000 0
-M  V30 5 C 12.9018 3.7993 0.5932 0
-M  V30 6 C 13.5659 2.5874 0.5996 0
-M  V30 7 C 14.7939 2.4749 -0.0171 0
-M  V30 8 C 15.4939 1.1926 -0.0090 0
-M  V30 9 C 16.8711 1.1292 -0.0077 0
-M  V30 10 C 17.5565 -0.0840 0.0004 0
-M  V30 11 C 16.8578 -1.2740 0.0075 0
-M  V30 12 C 15.4780 -1.2425 0.0064 0
-M  V30 13 C 14.7497 -2.4936 0.0146 0
-M  V30 14 C 13.5220 -2.5919 0.6235 0
-M  V30 15 C 12.8806 -3.8096 0.5967 0
-M  V30 16 N 13.4123 -4.8933 0.0000 0
-M  V30 17 C 14.6118 -4.8155 -0.6003 0
-M  V30 18 C 15.2647 -3.6219 -0.5866 0
-M  V30 19 C 14.8141 -0.0144 -0.0018 0
-M  V30 20 C 15.3148 3.5984 -0.6246 0
-M  V30 21 H 14.9944 5.6977 -1.0750 0
-M  V30 22 H 11.9249 3.8319 1.1009 0
-M  V30 23 H 13.1630 1.6997 1.0741 0
-M  V30 24 H 17.4342 2.0590 -0.0132 0
-M  V30 25 H 18.6349 -0.1061 0.0012 0
-M  V30 26 H 17.3723 -2.2363 0.0139 0
-M  V30 27 H 13.0431 -1.7455 1.1225 0
-M  V30 28 H 11.9020 -3.9029 1.0772 0
-M  V30 29 H 15.0316 -5.7081 -1.0820 0
-M  V30 30 H 16.2391 -3.5986 -1.0858 0
-M  V30 31 H 13.7460 0.0126 -0.0026 0
-M  V30 32 H 16.2634 3.5747 -1.1195 0
-M  V30 33 C 0.6066 4.7881 14.6172 0
-M  V30 34 N 0.0000 4.8933 13.4123 0
-M  V30 35 C -0.5932 3.7993 12.9018 0
-M  V30 36 C -0.5996 2.5874 13.5659 0
-M  V30 37 C 0.0171 2.4749 14.7939 0
-M  V30 38 C 0.0090 1.1926 15.4939 0
-M  V30 39 C 0.0077 1.1292 16.8711 0
-M  V30 40 C -0.0004 -0.0840 17.5565 0
-M  V30 41 C -0.0075 -1.2740 16.8578 0
-M  V30 42 C -0.0064 -1.2425 15.4780 0
-M  V30 43 C -0.0146 -2.4936 14.7497 0
-M  V30 44 C -0.6235 -2.5919 13.5220 0
-M  V30 45 C -0.5967 -3.8096 12.8806 0
-M  V30 46 N 0.0000 -4.8933 13.4123 0
-M  V30 47 C 0.6003 -4.8155 14.6118 0
-M  V30 48 C 0.5866 -3.6219 15.2647 0
-M  V30 49 C 0.0018 -0.0144 14.8141 0
-M  V30 50 C 0.6246 3.5984 15.3148 0
-M  V30 51 H 1.0750 5.6977 14.9944 0
-M  V30 52 H -1.1009 3.8319 11.9249 0
-M  V30 53 H -1.0741 1.6997 13.1630 0
-M  V30 54 H 0.0132 2.0590 17.4342 0
-M  V30 55 H -0.0012 -0.1061 18.6349 0
-M  V30 56 H -0.0139 -2.2363 17.3723 0
-M  V30 57 H -1.1225 -1.7455 13.0431 0
-M  V30 58 H -1.0772 -3.9029 11.9020 0
-M  V30 59 H 1.0820 -5.7081 15.0316 0
-M  V30 60 H 1.0858 -3.5986 16.2391 0
-M  V30 61 H 0.0026 0.0126 13.7460 0
-M  V30 62 H 1.1195 3.5747 16.2634 0
-M  V30 63 C -14.6172 4.7881 0.6066 0
-M  V30 64 N -13.4123 4.8933 0.0000 0
-M  V30 65 C -12.9018 3.7993 -0.5932 0
-M  V30 66 C -13.5659 2.5874 -0.5996 0
-M  V30 67 C -14.7939 2.4749 0.0171 0
-M  V30 68 C -15.4939 1.1926 0.0090 0
-M  V30 69 C -16.8711 1.1292 0.0077 0
-M  V30 70 C -17.5565 -0.0840 -0.0004 0
-M  V30 71 C -16.8578 -1.2740 -0.0075 0
-M  V30 72 C -15.4780 -1.2425 -0.0064 0
-M  V30 73 C -14.7497 -2.4936 -0.0146 0
-M  V30 74 C -13.5220 -2.5919 -0.6235 0
-M  V30 75 C -12.8806 -3.8096 -0.5967 0
-M  V30 76 N -13.4123 -4.8933 -0.0000 0
-M  V30 77 C -14.6118 -4.8155 0.6003 0
-M  V30 78 C -15.2647 -3.6219 0.5866 0
-M  V30 79 C -14.8141 -0.0144 0.0018 0
-M  V30 80 C -15.3148 3.5984 0.6246 0
-M  V30 81 H -14.9944 5.6977 1.0750 0
-M  V30 82 H -11.9249 3.8319 -1.1009 0
-M  V30 83 H -13.1630 1.6997 -1.0741 0
-M  V30 84 H -17.4342 2.0590 0.0132 0
-M  V30 85 H -18.6349 -0.1061 -0.0012 0
-M  V30 86 H -17.3723 -2.2363 -0.0139 0
-M  V30 87 H -13.0431 -1.7455 -1.1225 0
-M  V30 88 H -11.9020 -3.9029 -1.0772 0
-M  V30 89 H -15.0316 -5.7081 1.0820 0
-M  V30 90 H -16.2391 -3.5986 1.0858 0
-M  V30 91 H -13.7460 0.0126 0.0026 0
-M  V30 92 H -16.2634 3.5747 1.1195 0
-M  V30 93 C -0.6066 4.7881 -14.6172 0
-M  V30 94 N -0.0000 4.8933 -13.4123 0
-M  V30 95 C 0.5932 3.7993 -12.9018 0
-M  V30 96 C 0.5996 2.5874 -13.5659 0
-M  V30 97 C -0.0171 2.4749 -14.7939 0
-M  V30 98 C -0.0090 1.1926 -15.4939 0
-M  V30 99 C -0.0077 1.1292 -16.8711 0
-M  V30 100 C 0.0004 -0.0840 -17.5565 0
-M  V30 101 C 0.0075 -1.2740 -16.8578 0
-M  V30 102 C 0.0064 -1.2425 -15.4780 0
-M  V30 103 C 0.0146 -2.4936 -14.7497 0
-M  V30 104 C 0.6235 -2.5919 -13.5220 0
-M  V30 105 C 0.5967 -3.8096 -12.8806 0
-M  V30 106 N -0.0000 -4.8933 -13.4123 0
-M  V30 107 C -0.6003 -4.8155 -14.6118 0
-M  V30 108 C -0.5866 -3.6219 -15.2647 0
-M  V30 109 C -0.0018 -0.0144 -14.8141 0
-M  V30 110 C -0.6246 3.5984 -15.3148 0
-M  V30 111 H -1.0750 5.6977 -14.9944 0
-M  V30 112 H 1.1009 3.8319 -11.9249 0
-M  V30 113 H 1.0741 1.6997 -13.1630 0
-M  V30 114 H -0.0132 2.0590 -17.4342 0
-M  V30 115 H 0.0012 -0.1061 -18.6349 0
-M  V30 116 H 0.0139 -2.2363 -17.3723 0
-M  V30 117 H 1.1225 -1.7455 -13.0431 0
-M  V30 118 H 1.0772 -3.9029 -11.9020 0
-M  V30 119 H -1.0820 -5.7081 -15.0316 0
-M  V30 120 H -1.0858 -3.5986 -16.2391 0
-M  V30 121 H -0.0026 0.0126 -13.7460 0
-M  V30 122 H -1.1195 3.5747 -16.2634 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 2 3 4
-M  V30 2 1 4 5
-M  V30 3 2 5 6
-M  V30 4 1 6 7
-M  V30 5 1 7 8
-M  V30 6 2 8 9
-M  V30 7 1 9 10
-M  V30 8 2 10 11
-M  V30 9 1 11 12
-M  V30 10 1 12 13
-M  V30 11 2 13 14
-M  V30 12 1 14 15
-M  V30 13 2 15 16
-M  V30 14 1 16 17
-M  V30 15 2 17 18
-M  V30 16 2 12 19
-M  V30 17 2 7 20
-M  V30 18 1 20 3
-M  V30 19 1 19 8
-M  V30 20 1 18 13
-M  V30 21 1 3 21
-M  V30 22 1 5 22
-M  V30 23 1 6 23
-M  V30 24 1 9 24
-M  V30 25 1 10 25
-M  V30 26 1 11 26
-M  V30 27 1 14 27
-M  V30 28 1 15 28
-M  V30 29 1 17 29
-M  V30 30 1 18 30
-M  V30 31 1 19 31
-M  V30 32 1 20 32
-M  V30 33 2 33 34
-M  V30 34 1 34 35
-M  V30 35 2 35 36
-M  V30 36 1 36 37
-M  V30 37 1 37 38
-M  V30 38 2 38 39
-M  V30 39 1 39 40
-M  V30 40 2 40 41
-M  V30 41 1 41 42
-M  V30 42 1 42 43
-M  V30 43 2 43 44
-M  V30 44 1 44 45
-M  V30 45 2 45 46
-M  V30 46 1 46 47
-M  V30 47 2 47 48
-M  V30 48 2 42 49
-M  V30 49 2 37 50
-M  V30 50 1 50 33
-M  V30 51 1 49 38
-M  V30 52 1 48 43
-M  V30 53 1 33 51
-M  V30 54 1 35 52
-M  V30 55 1 36 53
-M  V30 56 1 39 54
-M  V30 57 1 40 55
-M  V30 58 1 41 56
-M  V30 59 1 44 57
-M  V30 60 1 45 58
-M  V30 61 1 47 59
-M  V30 62 1 48 60
-M  V30 63 1 49 61
-M  V30 64 1 50 62
-M  V30 65 2 63 64
-M  V30 66 1 64 65
-M  V30 67 2 65 66
-M  V30 68 1 66 67
-M  V30 69 1 67 68
-M  V30 70 2 68 69
-M  V30 71 1 69 70
-M  V30 72 2 70 71
-M  V30 73 1 71 72
-M  V30 74 1 72 73
-M  V30 75 2 73 74
-M  V30 76 1 74 75
-M  V30 77 2 75 76
-M  V30 78 1 76 77
-M  V30 79 2 77 78
-M  V30 80 2 72 79
-M  V30 81 2 67 80
-M  V30 82 1 80 63
-M  V30 83 1 79 68
-M  V30 84 1 78 73
-M  V30 85 1 63 81
-M  V30 86 1 65 82
-M  V30 87 1 66 83
-M  V30 88 1 69 84
-M  V30 89 1 70 85
-M  V30 90 1 71 86
-M  V30 91 1 74 87
-M  V30 92 1 75 88
-M  V30 93 1 77 89
-M  V30 94 1 78 90
-M  V30 95 1 79 91
-M  V30 96 1 80 92
-M  V30 97 2 93 94
-M  V30 98 1 94 95
-M  V30 99 2 95 96
-M  V30 100 1 96 97
-M  V30 101 1 97 98
-M  V30 102 2 98 99
-M  V30 103 1 99 100
-M  V30 104 2 100 101
-M  V30 105 1 101 102
-M  V30 106 1 102 103
-M  V30 107 2 103 104
-M  V30 108 1 104 105
-M  V30 109 2 105 106
-M  V30 110 1 106 107
-M  V30 111 2 107 108
-M  V30 112 2 102 109
-M  V30 113 2 97 110
-M  V30 114 1 110 93
-M  V30 115 1 109 98
-M  V30 116 1 108 103
-M  V30 117 1 93 111
-M  V30 118 1 95 112
-M  V30 119 1 96 113
-M  V30 120 1 99 114
-M  V30 121 1 100 115
-M  V30 122 1 101 116
-M  V30 123 1 104 117
-M  V30 124 1 105 118
-M  V30 125 1 107 119
-M  V30 126 1 108 120
-M  V30 127 1 109 121
-M  V30 128 1 110 122
-M  V30 129 9 4 1
-M  V30 130 9 34 1
-M  V30 131 9 64 1
-M  V30 132 9 94 1
-M  V30 133 9 16 2
-M  V30 134 9 46 2
-M  V30 135 9 76 2
-M  V30 136 9 106 2
-M  V30 END BOND
-M  V30 END CTAB
-M  END
-
-$$$$
diff --git a/python/examples/data/stkbuilt.xyz b/python/examples/data/stkbuilt.xyz
deleted file mode 100644
index a2b2b77c1..000000000
--- a/python/examples/data/stkbuilt.xyz
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-C -13.565877 2.587447 -0.599618
-C -14.793916 2.474878 0.017105
-C -15.493884 1.192641 0.008968
-C -16.871077 1.129187 0.007671
-C -17.556534 -0.083989 -0.000424
-C -16.857801 -1.274026 -0.007511
-C -15.478020 -1.242464 -0.006411
-C -14.749705 -2.493615 -0.014614
-C -13.522003 -2.591883 -0.623452
-C -12.880642 -3.809551 -0.596673
-N -13.412279 -4.893306 -0.000000
-C -14.611776 -4.815506 0.600290
-C -15.264750 -3.621907 0.586634
-C -14.814107 -0.014410 0.001813
-C -15.314784 3.598395 0.624584
-H -14.994387 5.697699 1.075037
-H -11.924946 3.831871 -1.100866
-H -13.163007 1.699657 -1.074149
-H -17.434224 2.059040 0.013178
-H -18.634873 -0.106053 -0.001236
-H -17.372346 -2.236272 -0.013913
-H -13.043071 -1.745509 -1.122496
-H -11.901981 -3.902911 -1.077175
-H -15.031603 -5.708122 1.081966
-H -16.239128 -3.598600 1.085790
-H -13.746032 0.012568 0.002636
-H -16.263366 3.574652 1.119470
-C -0.606619 4.788114 -14.617151
-N -0.000000 4.893306 -13.412279
-C 0.593223 3.799282 -12.901820
-C 0.599618 2.587447 -13.565877
-C -0.017105 2.474878 -14.793916
-C -0.008968 1.192641 -15.493884
-C -0.007671 1.129187 -16.871077
-C 0.000424 -0.083989 -17.556534
-C 0.007511 -1.274026 -16.857801
-C 0.006411 -1.242464 -15.478020
-C 0.014614 -2.493615 -14.749705
-C 0.623452 -2.591883 -13.522003
-C 0.596673 -3.809551 -12.880642
-N -0.000000 -4.893306 -13.412279
-C -0.600290 -4.815506 -14.611776
-C -0.586634 -3.621907 -15.264750
-C -0.001813 -0.014410 -14.814107
-C -0.624584 3.598395 -15.314784
-H -1.075037 5.697699 -14.994387
-H 1.100866 3.831871 -11.924946
-H 1.074149 1.699657 -13.163007
-H -0.013178 2.059040 -17.434224
-H 0.001236 -0.106053 -18.634873
-H 0.013913 -2.236272 -17.372346
-H 1.122496 -1.745509 -13.043071
-H 1.077175 -3.902911 -11.901981
-H -1.081966 -5.708122 -15.031603
-H -1.085790 -3.598600 -16.239128
-H -0.002636 0.012568 -13.746032
-H -1.119470 3.574652 -16.263366
diff --git a/python/examples/data/unoptcage.mol b/python/examples/data/unoptcage.mol
deleted file mode 100644
index d61446e47..000000000
--- a/python/examples/data/unoptcage.mol
+++ /dev/null
@@ -1,176 +0,0 @@
-
-     RDKit          3D
-
-  0  0  0  0  0  0  0  0  0  0999 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 80 82 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 C -1.2134 -0.7006 7.6921 0
-M  V30 2 C 0.0024 0.0195 8.1532 0
-M  V30 3 C 1.2289 -0.7128 7.6921 0
-M  V30 4 C -0.0155 1.4134 7.6921 0
-M  V30 5 H -1.4106 -0.8660 6.6467 0
-M  V30 6 H 0.0228 0.0328 9.2640 0
-M  V30 7 H 1.3779 -0.8508 6.6158 0
-M  V30 8 H 0.7696 2.1271 7.9093 0
-M  V30 9 C -6.6851 -3.8596 -1.2430 0
-M  V30 10 C -6.6459 -3.8550 -2.7289 0
-M  V30 11 C -6.6921 -2.4414 -3.2314 0
-M  V30 12 C -5.4646 -4.5773 -3.2177 0
-M  V30 13 H -5.9270 -3.3704 -0.6555 0
-M  V30 14 H -7.5451 -4.3758 -3.1221 0
-M  V30 15 H -5.8930 -1.7560 -2.9293 0
-M  V30 16 H -5.2299 -4.7022 -4.2675 0
-M  V30 17 C 6.6851 -3.8596 -1.2430 0
-M  V30 18 C 6.6615 -3.8280 -2.7289 0
-M  V30 19 C 5.4604 -4.5748 -3.2314 0
-M  V30 20 C 6.6963 -2.4438 -3.2177 0
-M  V30 21 H 5.8824 -3.4478 -0.6555 0
-M  V30 22 H 7.5621 -4.3463 -3.1221 0
-M  V30 23 H 4.4673 -4.2255 -2.9293 0
-M  V30 24 H 6.6872 -2.1781 -4.2675 0
-M  V30 25 C -0.0000 7.7193 -1.2430 0
-M  V30 26 C -0.0156 7.6830 -2.7289 0
-M  V30 27 C 1.2317 7.0162 -3.2314 0
-M  V30 28 C -1.2317 7.0211 -3.2177 0
-M  V30 29 H 0.0447 6.8181 -0.6555 0
-M  V30 30 H -0.0170 8.7221 -3.1221 0
-M  V30 31 H 1.4257 5.9815 -2.9293 0
-M  V30 32 H -1.4573 6.8803 -4.2675 0
-M  V30 33 N -3.2178 -1.8578 4.4191 0
-M  V30 34 C -4.6051 -2.2313 4.4421 0
-M  V30 35 C -4.9290 -3.2079 3.3152 0
-M  V30 36 N -4.6808 -2.7024 2.0300 0
-M  V30 37 H -5.2477 -1.3300 4.3651 0
-M  V30 38 H -4.7784 -2.7831 5.3911 0
-M  V30 39 H -4.2388 -4.0831 3.4884 0
-M  V30 40 H -5.9702 -3.5517 3.4212 0
-M  V30 41 N 3.2255 -1.8639 4.4191 0
-M  V30 42 C 4.2425 -2.8787 4.4421 0
-M  V30 43 C 5.2503 -2.6710 3.3153 0
-M  V30 44 N 4.6885 -2.7085 2.0300 0
-M  V30 45 H 3.7830 -3.8858 4.3649 0
-M  V30 46 H 4.8069 -2.7532 5.3911 0
-M  V30 47 H 5.6634 -1.6358 3.4886 0
-M  V30 48 H 6.0684 -3.4011 3.4212 0
-M  V30 49 N -0.0077 3.7216 4.4191 0
-M  V30 50 C 0.3608 5.1103 4.4424 0
-M  V30 51 C -0.3230 5.8783 3.3150 0
-M  V30 52 N -0.0077 5.4110 2.0300 0
-M  V30 53 H 1.4626 5.2174 4.3663 0
-M  V30 54 H -0.0316 5.5358 5.3911 0
-M  V30 55 H -1.4260 5.7170 3.4873 0
-M  V30 56 H -0.1013 6.9522 3.4211 0
-M  V30 57 N -1.4651 -4.5761 -3.2246 0
-M  V30 58 C -0.6824 -5.3003 -4.1877 0
-M  V30 59 C 0.6815 -5.6755 -3.6155 0
-M  V30 60 N 1.4609 -4.5761 -3.2246 0
-M  V30 61 H -0.5584 -4.6999 -5.1126 0
-M  V30 62 H -1.2113 -6.2578 -4.3839 0
-M  V30 63 H 0.4477 -6.2857 -2.6961 0
-M  V30 64 H 1.2149 -6.3136 -4.3380 0
-M  V30 65 N -4.6934 1.0229 -3.2246 0
-M  V30 66 C -5.2985 2.2760 -3.5825 0
-M  V30 67 C -4.2593 3.2509 -4.1283 0
-M  V30 68 N -3.2304 3.5569 -3.2246 0
-M  V30 69 H -5.8160 2.7179 -2.7060 0
-M  V30 70 H -6.0020 2.0714 -4.4183 0
-M  V30 71 H -3.8042 2.7182 -5.0123 0
-M  V30 72 H -4.7677 4.1603 -4.4863 0
-M  V30 73 N 4.6955 1.0192 -3.2246 0
-M  V30 74 C 4.9314 2.0591 -4.1877 0
-M  V30 75 C 4.5743 3.4280 -3.6155 0
-M  V30 76 N 3.2325 3.5532 -3.2246 0
-M  V30 77 H 4.3495 1.8663 -5.1126 0
-M  V30 78 H 6.0251 2.0799 -4.3839 0
-M  V30 79 H 5.2197 3.5306 -2.6961 0
-M  V30 80 H 4.8603 4.2089 -4.3380 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 1 1 2
-M  V30 2 1 2 3
-M  V30 3 1 2 4
-M  V30 4 1 1 5
-M  V30 5 1 2 6
-M  V30 6 1 3 7
-M  V30 7 1 4 8
-M  V30 8 1 9 10
-M  V30 9 1 10 11
-M  V30 10 1 10 12
-M  V30 11 1 9 13
-M  V30 12 1 10 14
-M  V30 13 1 11 15
-M  V30 14 1 12 16
-M  V30 15 1 17 18
-M  V30 16 1 18 19
-M  V30 17 1 18 20
-M  V30 18 1 17 21
-M  V30 19 1 18 22
-M  V30 20 1 19 23
-M  V30 21 1 20 24
-M  V30 22 1 25 26
-M  V30 23 1 26 27
-M  V30 24 1 26 28
-M  V30 25 1 25 29
-M  V30 26 1 26 30
-M  V30 27 1 27 31
-M  V30 28 1 28 32
-M  V30 29 1 33 34
-M  V30 30 1 34 35
-M  V30 31 1 35 36
-M  V30 32 1 34 37
-M  V30 33 1 34 38
-M  V30 34 1 35 39
-M  V30 35 1 35 40
-M  V30 36 1 41 42
-M  V30 37 1 42 43
-M  V30 38 1 43 44
-M  V30 39 1 42 45
-M  V30 40 1 42 46
-M  V30 41 1 43 47
-M  V30 42 1 43 48
-M  V30 43 1 49 50
-M  V30 44 1 50 51
-M  V30 45 1 51 52
-M  V30 46 1 50 53
-M  V30 47 1 50 54
-M  V30 48 1 51 55
-M  V30 49 1 51 56
-M  V30 50 1 57 58
-M  V30 51 1 58 59
-M  V30 52 1 59 60
-M  V30 53 1 58 61
-M  V30 54 1 58 62
-M  V30 55 1 59 63
-M  V30 56 1 59 64
-M  V30 57 1 65 66
-M  V30 58 1 66 67
-M  V30 59 1 67 68
-M  V30 60 1 66 69
-M  V30 61 1 66 70
-M  V30 62 1 67 71
-M  V30 63 1 67 72
-M  V30 64 1 73 74
-M  V30 65 1 74 75
-M  V30 66 1 75 76
-M  V30 67 1 74 77
-M  V30 68 1 74 78
-M  V30 69 1 75 79
-M  V30 70 1 75 80
-M  V30 71 2 1 33
-M  V30 72 2 9 36
-M  V30 73 2 3 41
-M  V30 74 2 17 44
-M  V30 75 2 4 49
-M  V30 76 2 25 52
-M  V30 77 2 12 57
-M  V30 78 2 19 60
-M  V30 79 2 11 65
-M  V30 80 2 28 68
-M  V30 81 2 20 73
-M  V30 82 2 27 76
-M  V30 END BOND
-M  V30 END CTAB
-M  END
-
-$$$$

From b0bb1e62c73dc3568ac33fc5404832d743fecb8f Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:26:49 +0200
Subject: [PATCH 08/35] Update tests.

---
 python/tests/create_input.py   | 605 +++++++++++++++++----------------
 python/tests/stk_structures.py | 143 ++++++++
 python/tests/write_input.py    |  47 +--
 3 files changed, 488 insertions(+), 307 deletions(-)
 create mode 100644 python/tests/stk_structures.py

diff --git a/python/tests/create_input.py b/python/tests/create_input.py
index 7a16586ae..81b3409c6 100644
--- a/python/tests/create_input.py
+++ b/python/tests/create_input.py
@@ -2,323 +2,354 @@
 
 import ase
 import numpy as np
+import stk
 
 from chemiscope import all_atomic_environments, create_input
 
+# These should be the same molecule!
 TEST_FRAMES = [ase.Atoms("CO2")]
+TEST_FRAMES_STK = [stk.BuildingBlock("O=C=O")]
 
 
 class TestCreateInputMeta(unittest.TestCase):
     def test_meta(self):
-        meta = {}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "<unknown>")
-        self.assertEqual(len(data["meta"].keys()), 1)
-
-        meta = {"name": ""}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "<unknown>")
-        self.assertEqual(len(data["meta"].keys()), 1)
-
-        meta = {"name": "foo"}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "foo")
-        self.assertEqual(len(data["meta"].keys()), 1)
-
-        meta = {"name": "foo", "description": "bar"}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "foo")
-        self.assertEqual(data["meta"]["description"], "bar")
-        self.assertEqual(len(data["meta"].keys()), 2)
-
-        meta = {"name": "foo", "references": ["bar"]}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "foo")
-        self.assertEqual(len(data["meta"]["references"]), 1)
-        self.assertEqual(data["meta"]["references"][0], "bar")
-        self.assertEqual(len(data["meta"].keys()), 2)
-
-        meta = {"name": "foo", "authors": ["bar"]}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "foo")
-        self.assertEqual(len(data["meta"]["authors"]), 1)
-        self.assertEqual(data["meta"]["authors"][0], "bar")
-        self.assertEqual(len(data["meta"].keys()), 2)
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            meta = {}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "<unknown>")
+            self.assertEqual(len(data["meta"].keys()), 1)
+
+            meta = {"name": ""}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "<unknown>")
+            self.assertEqual(len(data["meta"].keys()), 1)
+
+            meta = {"name": "foo"}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "foo")
+            self.assertEqual(len(data["meta"].keys()), 1)
+
+            meta = {"name": "foo", "description": "bar"}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "foo")
+            self.assertEqual(data["meta"]["description"], "bar")
+            self.assertEqual(len(data["meta"].keys()), 2)
+
+            meta = {"name": "foo", "references": ["bar"]}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "foo")
+            self.assertEqual(len(data["meta"]["references"]), 1)
+            self.assertEqual(data["meta"]["references"][0], "bar")
+            self.assertEqual(len(data["meta"].keys()), 2)
+
+            meta = {"name": "foo", "authors": ["bar"]}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "foo")
+            self.assertEqual(len(data["meta"]["authors"]), 1)
+            self.assertEqual(data["meta"]["authors"][0], "bar")
+            self.assertEqual(len(data["meta"].keys()), 2)
 
     def test_meta_unknown_keys_warning(self):
-        meta = {"name": "foo", "what_is_this": "I don't know"}
-        with self.assertWarns(UserWarning) as cm:
-            data = create_input(frames=TEST_FRAMES, meta=meta)
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            meta = {"name": "foo", "what_is_this": "I don't know"}
+            with self.assertWarns(UserWarning) as cm:
+                data = create_input(frames=TF, meta=meta)
 
-        self.assertEqual(data["meta"]["name"], "foo")
-        self.assertEqual(len(data["meta"].keys()), 1)
+            self.assertEqual(data["meta"]["name"], "foo")
+            self.assertEqual(len(data["meta"].keys()), 1)
 
-        self.assertEqual(str(cm.warning), "ignoring unexpected metadata: what_is_this")
+            self.assertEqual(
+                str(cm.warning), "ignoring unexpected metadata: what_is_this"
+            )
 
     def test_meta_conversions(self):
-        meta = {"name": 33}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "33")
-        self.assertEqual(len(data["meta"].keys()), 1)
-
-        meta = {"name": ["foo", "bar"], "description": False}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "['foo', 'bar']")
-        self.assertEqual(data["meta"]["description"], "False")
-        self.assertEqual(len(data["meta"].keys()), 2)
-
-        meta = {"name": "foo", "references": (3, False)}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "foo")
-        self.assertEqual(len(data["meta"]["references"]), 2)
-        self.assertEqual(data["meta"]["references"][0], "3")
-        self.assertEqual(data["meta"]["references"][1], "False")
-        self.assertEqual(len(data["meta"].keys()), 2)
-
-        meta = {"name": "foo", "authors": (3, False)}
-        data = create_input(frames=TEST_FRAMES, meta=meta)
-        self.assertEqual(data["meta"]["name"], "foo")
-        self.assertEqual(len(data["meta"]["authors"]), 2)
-        self.assertEqual(data["meta"]["authors"][0], "3")
-        self.assertEqual(data["meta"]["authors"][1], "False")
-        self.assertEqual(len(data["meta"].keys()), 2)
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            meta = {"name": 33}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "33")
+            self.assertEqual(len(data["meta"].keys()), 1)
+
+            meta = {"name": ["foo", "bar"], "description": False}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "['foo', 'bar']")
+            self.assertEqual(data["meta"]["description"], "False")
+            self.assertEqual(len(data["meta"].keys()), 2)
+
+            meta = {"name": "foo", "references": (3, False)}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "foo")
+            self.assertEqual(len(data["meta"]["references"]), 2)
+            self.assertEqual(data["meta"]["references"][0], "3")
+            self.assertEqual(data["meta"]["references"][1], "False")
+            self.assertEqual(len(data["meta"].keys()), 2)
+
+            meta = {"name": "foo", "authors": (3, False)}
+            data = create_input(frames=TF, meta=meta)
+            self.assertEqual(data["meta"]["name"], "foo")
+            self.assertEqual(len(data["meta"]["authors"]), 2)
+            self.assertEqual(data["meta"]["authors"][0], "3")
+            self.assertEqual(data["meta"]["authors"][1], "False")
+            self.assertEqual(len(data["meta"].keys()), 2)
 
 
 class TestCreateInputProperties(unittest.TestCase):
     def test_properties(self):
-        # values are numbers
-        properties = {"name": {"target": "atom", "values": [2, 3, 4]}}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "atom")
-        self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
-        self.assertEqual(len(data["properties"]["name"].keys()), 2)
-
-        # values are strings
-        properties = {"name": {"target": "atom", "values": ["2", "3", "4"]}}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "atom")
-        self.assertEqual(data["properties"]["name"]["values"], ["2", "3", "4"])
-        self.assertEqual(len(data["properties"]["name"].keys()), 2)
-
-        properties = {
-            "name": {
-                "target": "atom",
-                "values": [2, 3, 4],
-                "description": "foo",
-            },
-        }
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "atom")
-        self.assertEqual(data["properties"]["name"]["description"], "foo")
-        self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
-        self.assertEqual(len(data["properties"]["name"].keys()), 3)
-
-        properties = {
-            "name": {
-                "target": "atom",
-                "values": [2, 3, 4],
-                "units": "foo",
-            },
-        }
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "atom")
-        self.assertEqual(data["properties"]["name"]["units"], "foo")
-        self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
-        self.assertEqual(len(data["properties"]["name"].keys()), 3)
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            # values are numbers
+            properties = {"name": {"target": "atom", "values": [2, 3, 4]}}
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "atom")
+            self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
+            self.assertEqual(len(data["properties"]["name"].keys()), 2)
+
+            # values are strings
+            properties = {"name": {"target": "atom", "values": ["2", "3", "4"]}}
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "atom")
+            self.assertEqual(data["properties"]["name"]["values"], ["2", "3", "4"])
+            self.assertEqual(len(data["properties"]["name"].keys()), 2)
+
+            properties = {
+                "name": {
+                    "target": "atom",
+                    "values": [2, 3, 4],
+                    "description": "foo",
+                },
+            }
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "atom")
+            self.assertEqual(data["properties"]["name"]["description"], "foo")
+            self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
+            self.assertEqual(len(data["properties"]["name"].keys()), 3)
+
+            properties = {
+                "name": {
+                    "target": "atom",
+                    "values": [2, 3, 4],
+                    "units": "foo",
+                },
+            }
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "atom")
+            self.assertEqual(data["properties"]["name"]["units"], "foo")
+            self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
+            self.assertEqual(len(data["properties"]["name"].keys()), 3)
 
     def test_ndarray_properties(self):
-        # shape N
-        properties = {"name": {"target": "atom", "values": np.array([2, 3, 4])}}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "atom")
-        self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
-        self.assertEqual(len(data["properties"].keys()), 1)
-
-        # shape N
-        properties = {"name": {"target": "atom", "values": np.array(["2", "3", "4"])}}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "atom")
-        self.assertEqual(data["properties"]["name"]["values"], ["2", "3", "4"])
-        self.assertEqual(len(data["properties"].keys()), 1)
-
-        # shape N x 1
-        properties = {"name": {"target": "atom", "values": np.array([[2], [3], [4]])}}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "atom")
-        self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
-        self.assertEqual(len(data["properties"].keys()), 1)
-
-        # shape N x 3
-        properties = {
-            "name": {
-                "target": "atom",
-                "values": np.array([[1, 2, 4], [1, 2, 4], [1, 2, 4]]),
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            # shape N
+            properties = {"name": {"target": "atom", "values": np.array([2, 3, 4])}}
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "atom")
+            self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
+            self.assertEqual(len(data["properties"].keys()), 1)
+
+            # shape N
+            properties = {
+                "name": {"target": "atom", "values": np.array(["2", "3", "4"])}
             }
-        }
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name[1]"]["target"], "atom")
-        self.assertEqual(data["properties"]["name[1]"]["values"], [1, 1, 1])
-        self.assertEqual(data["properties"]["name[2]"]["target"], "atom")
-        self.assertEqual(data["properties"]["name[2]"]["values"], [2, 2, 2])
-        self.assertEqual(data["properties"]["name[3]"]["target"], "atom")
-        self.assertEqual(data["properties"]["name[3]"]["values"], [4, 4, 4])
-        self.assertEqual(len(data["properties"].keys()), 3)
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "atom")
+            self.assertEqual(data["properties"]["name"]["values"], ["2", "3", "4"])
+            self.assertEqual(len(data["properties"].keys()), 1)
+
+            # shape N x 1
+            properties = {
+                "name": {"target": "atom", "values": np.array([[2], [3], [4]])}
+            }
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "atom")
+            self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
+            self.assertEqual(len(data["properties"].keys()), 1)
+
+            # shape N x 3
+            properties = {
+                "name": {
+                    "target": "atom",
+                    "values": np.array([[1, 2, 4], [1, 2, 4], [1, 2, 4]]),
+                }
+            }
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name[1]"]["target"], "atom")
+            self.assertEqual(data["properties"]["name[1]"]["values"], [1, 1, 1])
+            self.assertEqual(data["properties"]["name[2]"]["target"], "atom")
+            self.assertEqual(data["properties"]["name[2]"]["values"], [2, 2, 2])
+            self.assertEqual(data["properties"]["name[3]"]["target"], "atom")
+            self.assertEqual(data["properties"]["name[3]"]["values"], [4, 4, 4])
+            self.assertEqual(len(data["properties"].keys()), 3)
 
     def test_shortened_properties(self):
-        # atom property
-        properties = {"name": [2, 3, 4]}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "atom")
-        self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
-        self.assertEqual(len(data["properties"]["name"].keys()), 2)
-
-        # frame property
-        properties = {"name": [2]}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["target"], "structure")
-        self.assertEqual(data["properties"]["name"]["values"], [2])
-        self.assertEqual(len(data["properties"]["name"].keys()), 2)
-
-        # ndarray frame property
-        properties = {"name": np.array([[2, 4]])}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name[1]"]["target"], "structure")
-        self.assertEqual(data["properties"]["name[1]"]["values"], [2])
-        self.assertEqual(len(data["properties"]["name[1]"].keys()), 2)
-
-        self.assertEqual(data["properties"]["name[2]"]["target"], "structure")
-        self.assertEqual(data["properties"]["name[2]"]["values"], [4])
-        self.assertEqual(len(data["properties"]["name[2]"].keys()), 2)
-
-        # the initial properties object must not be changed
-        self.assertEqual(type(properties["name"]), np.ndarray)
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            # atom property
+            properties = {"name": [2, 3, 4]}
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "atom")
+            self.assertEqual(data["properties"]["name"]["values"], [2, 3, 4])
+            self.assertEqual(len(data["properties"]["name"].keys()), 2)
+
+            # frame property
+            properties = {"name": [2]}
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["target"], "structure")
+            self.assertEqual(data["properties"]["name"]["values"], [2])
+            self.assertEqual(len(data["properties"]["name"].keys()), 2)
+
+            # ndarray frame property
+            properties = {"name": np.array([[2, 4]])}
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name[1]"]["target"], "structure")
+            self.assertEqual(data["properties"]["name[1]"]["values"], [2])
+            self.assertEqual(len(data["properties"]["name[1]"].keys()), 2)
+
+            self.assertEqual(data["properties"]["name[2]"]["target"], "structure")
+            self.assertEqual(data["properties"]["name[2]"]["values"], [4])
+            self.assertEqual(len(data["properties"]["name[2]"].keys()), 2)
+
+            # the initial properties object must not be changed
+            self.assertEqual(type(properties["name"]), np.ndarray)
 
     def test_shortened_properties_errors(self):
-        properties = {"name": ["2", "3"]}
-        with self.assertRaises(ValueError) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception),
-            "The length of property values is different from the number of "
-            "structures and the number of atoms, we can not guess the target. "
-            "Got n_atoms = 3, n_structures = 1, the length of property values "
-            "is 2, for the 'name' property",
-        )
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            properties = {"name": ["2", "3"]}
+            with self.assertRaises(ValueError) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception),
+                "The length of property values is different from the number of "
+                "structures and the number of atoms, we can not guess the target. "
+                "Got n_atoms = 3, n_structures = 1, the length of property values "
+                "is 2, for the 'name' property",
+            )
 
-        properties = {"name": ase.Atoms("CO2")}
-        with self.assertRaises(ValueError) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception),
-            "Property values should be either list or numpy array, got "
-            "<class 'ase.atoms.Atoms'> instead",
-        )
+            properties = {"name": ase.Atoms("CO2")}
+            with self.assertRaises(ValueError) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception),
+                "Property values should be either list or numpy array, got "
+                "<class 'ase.atoms.Atoms'> instead",
+            )
 
-        properties = {"name": ["2", "3"]}
-        frames_single_atoms = [ase.Atoms("C"), ase.Atoms("H")]
-        with self.assertWarns(UserWarning) as cm:
-            data = create_input(frames=frames_single_atoms, properties=properties)
+            properties = {"name": ["2", "3"]}
+            frames_single_atoms = [ase.Atoms("C"), ase.Atoms("H")]
+            with self.assertWarns(UserWarning) as cm:
+                data = create_input(frames=frames_single_atoms, properties=properties)
 
-        self.assertEqual(data["properties"]["name"]["target"], "structure")
+            self.assertEqual(data["properties"]["name"]["target"], "structure")
 
-        self.assertEqual(
-            cm.warning.args[0],
-            "The target of the property 'name' is ambiguous because there is the same "
-            "number of atoms and structures. We will assume target=structure",
-        )
+            self.assertEqual(
+                cm.warning.args[0],
+                "The target of the property 'name' is ambiguous because there "
+                "is the same number of atoms and structures. We will assume "
+                "target=structure",
+            )
 
     def test_invalid_name(self):
-        properties = {"": {"target": "atom", "values": [2, 3, 4]}}
-        with self.assertRaises(Exception) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception), "the name of a property can not be the empty string"
-        )
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            properties = {"": {"target": "atom", "values": [2, 3, 4]}}
+            with self.assertRaises(Exception) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception),
+                "the name of a property can not be the empty string",
+            )
 
-        properties = {False: {"target": "atom", "values": [2, 3, 4]}}
-        with self.assertRaises(Exception) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception),
-            "the name of a property name must be a string, "
-            "got 'False' of type <class 'bool'>",
-        )
+            properties = {False: {"target": "atom", "values": [2, 3, 4]}}
+            with self.assertRaises(Exception) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception),
+                "the name of a property name must be a string, "
+                "got 'False' of type <class 'bool'>",
+            )
 
     def test_invalid_target(self):
-        properties = {"name": {"values": [2, 3, 4]}}
-        with self.assertRaises(Exception) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(str(cm.exception), "missing 'target' for the 'name' property")
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            properties = {"name": {"values": [2, 3, 4]}}
+            with self.assertRaises(Exception) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception), "missing 'target' for the 'name' property"
+            )
 
-        properties = {"name": {"target": "atoms", "values": [2, 3, 4]}}
-        with self.assertRaises(Exception) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception),
-            "the target must be 'atom' or 'structure' for the 'name' property",
-        )
+            properties = {"name": {"target": "atoms", "values": [2, 3, 4]}}
+            with self.assertRaises(Exception) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception),
+                "the target must be 'atom' or 'structure' for the 'name' property",
+            )
 
     def test_invalid_types_metadata(self):
-        properties = {"name": {"target": "atom", "values": [2, 3, 4], "units": False}}
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["units"], "False")
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            properties = {
+                "name": {"target": "atom", "values": [2, 3, 4], "units": False}
+            }
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["units"], "False")
 
-        properties = {
-            "name": {"target": "atom", "values": [2, 3, 4], "description": False}
-        }
-        data = create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(data["properties"]["name"]["description"], "False")
+            properties = {
+                "name": {"target": "atom", "values": [2, 3, 4], "description": False}
+            }
+            data = create_input(frames=TF, properties=properties)
+            self.assertEqual(data["properties"]["name"]["description"], "False")
 
     def test_property_unknown_keys_warning(self):
-        properties = {"name": {"target": "atom", "values": [2, 3, 4], "what": False}}
-        with self.assertWarns(UserWarning) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(str(cm.warning), "ignoring unexpected property key: what")
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            properties = {
+                "name": {"target": "atom", "values": [2, 3, 4], "what": False}
+            }
+            with self.assertWarns(UserWarning) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(str(cm.warning), "ignoring unexpected property key: what")
 
     def test_invalid_values_types(self):
-        properties = {"name": {"target": "atom", "values": 3}}
-        with self.assertRaises(Exception) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception), "unknown type (<class 'int'>) for property 'name'"
-        )
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            properties = {"name": {"target": "atom", "values": 3}}
+            with self.assertRaises(Exception) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception), "unknown type (<class 'int'>) for property 'name'"
+            )
 
-        properties = {"name": {"target": "atom", "values": {"test": "bad"}}}
-        with self.assertRaises(Exception) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception), "unknown type (<class 'dict'>) for property 'name'"
-        )
+            properties = {"name": {"target": "atom", "values": {"test": "bad"}}}
+            with self.assertRaises(Exception) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception), "unknown type (<class 'dict'>) for property 'name'"
+            )
 
-        properties = {"name": {"target": "atom", "values": [{}, {}, {}]}}
-        with self.assertRaises(Exception) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception),
-            "unsupported type in property 'name' values: should be string or number",
-        )
+            properties = {"name": {"target": "atom", "values": [{}, {}, {}]}}
+            with self.assertRaises(Exception) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception),
+                "unsupported type in property 'name' values: should be string"
+                " or number",
+            )
 
     def test_wrong_number_of_values(self):
-        properties = {"name": {"target": "atom", "values": [2, 3]}}
-        environments = [(0, 0, 3), (0, 1, 3), (0, 2, 3)]
-        with self.assertRaises(Exception) as cm:
-            create_input(
-                frames=TEST_FRAMES, properties=properties, environments=environments
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            properties = {"name": {"target": "atom", "values": [2, 3]}}
+            environments = [(0, 0, 3), (0, 1, 3), (0, 2, 3)]
+            with self.assertRaises(Exception) as cm:
+                create_input(
+                    frames=TF, properties=properties, environments=environments
+                )
+            self.assertEqual(
+                str(cm.exception),
+                "wrong size for the property 'name' with target=='atom': "
+                "expected 3 values, got 2",
             )
-        self.assertEqual(
-            str(cm.exception),
-            "wrong size for the property 'name' with target=='atom': "
-            "expected 3 values, got 2",
-        )
 
-        properties = {"name": {"target": "structure", "values": [2, 3, 5]}}
-        with self.assertRaises(Exception) as cm:
-            create_input(frames=TEST_FRAMES, properties=properties)
-        self.assertEqual(
-            str(cm.exception),
-            "wrong size for the property 'name' with target=='structure': "
-            "expected 1 values, got 3",
-        )
+            properties = {"name": {"target": "structure", "values": [2, 3, 5]}}
+            with self.assertRaises(Exception) as cm:
+                create_input(frames=TF, properties=properties)
+            self.assertEqual(
+                str(cm.exception),
+                "wrong size for the property 'name' with target=='structure': "
+                "expected 1 values, got 3",
+            )
 
     def test_property_only(self):
         properties = {"name": [2, 3, 4]}
@@ -358,25 +389,27 @@ def test_property_only(self):
 
 class TestCreateInputEnvironments(unittest.TestCase):
     def test_manual_environments_list(self):
-        environments = [
-            (0, 0, 3.5),
-            (1, 1, 2.5),
-            (1, 2, 3),
-        ]
-        data = create_input(frames=TEST_FRAMES + TEST_FRAMES, environments=environments)
-        self.assertEqual(len(data["environments"]), 3)
-
-        for i, env in enumerate(data["environments"]):
-            self.assertEqual(env["structure"], environments[i][0])
-            self.assertEqual(env["center"], environments[i][1])
-            self.assertEqual(env["cutoff"], environments[i][2])
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            environments = [
+                (0, 0, 3.5),
+                (1, 1, 2.5),
+                (1, 2, 3),
+            ]
+            data = create_input(frames=TF + TF, environments=environments)
+            self.assertEqual(len(data["environments"]), 3)
+
+            for i, env in enumerate(data["environments"]):
+                self.assertEqual(env["structure"], environments[i][0])
+                self.assertEqual(env["center"], environments[i][1])
+                self.assertEqual(env["cutoff"], environments[i][2])
 
     def test_all_environments(self):
-        environments = all_atomic_environments(TEST_FRAMES, cutoff=6)
-        for i, (structure, center, cutoff) in enumerate(environments):
-            self.assertEqual(structure, 0)
-            self.assertEqual(center, i)
-            self.assertEqual(cutoff, 6)
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            environments = all_atomic_environments(TF, cutoff=6)
+            for i, (structure, center, cutoff) in enumerate(environments):
+                self.assertEqual(structure, 0)
+                self.assertEqual(center, i)
+                self.assertEqual(cutoff, 6)
 
 
 if __name__ == "__main__":
diff --git a/python/tests/stk_structures.py b/python/tests/stk_structures.py
new file mode 100644
index 000000000..844aeb711
--- /dev/null
+++ b/python/tests/stk_structures.py
@@ -0,0 +1,143 @@
+import unittest
+
+import stk
+
+import chemiscope
+
+BASE_FRAME = stk.BuildingBlock("N#CC")
+
+
+class TestStructures(unittest.TestCase):
+    """Conversion of structure data to chemiscope JSON"""
+
+    def test_structures(self):
+        data = chemiscope.create_input(BASE_FRAME)
+        self.assertEqual(len(data["structures"]), 1)
+        self.assertEqual(data["structures"][0]["size"], 6)
+        self.assertEqual(
+            data["structures"][0]["names"],
+            ["N", "C", "C", "H", "H", "H"],
+        )
+        self.assertEqual(
+            data["structures"][0]["x"],
+            [
+                1.6991195138834223,
+                0.7737143493209756,
+                -0.41192204250544034,
+                -0.7778845126633998,
+                -1.1777543806588109,
+                -0.10527292738297804,
+            ],
+        )
+        self.assertEqual(
+            data["structures"][0]["y"],
+            [
+                -1.2265369887154756,
+                -0.5721898035707434,
+                0.28832060028277334,
+                0.6076276888433211,
+                -0.27163665176706653,
+                1.1744151549238042,
+            ],
+        )
+        self.assertEqual(
+            data["structures"][0]["z"],
+            [
+                -0.19321573000005213,
+                -0.10192268845612924,
+                0.03435599430880268,
+                -0.9630155400427929,
+                0.6165952621860082,
+                0.6072027020039786,
+            ],
+        )
+        self.assertEqual(data["structures"][0].get("cell"), None)
+
+        # Not testing cell because stk implementation does not have that yet.
+
+        frame = BASE_FRAME.clone()
+        data = chemiscope.create_input([frame])
+        self.assertEqual(len(data["structures"]), 1)
+        self.assertEqual(data["structures"][0]["size"], 6)
+        self.assertEqual(
+            data["structures"][0]["names"],
+            ["N", "C", "C", "H", "H", "H"],
+        )
+        self.assertEqual(
+            data["structures"][0]["x"],
+            [
+                1.6991195138834223,
+                0.7737143493209756,
+                -0.41192204250544034,
+                -0.7778845126633998,
+                -1.1777543806588109,
+                -0.10527292738297804,
+            ],
+        )
+        self.assertEqual(
+            data["structures"][0]["y"],
+            [
+                -1.2265369887154756,
+                -0.5721898035707434,
+                0.28832060028277334,
+                0.6076276888433211,
+                -0.27163665176706653,
+                1.1744151549238042,
+            ],
+        )
+        self.assertEqual(
+            data["structures"][0]["z"],
+            [
+                -0.19321573000005213,
+                -0.10192268845612924,
+                0.03435599430880268,
+                -0.9630155400427929,
+                0.6165952621860082,
+                0.6072027020039786,
+            ],
+        )
+        self.assertEqual(data["structures"][0].get("cell"), None)
+
+
+class TestExtractProperties(unittest.TestCase):
+    """Properties extraction"""
+
+    def test_exception(self):
+        with self.assertRaises(RuntimeError):
+            chemiscope.extract_properties(BASE_FRAME)
+
+
+class TestCompositionProperties(unittest.TestCase):
+    """Composition properties"""
+
+    def test_composition(self):
+        properties = chemiscope.composition_properties([BASE_FRAME, BASE_FRAME])
+
+        self.assertEqual(len(properties.keys()), 6)
+
+        self.assertEqual(properties["composition"]["target"], "structure")
+        self.assertEqual(properties["composition"]["values"], ["C2H3N1", "C2H3N1"])
+
+        self.assertEqual(properties["n_C"]["target"], "structure")
+        self.assertEqual(properties["n_C"]["values"], [2, 2])
+
+        self.assertEqual(properties["n_N"]["target"], "structure")
+        self.assertEqual(properties["n_N"]["values"], [1, 1])
+
+        self.assertEqual(properties["n_H"]["target"], "structure")
+        self.assertEqual(properties["n_H"]["values"], [3, 3])
+
+        self.assertEqual(properties["symbol"]["target"], "atom")
+        self.assertEqual(
+            properties["symbol"]["values"],
+            ["N", "C", "C", "H", "H", "H", "N", "C", "C", "H", "H", "H"],
+        )
+
+        self.assertEqual(properties["number"]["target"], "atom")
+        self.assertEqual(
+            properties["number"]["values"], [7, 6, 6, 1, 1, 1, 7, 6, 6, 1, 1, 1]
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/python/tests/write_input.py b/python/tests/write_input.py
index 193d95e96..55cf17543 100644
--- a/python/tests/write_input.py
+++ b/python/tests/write_input.py
@@ -4,10 +4,12 @@
 import unittest
 
 import ase
+import stk
 
 from chemiscope import write_input
 
 TEST_FRAMES = [ase.Atoms("CO2")]
+TEST_FRAMES_STK = [stk.BuildingBlock("NCCN")]
 
 
 def is_gz_file(filepath):
@@ -18,34 +20,37 @@ def is_gz_file(filepath):
 
 class TestWriteInput(unittest.TestCase):
     def test_file_path_as_dataset_name(self):
-        with tempfile.TemporaryDirectory() as dirname:
-            path = os.path.join(dirname, "test.json")
-            write_input(path, TEST_FRAMES)
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            with tempfile.TemporaryDirectory() as dirname:
+                path = os.path.join(dirname, "test.json")
+                write_input(path, TF)
 
-            with open(path) as fd:
-                data = json.load(fd)
+                with open(path) as fd:
+                    data = json.load(fd)
 
-            self.assertEqual(data["meta"]["name"], "test")
+                self.assertEqual(data["meta"]["name"], "test")
 
     def test_create_gz_file(self):
-        with tempfile.TemporaryDirectory() as dirname:
-            path = os.path.join(dirname, "test.json")
-            write_input(path, TEST_FRAMES)
-            self.assertFalse(is_gz_file(path))
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            with tempfile.TemporaryDirectory() as dirname:
+                path = os.path.join(dirname, "test.json")
+                write_input(path, TF)
+                self.assertFalse(is_gz_file(path))
 
-            path = os.path.join(dirname, "test.json.gz")
-            write_input(path, TEST_FRAMES)
-            self.assertTrue(is_gz_file(path))
+                path = os.path.join(dirname, "test.json.gz")
+                write_input(path, TF)
+                self.assertTrue(is_gz_file(path))
 
     def test_wrong_path(self):
-        with tempfile.TemporaryDirectory() as dirname:
-            path = os.path.join(dirname, "test.tmp")
-            with self.assertRaises(Exception) as cm:
-                write_input(path, TEST_FRAMES)
-
-            self.assertEqual(
-                str(cm.exception), "path should end with .json or .json.gz"
-            )
+        for TF in (TEST_FRAMES, TEST_FRAMES_STK):
+            with tempfile.TemporaryDirectory() as dirname:
+                path = os.path.join(dirname, "test.tmp")
+                with self.assertRaises(Exception) as cm:
+                    write_input(path, TF)
+
+                self.assertEqual(
+                    str(cm.exception), "path should end with .json or .json.gz"
+                )
 
 
 if __name__ == "__main__":

From ac40440e9f662f9695545b184657f9549d5ae63f Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:27:01 +0200
Subject: [PATCH 09/35] Minor formatting.

---
 python/chemiscope/jupyter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/chemiscope/jupyter.py b/python/chemiscope/jupyter.py
index d690190b7..2364a54e4 100644
--- a/python/chemiscope/jupyter.py
+++ b/python/chemiscope/jupyter.py
@@ -155,7 +155,7 @@ def show_input(path, mode="default"):
     try:
         meta = dict_input["meta"]
 
-        if meta is {"name": " "}:
+        if meta == {"name": " "}:
             has_metadata = False
         else:
             has_metadata = True

From fccaf60bf0dde715c431c13f9229570e2e380240 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:27:23 +0200
Subject: [PATCH 10/35] Handle properties not in stk.

---
 python/chemiscope/input.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/python/chemiscope/input.py b/python/chemiscope/input.py
index 3b5a4060a..4c9490b7a 100644
--- a/python/chemiscope/input.py
+++ b/python/chemiscope/input.py
@@ -2,6 +2,7 @@
 """
 Generate JSON input files for the default chemiscope visualizer.
 """
+
 import gzip
 import json
 import os
@@ -10,6 +11,7 @@
 import numpy as np
 
 from .structures import (
+    _guess_adapter,
     _list_atom_properties,
     _list_structure_properties,
     frames_to_json,
@@ -282,6 +284,8 @@ def create_input(
         data["structures"] = frames_to_json(frames)
         n_structures = len(data["structures"])
         n_atoms = sum(s["size"] for s in data["structures"])
+        _, adapter = _guess_adapter(frames)
+        from_stk = True if adapter == "stk" else False
     else:
         n_atoms = 0
 
@@ -376,8 +380,10 @@ def create_input(
     # Check to tell the user they might have forgotten some properties coming
     # from the frames (that chemiscope used to automatically extract). This code
     # should be removed in version 0.6 of chemiscope.
-    if frames is not None:
+    # stk cannot have atom properties or structure properties, so skipping.
+    if frames is not None and not from_stk:
         found_one_from_frame = False
+
         atom_properties = _list_atom_properties(frames)
         for name in atom_properties:
             if name in data["properties"]:

From 86f2bf41a320effe59d9401934a70e103d055469 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:27:37 +0200
Subject: [PATCH 11/35] Import necessary code.

---
 python/chemiscope/structures/__init__.py | 44 ++++++++++++++++++++++--
 1 file changed, 41 insertions(+), 3 deletions(-)

diff --git a/python/chemiscope/structures/__init__.py b/python/chemiscope/structures/__init__.py
index ca8041ee9..28124eebb 100644
--- a/python/chemiscope/structures/__init__.py
+++ b/python/chemiscope/structures/__init__.py
@@ -20,6 +20,13 @@
     ase_tensors_to_ellipsoids,
     ase_vectors_to_arrows,
 )
+from ._stk import (
+    _stk_valid_structures,
+    _stk_to_json,
+    convert_stk_bonds_as_shapes,
+    _stk_all_atomic_environments,
+    _stk_composition_properties,
+)
 
 __all__ = [
     "convert_stk_bonds_as_shapes",
@@ -32,9 +39,16 @@ def _guess_adapter(frames):
     frames as a list and a string describing which adapter should be used.
     """
 
-    ase_frames, use_ase = _ase_valid_structures(frames)
-    if use_ase:
-        return ase_frames, "ASE"
+    try:
+        ase_frames, use_ase = _ase_valid_structures(frames)
+        if use_ase:
+            return ase_frames, "ASE"
+    except TypeError:
+        # Error associated with it being an stk list.
+        pass
+    stk_frames, use_stk = _stk_valid_structures(frames)
+    if use_stk:
+        return stk_frames, "stk"
 
     raise Exception(f"unknown frame type: '{frames[0].__class__.__name__}'")
 
@@ -52,6 +66,8 @@ def frames_to_json(frames):
 
     if adapter == "ASE":
         return [_ase_to_json(frame) for frame in frames]
+    elif adapter == "stk":
+        return [_stk_to_json(frame) for frame in frames]
     else:
         raise Exception("reached unreachable code")
 
@@ -66,6 +82,10 @@ def _list_atom_properties(frames):
 
     if adapter == "ASE":
         return _ase_list_atom_properties(frames)
+    elif adapter == "stk":
+        # Do not check, because stk does not contain its own properties
+        # and a dictionary must be added.
+        pass
     else:
         raise Exception("reached unreachable code")
 
@@ -80,6 +100,10 @@ def _list_structure_properties(frames):
 
     if adapter == "ASE":
         return _ase_list_structure_properties(frames)
+    elif adapter == "stk":
+        # Do not check, because stk does not contain its own properties
+        # and a dictionary must be added.
+        pass
     else:
         raise Exception("reached unreachable code")
 
@@ -100,6 +124,14 @@ def extract_properties(frames, only=None, environments=None):
 
     if adapter == "ASE":
         return _ase_extract_properties(frames, only, environments)
+
+    elif adapter == "stk":
+        msg = (
+            "stk molecules do not contain properties, you must write your "
+            "own dictionary as in example 8."
+        )
+        raise RuntimeError(msg)
+
     else:
         raise Exception("reached unreachable code")
 
@@ -123,6 +155,10 @@ def composition_properties(frames, environments=None):
 
     if adapter == "ASE":
         return _ase_composition_properties(frames, environments)
+
+    elif adapter == "stk":
+        return _stk_composition_properties(frames, environments)
+
     else:
         raise Exception("reached unreachable code")
 
@@ -141,6 +177,8 @@ def all_atomic_environments(frames, cutoff=3.5):
 
     if adapter == "ASE":
         return _ase_all_atomic_environments(frames, cutoff)
+    elif adapter == "stk":
+        return _stk_all_atomic_environments(frames, cutoff)
     else:
         raise Exception("reached unreachable code")
 

From 77029bac893f7a8321cd52b252777b6c383cd330 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:28:00 +0200
Subject: [PATCH 12/35] Write all stk handling functions.

---
 python/chemiscope/structures/_stk.py | 103 +++++++++++++++++++++++++++
 1 file changed, 103 insertions(+)

diff --git a/python/chemiscope/structures/_stk.py b/python/chemiscope/structures/_stk.py
index a406dd537..6c6d6b80e 100644
--- a/python/chemiscope/structures/_stk.py
+++ b/python/chemiscope/structures/_stk.py
@@ -1,3 +1,4 @@
+from collections import Counter
 
 try:
     import stk
@@ -7,6 +8,108 @@
     HAVE_STK = False
 
 
+def _stk_valid_structures(
+    frames: stk.Molecule | list[stk.Molecule],
+) -> tuple[list[stk.Molecule], bool]:
+    if HAVE_STK and isinstance(frames, stk.Molecule):
+        # deal with the user passing a single frame
+        return [frames], True
+    elif HAVE_STK and isinstance(frames[0], stk.Molecule):
+        for frame in frames:
+            assert isinstance(frame, stk.Molecule)
+        return frames, True
+    else:
+        return frames, False
+
+
+def _stk_to_json(molecule: stk.Molecule) -> dict[str : int | list]:
+    """Implementation of frame_to_json for stk.Molcule.
+
+    The current implementation assumes no periodic information, which is safe
+    for the majority of stk molecules. If necessary, we can add cell information
+    in the future.
+
+    """
+    pos_mat = molecule.get_position_matrix()
+    data = {}
+    data["size"] = molecule.get_num_atoms()
+    data["names"] = [atom.__class__.__name__ for atom in molecule.get_atoms()]
+    data["x"] = [float(pos_mat[atom.get_id()][0]) for atom in molecule.get_atoms()]
+    data["y"] = [float(pos_mat[atom.get_id()][1]) for atom in molecule.get_atoms()]
+    data["z"] = [float(pos_mat[atom.get_id()][2]) for atom in molecule.get_atoms()]
+
+    return data
+
+
+def _stk_all_atomic_environments(frames, cutoff):
+    "Extract all atomic environments out of a set of ASE Atoms objects"
+    environments = []
+    for structure_i, frame in enumerate(frames):
+        for atom in frame.get_atoms():
+            environments.append((structure_i, atom.get_id(), cutoff))
+
+    return environments
+
+
+def _stk_composition_properties(frames, environments=None):
+    all_elements = set()
+    for frame in frames:
+        all_elements.update([atom.__class__.__name__ for atom in frame.get_atoms()])
+    all_elements = set(all_elements)
+
+    composition = []
+    elements_count = {element: [] for element in all_elements}
+    for frame in frames:
+        counter = Counter([atom.__class__.__name__ for atom in frame.get_atoms()])
+
+        composition.append("".join(f"{i}{counter[i]}" for i in sorted(counter)))
+
+        dict_composition = dict(counter)
+
+        for element in all_elements:
+            if element in dict_composition:
+                elements_count[element].append(dict_composition[element])
+            else:
+                elements_count[element].append(0)
+
+    properties = {
+        f"n_{element}": {"values": values, "target": "structure"}
+        for element, values in elements_count.items()
+    }
+
+    properties["composition"] = {"values": composition, "target": "structure"}
+
+    if environments is not None:
+        atoms_mask = [[False] * len(f) for f in frames]
+        for structure, center, _ in environments:
+            atoms_mask[structure][center] = True
+    else:
+        atoms_mask = None
+
+    symbols = []
+    numbers = []
+    for i, frame in enumerate(frames):
+        if atoms_mask is None:
+            frame_symbols = [atom.__class__.__name__ for atom in frame.get_atoms()]
+            frame_numbers = [atom.get_atomic_number() for atom in frame.get_atoms()]
+
+        else:
+            frame_symbols = [atom.__class__.__name__ for atom in frame.get_atoms()][
+                atoms_mask[i]
+            ]
+            frame_numbers = [atom.get_atomic_number() for atom in frame.get_atoms()][
+                atoms_mask[i]
+            ]
+
+        symbols.extend(frame_symbols)
+        numbers.extend(frame_numbers)
+
+    properties["symbol"] = {"values": symbols, "target": "atom"}
+    properties["number"] = {"values": numbers, "target": "atom"}
+
+    return properties
+
+
 def convert_stk_bonds_as_shapes(
     frames: list[stk.Molecule],
     bond_color: str,

From acb01ab5b2bb94578ed325fd759c598edc60d698 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 17:28:13 +0200
Subject: [PATCH 13/35] Add example output.

---
 python/examples/data/stk_0.mol |  37 ++++
 python/examples/data/stk_1.mol | 176 ++++++++++++++++
 python/examples/data/stk_2.mol | 272 ++++++++++++++++++++++++
 python/examples/data/stk_3.mol | 365 +++++++++++++++++++++++++++++++++
 python/examples/data/stk_4.mol |  44 ++++
 5 files changed, 894 insertions(+)
 create mode 100644 python/examples/data/stk_0.mol
 create mode 100644 python/examples/data/stk_1.mol
 create mode 100644 python/examples/data/stk_2.mol
 create mode 100644 python/examples/data/stk_3.mol
 create mode 100644 python/examples/data/stk_4.mol

diff --git a/python/examples/data/stk_0.mol b/python/examples/data/stk_0.mol
new file mode 100644
index 000000000..cd294ed00
--- /dev/null
+++ b/python/examples/data/stk_0.mol
@@ -0,0 +1,37 @@
+
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 12 11 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 N -1.3789 -0.7953 0.3238 0
+M  V30 2 C -0.6980 0.4411 0.5929 0
+M  V30 3 C 0.4802 0.6365 -0.3568 0
+M  V30 4 N 1.4531 -0.3716 -0.2778 0
+M  V30 5 H -1.8591 -0.7562 -0.6012 0
+M  V30 6 H -0.7320 -1.6254 0.3496 0
+M  V30 7 H -0.3501 0.4675 1.6463 0
+M  V30 8 H -1.4140 1.2621 0.3731 0
+M  V30 9 H 0.0242 0.6054 -1.3880 0
+M  V30 10 H 0.9168 1.6345 -0.1926 0
+M  V30 11 H 1.4680 -1.1058 -0.9708 0
+M  V30 12 H 2.0898 -0.3929 0.5016 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 3 4
+M  V30 4 1 1 5
+M  V30 5 1 1 6
+M  V30 6 1 2 7
+M  V30 7 1 2 8
+M  V30 8 1 3 9
+M  V30 9 1 3 10
+M  V30 10 1 4 11
+M  V30 11 1 4 12
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+
+$$$$
diff --git a/python/examples/data/stk_1.mol b/python/examples/data/stk_1.mol
new file mode 100644
index 000000000..9b327414e
--- /dev/null
+++ b/python/examples/data/stk_1.mol
@@ -0,0 +1,176 @@
+
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 80 82 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -1.2556 -0.4225 4.0772 0
+M  V30 2 C -0.0397 0.2975 4.5383 0
+M  V30 3 C 1.1868 -0.4347 4.0772 0
+M  V30 4 C -0.0576 1.6914 4.0772 0
+M  V30 5 H -1.4528 -0.5880 3.0318 0
+M  V30 6 H -0.0193 0.3109 5.6490 0
+M  V30 7 H 1.3357 -0.5727 3.0009 0
+M  V30 8 H 0.7275 2.4052 4.2944 0
+M  V30 9 C -3.7498 -1.7805 0.1839 0
+M  V30 10 C -3.7106 -1.7760 -1.3020 0
+M  V30 11 C -3.7569 -0.3623 -1.8045 0
+M  V30 12 C -2.5293 -2.4982 -1.7907 0
+M  V30 13 H -2.9918 -1.2913 0.7714 0
+M  V30 14 H -4.6098 -2.2967 -1.6952 0
+M  V30 15 H -2.9577 0.3230 -1.5023 0
+M  V30 16 H -2.2946 -2.6232 -2.8406 0
+M  V30 17 C 3.6233 -2.0364 -0.2630 0
+M  V30 18 C 3.5997 -2.0048 -1.7488 0
+M  V30 19 C 2.3985 -2.7516 -2.2514 0
+M  V30 20 C 3.6345 -0.6206 -2.2376 0
+M  V30 21 H 2.8205 -1.6246 0.3245 0
+M  V30 22 H 4.5003 -2.5231 -2.1420 0
+M  V30 23 H 1.4054 -2.4023 -1.9492 0
+M  V30 24 H 3.6254 -0.3549 -3.2875 0
+M  V30 25 C -0.1654 5.0154 -0.1294 0
+M  V30 26 C -0.1810 4.9791 -1.6153 0
+M  V30 27 C 1.0664 4.3124 -2.1178 0
+M  V30 28 C -1.3971 4.3173 -2.1040 0
+M  V30 29 H -0.1207 4.1143 0.4581 0
+M  V30 30 H -0.1824 6.0182 -2.0084 0
+M  V30 31 H 1.2603 3.2776 -1.8156 0
+M  V30 32 H -1.6227 4.1765 -3.1539 0
+M  V30 33 N -2.4870 -1.4284 4.1027 0
+M  V30 34 C -3.8743 -1.8020 4.1257 0
+M  V30 35 C -4.1982 -2.7786 2.9988 0
+M  V30 36 N -3.9500 -2.2731 1.7136 0
+M  V30 37 H -4.5169 -0.9007 4.0487 0
+M  V30 38 H -4.0476 -2.3537 5.0747 0
+M  V30 39 H -3.5080 -3.6538 3.1720 0
+M  V30 40 H -5.2394 -3.1223 3.1048 0
+M  V30 41 N 2.4914 -1.4606 3.6815 0
+M  V30 42 C 3.5084 -2.4755 3.7045 0
+M  V30 43 C 4.5162 -2.2677 2.5777 0
+M  V30 44 N 3.9544 -2.3053 1.2924 0
+M  V30 45 H 3.0489 -3.4825 3.6273 0
+M  V30 46 H 4.0728 -2.3500 4.6535 0
+M  V30 47 H 4.9293 -1.2325 2.7510 0
+M  V30 48 H 5.3343 -2.9978 2.6836 0
+M  V30 49 N -0.0432 3.5590 3.9060 0
+M  V30 50 C 0.3254 4.9476 3.9293 0
+M  V30 51 C -0.3584 5.7156 2.8019 0
+M  V30 52 N -0.0432 5.2483 1.5169 0
+M  V30 53 H 1.4272 5.0547 3.8532 0
+M  V30 54 H -0.0670 5.3731 4.8780 0
+M  V30 55 H -1.4614 5.5543 2.9742 0
+M  V30 56 H -0.1367 6.7895 2.9081 0
+M  V30 57 N -1.5947 -3.7958 -2.6583 0
+M  V30 58 C -0.8120 -4.5200 -3.6214 0
+M  V30 59 C 0.5519 -4.8952 -3.0492 0
+M  V30 60 N 1.3313 -3.7958 -2.6583 0
+M  V30 61 H -0.6881 -3.9197 -4.5463 0
+M  V30 62 H -1.3409 -5.4775 -3.8176 0
+M  V30 63 H 0.3181 -5.5054 -2.1299 0
+M  V30 64 H 1.0853 -5.5334 -3.7717 0
+M  V30 65 N -4.0129 0.8090 -2.7690 0
+M  V30 66 C -4.6181 2.0621 -3.1270 0
+M  V30 67 C -3.5788 3.0371 -3.6728 0
+M  V30 68 N -2.5499 3.3430 -2.7690 0
+M  V30 69 H -5.1355 2.5040 -2.2505 0
+M  V30 70 H -5.3215 1.8575 -3.9627 0
+M  V30 71 H -3.1237 2.5043 -4.5568 0
+M  V30 72 H -4.0872 3.9465 -4.0307 0
+M  V30 73 N 3.8995 1.1677 -2.7340 0
+M  V30 74 C 4.1353 2.2077 -3.6971 0
+M  V30 75 C 3.7783 3.5765 -3.1249 0
+M  V30 76 N 2.4365 3.7017 -2.7340 0
+M  V30 77 H 3.5534 2.0149 -4.6220 0
+M  V30 78 H 5.2290 2.2284 -3.8933 0
+M  V30 79 H 4.4236 3.6791 -2.2055 0
+M  V30 80 H 4.0643 4.3575 -3.8474 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 3
+M  V30 3 1 2 4
+M  V30 4 1 1 5
+M  V30 5 1 2 6
+M  V30 6 1 3 7
+M  V30 7 1 4 8
+M  V30 8 1 9 10
+M  V30 9 1 10 11
+M  V30 10 1 10 12
+M  V30 11 1 9 13
+M  V30 12 1 10 14
+M  V30 13 1 11 15
+M  V30 14 1 12 16
+M  V30 15 1 17 18
+M  V30 16 1 18 19
+M  V30 17 1 18 20
+M  V30 18 1 17 21
+M  V30 19 1 18 22
+M  V30 20 1 19 23
+M  V30 21 1 20 24
+M  V30 22 1 25 26
+M  V30 23 1 26 27
+M  V30 24 1 26 28
+M  V30 25 1 25 29
+M  V30 26 1 26 30
+M  V30 27 1 27 31
+M  V30 28 1 28 32
+M  V30 29 1 33 34
+M  V30 30 1 34 35
+M  V30 31 1 35 36
+M  V30 32 1 34 37
+M  V30 33 1 34 38
+M  V30 34 1 35 39
+M  V30 35 1 35 40
+M  V30 36 1 41 42
+M  V30 37 1 42 43
+M  V30 38 1 43 44
+M  V30 39 1 42 45
+M  V30 40 1 42 46
+M  V30 41 1 43 47
+M  V30 42 1 43 48
+M  V30 43 1 49 50
+M  V30 44 1 50 51
+M  V30 45 1 51 52
+M  V30 46 1 50 53
+M  V30 47 1 50 54
+M  V30 48 1 51 55
+M  V30 49 1 51 56
+M  V30 50 1 57 58
+M  V30 51 1 58 59
+M  V30 52 1 59 60
+M  V30 53 1 58 61
+M  V30 54 1 58 62
+M  V30 55 1 59 63
+M  V30 56 1 59 64
+M  V30 57 1 65 66
+M  V30 58 1 66 67
+M  V30 59 1 67 68
+M  V30 60 1 66 69
+M  V30 61 1 66 70
+M  V30 62 1 67 71
+M  V30 63 1 67 72
+M  V30 64 1 73 74
+M  V30 65 1 74 75
+M  V30 66 1 75 76
+M  V30 67 1 74 77
+M  V30 68 1 74 78
+M  V30 69 1 75 79
+M  V30 70 1 75 80
+M  V30 71 2 1 33
+M  V30 72 2 9 36
+M  V30 73 2 3 41
+M  V30 74 2 17 44
+M  V30 75 2 4 49
+M  V30 76 2 25 52
+M  V30 77 2 12 57
+M  V30 78 2 19 60
+M  V30 79 2 11 65
+M  V30 80 2 28 68
+M  V30 81 2 20 73
+M  V30 82 2 27 76
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+
+$$$$
diff --git a/python/examples/data/stk_2.mol b/python/examples/data/stk_2.mol
new file mode 100644
index 000000000..f0dfe7c02
--- /dev/null
+++ b/python/examples/data/stk_2.mol
@@ -0,0 +1,272 @@
+
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 122 136 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 Pd 0.0000 6.7061 0.0000 0 CHG=2
+M  V30 2 Pd 0.0000 -6.7061 0.0000 0 CHG=2
+M  V30 3 C 14.6172 4.7881 -0.6066 0
+M  V30 4 N 13.4123 4.8933 -0.0000 0
+M  V30 5 C 12.9018 3.7993 0.5932 0
+M  V30 6 C 13.5659 2.5874 0.5996 0
+M  V30 7 C 14.7939 2.4749 -0.0171 0
+M  V30 8 C 15.4939 1.1926 -0.0090 0
+M  V30 9 C 16.8711 1.1292 -0.0077 0
+M  V30 10 C 17.5565 -0.0840 0.0004 0
+M  V30 11 C 16.8578 -1.2740 0.0075 0
+M  V30 12 C 15.4780 -1.2425 0.0064 0
+M  V30 13 C 14.7497 -2.4936 0.0146 0
+M  V30 14 C 13.5220 -2.5919 0.6235 0
+M  V30 15 C 12.8806 -3.8096 0.5967 0
+M  V30 16 N 13.4123 -4.8933 0.0000 0
+M  V30 17 C 14.6118 -4.8155 -0.6003 0
+M  V30 18 C 15.2647 -3.6219 -0.5866 0
+M  V30 19 C 14.8141 -0.0144 -0.0018 0
+M  V30 20 C 15.3148 3.5984 -0.6246 0
+M  V30 21 H 14.9944 5.6977 -1.0750 0
+M  V30 22 H 11.9249 3.8319 1.1009 0
+M  V30 23 H 13.1630 1.6997 1.0741 0
+M  V30 24 H 17.4342 2.0590 -0.0132 0
+M  V30 25 H 18.6349 -0.1061 0.0012 0
+M  V30 26 H 17.3723 -2.2363 0.0139 0
+M  V30 27 H 13.0431 -1.7455 1.1225 0
+M  V30 28 H 11.9020 -3.9029 1.0772 0
+M  V30 29 H 15.0316 -5.7081 -1.0820 0
+M  V30 30 H 16.2391 -3.5986 -1.0858 0
+M  V30 31 H 13.7460 0.0126 -0.0026 0
+M  V30 32 H 16.2634 3.5747 -1.1195 0
+M  V30 33 C 0.6066 4.7881 14.6172 0
+M  V30 34 N 0.0000 4.8933 13.4123 0
+M  V30 35 C -0.5932 3.7993 12.9018 0
+M  V30 36 C -0.5996 2.5874 13.5659 0
+M  V30 37 C 0.0171 2.4749 14.7939 0
+M  V30 38 C 0.0090 1.1926 15.4939 0
+M  V30 39 C 0.0077 1.1292 16.8711 0
+M  V30 40 C -0.0004 -0.0840 17.5565 0
+M  V30 41 C -0.0075 -1.2740 16.8578 0
+M  V30 42 C -0.0064 -1.2425 15.4780 0
+M  V30 43 C -0.0146 -2.4936 14.7497 0
+M  V30 44 C -0.6235 -2.5919 13.5220 0
+M  V30 45 C -0.5967 -3.8096 12.8806 0
+M  V30 46 N 0.0000 -4.8933 13.4123 0
+M  V30 47 C 0.6003 -4.8155 14.6118 0
+M  V30 48 C 0.5866 -3.6219 15.2647 0
+M  V30 49 C 0.0018 -0.0144 14.8141 0
+M  V30 50 C 0.6246 3.5984 15.3148 0
+M  V30 51 H 1.0750 5.6977 14.9944 0
+M  V30 52 H -1.1009 3.8319 11.9249 0
+M  V30 53 H -1.0741 1.6997 13.1630 0
+M  V30 54 H 0.0132 2.0590 17.4342 0
+M  V30 55 H -0.0012 -0.1061 18.6349 0
+M  V30 56 H -0.0139 -2.2363 17.3723 0
+M  V30 57 H -1.1225 -1.7455 13.0431 0
+M  V30 58 H -1.0772 -3.9029 11.9020 0
+M  V30 59 H 1.0820 -5.7081 15.0316 0
+M  V30 60 H 1.0858 -3.5986 16.2391 0
+M  V30 61 H 0.0026 0.0126 13.7460 0
+M  V30 62 H 1.1195 3.5747 16.2634 0
+M  V30 63 C -14.6172 4.7881 0.6066 0
+M  V30 64 N -13.4123 4.8933 0.0000 0
+M  V30 65 C -12.9018 3.7993 -0.5932 0
+M  V30 66 C -13.5659 2.5874 -0.5996 0
+M  V30 67 C -14.7939 2.4749 0.0171 0
+M  V30 68 C -15.4939 1.1926 0.0090 0
+M  V30 69 C -16.8711 1.1292 0.0077 0
+M  V30 70 C -17.5565 -0.0840 -0.0004 0
+M  V30 71 C -16.8578 -1.2740 -0.0075 0
+M  V30 72 C -15.4780 -1.2425 -0.0064 0
+M  V30 73 C -14.7497 -2.4936 -0.0146 0
+M  V30 74 C -13.5220 -2.5919 -0.6235 0
+M  V30 75 C -12.8806 -3.8096 -0.5967 0
+M  V30 76 N -13.4123 -4.8933 -0.0000 0
+M  V30 77 C -14.6118 -4.8155 0.6003 0
+M  V30 78 C -15.2647 -3.6219 0.5866 0
+M  V30 79 C -14.8141 -0.0144 0.0018 0
+M  V30 80 C -15.3148 3.5984 0.6246 0
+M  V30 81 H -14.9944 5.6977 1.0750 0
+M  V30 82 H -11.9249 3.8319 -1.1009 0
+M  V30 83 H -13.1630 1.6997 -1.0741 0
+M  V30 84 H -17.4342 2.0590 0.0132 0
+M  V30 85 H -18.6349 -0.1061 -0.0012 0
+M  V30 86 H -17.3723 -2.2363 -0.0139 0
+M  V30 87 H -13.0431 -1.7455 -1.1225 0
+M  V30 88 H -11.9020 -3.9029 -1.0772 0
+M  V30 89 H -15.0316 -5.7081 1.0820 0
+M  V30 90 H -16.2391 -3.5986 1.0858 0
+M  V30 91 H -13.7460 0.0126 0.0026 0
+M  V30 92 H -16.2634 3.5747 1.1195 0
+M  V30 93 C -0.6066 4.7881 -14.6172 0
+M  V30 94 N -0.0000 4.8933 -13.4123 0
+M  V30 95 C 0.5932 3.7993 -12.9018 0
+M  V30 96 C 0.5996 2.5874 -13.5659 0
+M  V30 97 C -0.0171 2.4749 -14.7939 0
+M  V30 98 C -0.0090 1.1926 -15.4939 0
+M  V30 99 C -0.0077 1.1292 -16.8711 0
+M  V30 100 C 0.0004 -0.0840 -17.5565 0
+M  V30 101 C 0.0075 -1.2740 -16.8578 0
+M  V30 102 C 0.0064 -1.2425 -15.4780 0
+M  V30 103 C 0.0146 -2.4936 -14.7497 0
+M  V30 104 C 0.6235 -2.5919 -13.5220 0
+M  V30 105 C 0.5967 -3.8096 -12.8806 0
+M  V30 106 N -0.0000 -4.8933 -13.4123 0
+M  V30 107 C -0.6003 -4.8155 -14.6118 0
+M  V30 108 C -0.5866 -3.6219 -15.2647 0
+M  V30 109 C -0.0018 -0.0144 -14.8141 0
+M  V30 110 C -0.6246 3.5984 -15.3148 0
+M  V30 111 H -1.0750 5.6977 -14.9944 0
+M  V30 112 H 1.1009 3.8319 -11.9249 0
+M  V30 113 H 1.0741 1.6997 -13.1630 0
+M  V30 114 H -0.0132 2.0590 -17.4342 0
+M  V30 115 H 0.0012 -0.1061 -18.6349 0
+M  V30 116 H 0.0139 -2.2363 -17.3723 0
+M  V30 117 H 1.1225 -1.7455 -13.0431 0
+M  V30 118 H 1.0772 -3.9029 -11.9020 0
+M  V30 119 H -1.0820 -5.7081 -15.0316 0
+M  V30 120 H -1.0858 -3.5986 -16.2391 0
+M  V30 121 H -0.0026 0.0126 -13.7460 0
+M  V30 122 H -1.1195 3.5747 -16.2634 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 3 4
+M  V30 2 1 4 5
+M  V30 3 2 5 6
+M  V30 4 1 6 7
+M  V30 5 1 7 8
+M  V30 6 2 8 9
+M  V30 7 1 9 10
+M  V30 8 2 10 11
+M  V30 9 1 11 12
+M  V30 10 1 12 13
+M  V30 11 2 13 14
+M  V30 12 1 14 15
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+M  V30 16 2 12 19
+M  V30 17 2 7 20
+M  V30 18 1 20 3
+M  V30 19 1 19 8
+M  V30 20 1 18 13
+M  V30 21 1 3 21
+M  V30 22 1 5 22
+M  V30 23 1 6 23
+M  V30 24 1 9 24
+M  V30 25 1 10 25
+M  V30 26 1 11 26
+M  V30 27 1 14 27
+M  V30 28 1 15 28
+M  V30 29 1 17 29
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+M  V30 33 2 33 34
+M  V30 34 1 34 35
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+M  V30 50 1 50 33
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+M  V30 98 1 94 95
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+M  V30 100 1 96 97
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+M  V30 105 1 101 102
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+M  V30 115 1 109 98
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+M  V30 122 1 101 116
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+M  V30 124 1 105 118
+M  V30 125 1 107 119
+M  V30 126 1 108 120
+M  V30 127 1 109 121
+M  V30 128 1 110 122
+M  V30 129 9 4 1
+M  V30 130 9 34 1
+M  V30 131 9 64 1
+M  V30 132 9 94 1
+M  V30 133 9 16 2
+M  V30 134 9 46 2
+M  V30 135 9 76 2
+M  V30 136 9 106 2
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+
+$$$$
diff --git a/python/examples/data/stk_3.mol b/python/examples/data/stk_3.mol
new file mode 100644
index 000000000..e6f366ee0
--- /dev/null
+++ b/python/examples/data/stk_3.mol
@@ -0,0 +1,365 @@
+
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 170 181 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -2.5393 -1.2587 5.2649 0
+M  V30 2 C -1.2725 -0.5338 5.2649 0
+M  V30 3 C -1.2400 0.8527 5.2649 0
+M  V30 4 C -0.0713 1.5643 5.2649 0
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+M  V30 6 C 1.0968 0.8497 5.2649 0
+M  V30 7 C 1.1356 -0.5436 5.2649 0
+M  V30 8 C 2.4110 -1.2491 5.2649 0
+M  V30 9 C -0.0685 -1.1963 5.2649 0
+M  V30 10 H -2.5200 -2.3313 5.2649 0
+M  V30 11 H -2.1982 1.3669 5.2649 0
+M  V30 12 H 0.8725 3.5663 5.2649 0
+M  V30 13 H 2.0496 1.3873 5.2649 0
+M  V30 14 H 3.3080 -0.6695 5.2649 0
+M  V30 15 H -0.0712 -2.2788 5.2649 0
+M  V30 16 C -5.3748 -3.1335 1.1212 0
+M  V30 17 C -4.9564 -2.8854 -0.2548 0
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+M  V30 30 H -5.9638 -1.0285 -0.4132 0
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+M  V30 122 N 1.4295 -5.3789 -3.4557 0
+M  V30 123 H -0.4110 -5.3291 -5.1981 0
+M  V30 124 H -1.9640 -7.7118 -4.0872 0
+M  V30 125 H -2.1892 -6.8320 -5.6919 0
+M  V30 126 H -0.5195 -9.1840 -5.0080 0
+M  V30 127 H -1.0501 -8.5716 -6.6120 0
+M  V30 128 H 1.3358 -8.4000 -6.4027 0
+M  V30 129 H 0.7376 -6.7007 -6.2275 0
+M  V30 130 H 1.0024 -8.5930 -3.8187 0
+M  V30 131 H 2.3913 -7.5435 -4.2950 0
+M  V30 132 H 0.2377 -6.8315 -2.6098 0
+M  V30 133 N -5.2458 1.4088 -3.6806 0
+M  V30 134 C -5.7902 2.7297 -4.0283 0
+M  V30 135 C -6.9776 2.4724 -4.9287 0
+M  V30 136 C -7.4236 3.6865 -5.6801 0
+M  V30 137 C -6.6552 4.8773 -5.0970 0
+M  V30 138 C -5.2077 4.6558 -5.5272 0
+M  V30 139 C -4.6944 3.4888 -4.7029 0
+M  V30 140 N -3.7701 3.9648 -3.6806 0
+M  V30 141 H -6.0994 3.1844 -3.0548 0
+M  V30 142 H -6.6539 1.7112 -5.6712 0
+M  V30 143 H -7.8241 2.1269 -4.3083 0
+M  V30 144 H -7.1073 3.6410 -6.7539 0
+M  V30 145 H -8.5067 3.8363 -5.6435 0
+M  V30 146 H -7.0934 5.7753 -5.5511 0
+M  V30 147 H -6.7605 4.8923 -4.0066 0
+M  V30 148 H -5.2049 4.3000 -6.5916 0
+M  V30 149 H -4.5975 5.5531 -5.4435 0
+M  V30 150 H -4.0930 2.7751 -5.3318 0
+M  V30 151 N 5.7193 1.4642 -4.0422 0
+M  V30 152 C 5.8932 2.5711 -4.9943 0
+M  V30 153 C 7.2958 2.4380 -5.5438 0
+M  V30 154 C 7.7810 3.6748 -6.2310 0
+M  V30 155 C 6.5769 4.6140 -6.3587 0
+M  V30 156 C 6.2698 5.0510 -4.9290 0
+M  V30 157 C 5.6777 3.8384 -4.2331 0
+M  V30 158 N 4.2436 4.0201 -4.0422 0
+M  V30 159 H 5.1208 2.4013 -5.7847 0
+M  V30 160 H 7.9608 2.2477 -4.6737 0
+M  V30 161 H 7.3114 1.6128 -6.2785 0
+M  V30 162 H 8.5135 4.2348 -5.5945 0
+M  V30 163 H 8.2484 3.4691 -7.1986 0
+M  V30 164 H 6.9069 5.4495 -6.9892 0
+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 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 2 2 3
+M  V30 3 1 3 4
+M  V30 4 1 4 5
+M  V30 5 2 4 6
+M  V30 6 1 6 7
+M  V30 7 1 7 8
+M  V30 8 2 7 9
+M  V30 9 1 9 2
+M  V30 10 1 1 10
+M  V30 11 1 3 11
+M  V30 12 1 5 12
+M  V30 13 1 6 13
+M  V30 14 1 8 14
+M  V30 15 1 9 15
+M  V30 16 1 16 17
+M  V30 17 2 17 18
+M  V30 18 1 18 19
+M  V30 19 1 19 20
+M  V30 20 2 19 21
+M  V30 21 1 21 22
+M  V30 22 1 22 23
+M  V30 23 2 22 24
+M  V30 24 1 24 17
+M  V30 25 1 16 25
+M  V30 26 1 18 26
+M  V30 27 1 20 27
+M  V30 28 1 21 28
+M  V30 29 1 23 29
+M  V30 30 1 24 30
+M  V30 31 1 31 32
+M  V30 32 2 32 33
+M  V30 33 1 33 34
+M  V30 34 1 34 35
+M  V30 35 2 34 36
+M  V30 36 1 36 37
+M  V30 37 1 37 38
+M  V30 38 2 37 39
+M  V30 39 1 39 32
+M  V30 40 1 31 40
+M  V30 41 1 33 41
+M  V30 42 1 35 42
+M  V30 43 1 36 43
+M  V30 44 1 38 44
+M  V30 45 1 39 45
+M  V30 46 1 46 47
+M  V30 47 2 47 48
+M  V30 48 1 48 49
+M  V30 49 1 49 50
+M  V30 50 2 49 51
+M  V30 51 1 51 52
+M  V30 52 1 52 53
+M  V30 53 2 52 54
+M  V30 54 1 54 47
+M  V30 55 1 46 55
+M  V30 56 1 48 56
+M  V30 57 1 50 57
+M  V30 58 1 51 58
+M  V30 59 1 53 59
+M  V30 60 1 54 60
+M  V30 61 1 61 62
+M  V30 62 1 62 63
+M  V30 63 1 63 64
+M  V30 64 1 64 65
+M  V30 65 1 65 66
+M  V30 66 1 66 67
+M  V30 67 1 67 68
+M  V30 68 1 67 62
+M  V30 69 1 62 69
+M  V30 70 1 63 70
+M  V30 71 1 63 71
+M  V30 72 1 64 72
+M  V30 73 1 64 73
+M  V30 74 1 65 74
+M  V30 75 1 65 75
+M  V30 76 1 66 76
+M  V30 77 1 66 77
+M  V30 78 1 67 78
+M  V30 79 1 79 80
+M  V30 80 1 80 81
+M  V30 81 1 81 82
+M  V30 82 1 82 83
+M  V30 83 1 83 84
+M  V30 84 1 84 85
+M  V30 85 1 85 86
+M  V30 86 1 85 80
+M  V30 87 1 80 87
+M  V30 88 1 81 88
+M  V30 89 1 81 89
+M  V30 90 1 82 90
+M  V30 91 1 82 91
+M  V30 92 1 83 92
+M  V30 93 1 83 93
+M  V30 94 1 84 94
+M  V30 95 1 84 95
+M  V30 96 1 85 96
+M  V30 97 1 97 98
+M  V30 98 1 98 99
+M  V30 99 1 99 100
+M  V30 100 1 100 101
+M  V30 101 1 101 102
+M  V30 102 1 102 103
+M  V30 103 1 103 104
+M  V30 104 1 103 98
+M  V30 105 1 98 105
+M  V30 106 1 99 106
+M  V30 107 1 99 107
+M  V30 108 1 100 108
+M  V30 109 1 100 109
+M  V30 110 1 101 110
+M  V30 111 1 101 111
+M  V30 112 1 102 112
+M  V30 113 1 102 113
+M  V30 114 1 103 114
+M  V30 115 1 115 116
+M  V30 116 1 116 117
+M  V30 117 1 117 118
+M  V30 118 1 118 119
+M  V30 119 1 119 120
+M  V30 120 1 120 121
+M  V30 121 1 121 122
+M  V30 122 1 121 116
+M  V30 123 1 116 123
+M  V30 124 1 117 124
+M  V30 125 1 117 125
+M  V30 126 1 118 126
+M  V30 127 1 118 127
+M  V30 128 1 119 128
+M  V30 129 1 119 129
+M  V30 130 1 120 130
+M  V30 131 1 120 131
+M  V30 132 1 121 132
+M  V30 133 1 133 134
+M  V30 134 1 134 135
+M  V30 135 1 135 136
+M  V30 136 1 136 137
+M  V30 137 1 137 138
+M  V30 138 1 138 139
+M  V30 139 1 139 140
+M  V30 140 1 139 134
+M  V30 141 1 134 141
+M  V30 142 1 135 142
+M  V30 143 1 135 143
+M  V30 144 1 136 144
+M  V30 145 1 136 145
+M  V30 146 1 137 146
+M  V30 147 1 137 147
+M  V30 148 1 138 148
+M  V30 149 1 138 149
+M  V30 150 1 139 150
+M  V30 151 1 151 152
+M  V30 152 1 152 153
+M  V30 153 1 153 154
+M  V30 154 1 154 155
+M  V30 155 1 155 156
+M  V30 156 1 156 157
+M  V30 157 1 157 158
+M  V30 158 1 157 152
+M  V30 159 1 152 159
+M  V30 160 1 153 160
+M  V30 161 1 153 161
+M  V30 162 1 154 162
+M  V30 163 1 154 163
+M  V30 164 1 155 164
+M  V30 165 1 155 165
+M  V30 166 1 156 166
+M  V30 167 1 156 167
+M  V30 168 1 157 168
+M  V30 169 2 1 61
+M  V30 170 2 16 68
+M  V30 171 2 8 79
+M  V30 172 2 31 86
+M  V30 173 2 5 97
+M  V30 174 2 46 104
+M  V30 175 2 20 115
+M  V30 176 2 38 122
+M  V30 177 2 23 133
+M  V30 178 2 50 140
+M  V30 179 2 35 151
+M  V30 180 2 53 158
+M  V30 181 1 169 170
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+
+$$$$
diff --git a/python/examples/data/stk_4.mol b/python/examples/data/stk_4.mol
new file mode 100644
index 000000000..7195b102e
--- /dev/null
+++ b/python/examples/data/stk_4.mol
@@ -0,0 +1,44 @@
+
+     RDKit          3D
+
+  0  0  0  0  0  0  0  0  0  0999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 15 15 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 2.2158 0.0324 -0.0218 0
+M  V30 2 C 0.7287 0.0297 -0.0118 0
+M  V30 3 C 0.0383 -1.1614 0.0667 0
+M  V30 4 C -1.3527 -1.1977 0.0782 0
+M  V30 5 C -2.0901 -0.0334 0.0108 0
+M  V30 6 C -1.3920 1.1548 -0.0676 0
+M  V30 7 C -0.0036 1.1972 -0.0794 0
+M  V30 8 H 2.6349 -0.0844 1.0025 0
+M  V30 9 H 2.5646 -0.8265 -0.6062 0
+M  V30 10 H 2.5418 1.0131 -0.3925 0
+M  V30 11 H 0.6086 -2.1021 0.1214 0
+M  V30 12 H -1.8853 -2.1304 0.1396 0
+M  V30 13 H -3.1787 -0.0848 0.0212 0
+M  V30 14 H -1.9686 2.0588 -0.1199 0
+M  V30 15 H 0.5383 2.1347 -0.1412 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 2 2 3
+M  V30 3 1 3 4
+M  V30 4 2 4 5
+M  V30 5 1 5 6
+M  V30 6 2 6 7
+M  V30 7 1 7 2
+M  V30 8 1 1 8
+M  V30 9 1 1 9
+M  V30 10 1 1 10
+M  V30 11 1 3 11
+M  V30 12 1 4 12
+M  V30 13 1 5 13
+M  V30 14 1 6 14
+M  V30 15 1 7 15
+M  V30 END BOND
+M  V30 END CTAB
+M  END
+
+$$$$

From d649250a42b1befb03ff9d18e53f6dc10a33164a Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 23:25:57 +0200
Subject: [PATCH 14/35] Shift handling to stk functions.

---
 python/chemiscope/input.py               |  3 +--
 python/chemiscope/structures/__init__.py | 13 +++++++------
 python/chemiscope/structures/_stk.py     | 17 +++++++++++++++--
 3 files changed, 23 insertions(+), 10 deletions(-)

diff --git a/python/chemiscope/input.py b/python/chemiscope/input.py
index 4c9490b7a..3ac232d45 100644
--- a/python/chemiscope/input.py
+++ b/python/chemiscope/input.py
@@ -380,8 +380,7 @@ def create_input(
     # Check to tell the user they might have forgotten some properties coming
     # from the frames (that chemiscope used to automatically extract). This code
     # should be removed in version 0.6 of chemiscope.
-    # stk cannot have atom properties or structure properties, so skipping.
-    if frames is not None and not from_stk:
+    if frames is not None:
         found_one_from_frame = False
 
         atom_properties = _list_atom_properties(frames)
diff --git a/python/chemiscope/structures/__init__.py b/python/chemiscope/structures/__init__.py
index 28124eebb..9aa8c6506 100644
--- a/python/chemiscope/structures/__init__.py
+++ b/python/chemiscope/structures/__init__.py
@@ -26,6 +26,8 @@
     convert_stk_bonds_as_shapes,
     _stk_all_atomic_environments,
     _stk_composition_properties,
+    _stk_list_atom_properties,
+    _stk_list_structure_properties,
 )
 
 __all__ = [
@@ -83,9 +85,9 @@ def _list_atom_properties(frames):
     if adapter == "ASE":
         return _ase_list_atom_properties(frames)
     elif adapter == "stk":
-        # Do not check, because stk does not contain its own properties
-        # and a dictionary must be added.
-        pass
+        # stk does not contain properties inside the structure objects.
+        return _stk_list_atom_properties(frames)
+
     else:
         raise Exception("reached unreachable code")
 
@@ -101,9 +103,8 @@ def _list_structure_properties(frames):
     if adapter == "ASE":
         return _ase_list_structure_properties(frames)
     elif adapter == "stk":
-        # Do not check, because stk does not contain its own properties
-        # and a dictionary must be added.
-        pass
+        # stk does not contain properties inside the structure objects.
+        return _stk_list_structure_properties(frames)
     else:
         raise Exception("reached unreachable code")
 
diff --git a/python/chemiscope/structures/_stk.py b/python/chemiscope/structures/_stk.py
index 6c6d6b80e..4ffb34b60 100644
--- a/python/chemiscope/structures/_stk.py
+++ b/python/chemiscope/structures/_stk.py
@@ -41,8 +41,11 @@ def _stk_to_json(molecule: stk.Molecule) -> dict[str : int | list]:
     return data
 
 
-def _stk_all_atomic_environments(frames, cutoff):
-    "Extract all atomic environments out of a set of ASE Atoms objects"
+def _stk_all_atomic_environments(
+    frames: list[stk.Molecule],
+    cutoff: float,
+) -> list[tuple[int, int, float]]:
+    "Extract all atomic environments out of a set of stk Molecule objects"
     environments = []
     for structure_i, frame in enumerate(frames):
         for atom in frame.get_atoms():
@@ -196,3 +199,13 @@ def convert_stk_bonds_as_shapes(
                 shape_dict[bname]["parameters"]["structure"].append(fake_bond)
 
     return shape_dict
+
+
+def _stk_list_atom_properties(frames: list[stk.Molecule]) -> list:
+    # stk cannot have atom properties or structure properties, so skipping.
+    return []
+
+
+def _stk_list_structure_properties(frames: list[stk.Molecule]) -> list:
+    # stk cannot have atom properties or structure properties, so skipping.
+    return []

From af545bb6e39751c652cd9cfbbc91334b10562634 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 23:26:47 +0200
Subject: [PATCH 15/35] Fix lint.

---
 python/chemiscope/input.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/python/chemiscope/input.py b/python/chemiscope/input.py
index 3ac232d45..6ef495ef4 100644
--- a/python/chemiscope/input.py
+++ b/python/chemiscope/input.py
@@ -11,7 +11,6 @@
 import numpy as np
 
 from .structures import (
-    _guess_adapter,
     _list_atom_properties,
     _list_structure_properties,
     frames_to_json,
@@ -284,8 +283,7 @@ def create_input(
         data["structures"] = frames_to_json(frames)
         n_structures = len(data["structures"])
         n_atoms = sum(s["size"] for s in data["structures"])
-        _, adapter = _guess_adapter(frames)
-        from_stk = True if adapter == "stk" else False
+
     else:
         n_atoms = 0
 

From be13c12f187b6f131911317de8ecb755fda0f784 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Tue, 24 Sep 2024 23:26:58 +0200
Subject: [PATCH 16/35] Add more detail.

---
 python/examples/8-showing_custom_bonds.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/python/examples/8-showing_custom_bonds.py b/python/examples/8-showing_custom_bonds.py
index c806d9e7a..6ef6f58f4 100644
--- a/python/examples/8-showing_custom_bonds.py
+++ b/python/examples/8-showing_custom_bonds.py
@@ -5,9 +5,13 @@
 This example demonstrates how to add shapes into the chemiscope output such
 that custom bonds that would not normally be assigned by ASE can be rendered.
 
-This is done by using stk to generate and analyse molecules, which comes with
-topology/bonding information by default (using the cheminformatic software
-rdkit).
+This is done by using `stk <https://stk.readthedocs.io/en/stable/>`_ to
+generate and analyse molecules, which comes with topology/bonding information
+by default (using the cheminformatic software rdkit).
+
+We use `stko <https://stko-docs.readthedocs.io/en/latest/>`_ to calculate
+some rudimentary properties of `stk` molecules. `stko` can be installed with
+``pip install stko``.
 
 """
 

From db8f7bb0acad08999b5d87233c730f68c8304102 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Wed, 25 Sep 2024 15:25:56 +0200
Subject: [PATCH 17/35] Update requirements.

---
 docs/requirements.txt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 8d5e7895e..1377149f5 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -8,6 +8,8 @@ numpy
 ipywidgets
 matplotlib
 ase==3.22.1
+rdkit==2024.3.4
+stk
 
 # required for the examples of chemiscope.explore
 mace-torch

From 5222fa03acee1bd3fba39c993e888826ef97351c Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Wed, 25 Sep 2024 15:26:13 +0200
Subject: [PATCH 18/35] Change typing to work with Python 3.9.

---
 python/chemiscope/structures/_stk.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/python/chemiscope/structures/_stk.py b/python/chemiscope/structures/_stk.py
index 4ffb34b60..9f2aab13b 100644
--- a/python/chemiscope/structures/_stk.py
+++ b/python/chemiscope/structures/_stk.py
@@ -1,3 +1,4 @@
+import typing
 from collections import Counter
 
 try:
@@ -9,7 +10,7 @@
 
 
 def _stk_valid_structures(
-    frames: stk.Molecule | list[stk.Molecule],
+    frames: typing.Union(stk.Molecule, list[stk.Molecule]),
 ) -> tuple[list[stk.Molecule], bool]:
     if HAVE_STK and isinstance(frames, stk.Molecule):
         # deal with the user passing a single frame

From 3c86f2fa473a2d2a6c28c71172f018fd1430aad9 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Wed, 25 Sep 2024 15:27:03 +0200
Subject: [PATCH 19/35] Bug fix.

---
 python/chemiscope/structures/_stk.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/chemiscope/structures/_stk.py b/python/chemiscope/structures/_stk.py
index 9f2aab13b..c01a566c7 100644
--- a/python/chemiscope/structures/_stk.py
+++ b/python/chemiscope/structures/_stk.py
@@ -10,7 +10,7 @@
 
 
 def _stk_valid_structures(
-    frames: typing.Union(stk.Molecule, list[stk.Molecule]),
+    frames: typing.Union[stk.Molecule, list[stk.Molecule]],
 ) -> tuple[list[stk.Molecule], bool]:
     if HAVE_STK and isinstance(frames, stk.Molecule):
         # deal with the user passing a single frame

From 9dd4f45955e52aec2d636d8bcdc5de6358b91c4b Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Wed, 25 Sep 2024 15:40:36 +0200
Subject: [PATCH 20/35] Add stko dependancy for docs, remove use of __file__
 for doc tests.

---
 docs/requirements.txt                     | 1 +
 python/examples/8-showing_custom_bonds.py | 9 +--------
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 1377149f5..741eef5a1 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -10,6 +10,7 @@ matplotlib
 ase==3.22.1
 rdkit==2024.3.4
 stk
+stko
 
 # 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 6ef6f58f4..5afba39cd 100644
--- a/python/examples/8-showing_custom_bonds.py
+++ b/python/examples/8-showing_custom_bonds.py
@@ -15,16 +15,12 @@
 
 """
 
-import pathlib
-
 import stk
 import stko
 from rdkit.Chem import AllChem as rdkit
 
 import chemiscope
 
-working_path = pathlib.Path(__file__).resolve().parent
-data_path = working_path / "data"
 
 # %%
 #
@@ -131,7 +127,7 @@
 
 # Write to file for sanity checks.
 for i, struct in enumerate(structures):
-    struct.write(data_path / f"stk_{i}.mol")
+    struct.write(f"data/stk_{i}.mol")
 
 # %%
 #
@@ -215,6 +211,3 @@
     ),
     shapes=shape_dict,
 )
-
-
-raise SystemExit

From 93ee3ed74dc8d6f8e6047a791e9adf9c8cb768b3 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Wed, 25 Sep 2024 15:59:04 +0200
Subject: [PATCH 21/35] Handle Python 3.9 typing.

---
 python/chemiscope/structures/_stk.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/chemiscope/structures/_stk.py b/python/chemiscope/structures/_stk.py
index c01a566c7..b2459d1b0 100644
--- a/python/chemiscope/structures/_stk.py
+++ b/python/chemiscope/structures/_stk.py
@@ -23,7 +23,7 @@ def _stk_valid_structures(
         return frames, False
 
 
-def _stk_to_json(molecule: stk.Molecule) -> dict[str : int | list]:
+def _stk_to_json(molecule: stk.Molecule) -> dict[str : typing.Union[int, list]]:
     """Implementation of frame_to_json for stk.Molcule.
 
     The current implementation assumes no periodic information, which is safe

From 7eeb7989d172e15515346fce62335fb6826e62d2 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Wed, 25 Sep 2024 15:59:42 +0200
Subject: [PATCH 22/35] Minor.

---
 python/examples/8-showing_custom_bonds.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/python/examples/8-showing_custom_bonds.py b/python/examples/8-showing_custom_bonds.py
index 5afba39cd..24e9a3de6 100644
--- a/python/examples/8-showing_custom_bonds.py
+++ b/python/examples/8-showing_custom_bonds.py
@@ -21,7 +21,6 @@
 
 import chemiscope
 
-
 # %%
 #
 # Generate a list of stk BuildingBlocks (representation of a molecule) with

From 3e72ec1647251e873802e37f38e3750b5b3be580 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Wed, 25 Sep 2024 16:50:15 +0200
Subject: [PATCH 23/35] Provide stricter requirements for rdkit and stko.

---
 docs/requirements.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 741eef5a1..6ff7f3c45 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -8,9 +8,9 @@ numpy
 ipywidgets
 matplotlib
 ase==3.22.1
-rdkit==2024.3.4
-stk
-stko
+rdkit==2023.9.5
+stk==2024.9.23.1
+stko==v2024.8.29.1
 
 # required for the examples of chemiscope.explore
 mace-torch

From a32eedc22f01ba74f3f20a2a7f4e303e06e66f0b Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Thu, 26 Sep 2024 11:48:37 +0200
Subject: [PATCH 24/35] For tests, use Python 3.10 stk,stko.

---
 docs/requirements.txt                     |  6 +++---
 python/examples/8-showing_custom_bonds.py | 14 ++++++++------
 python/examples/data/stk_3.mol            |  4 ++--
 3 files changed, 13 insertions(+), 11 deletions(-)

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

From 4f0ad7afebe2af33790a12c67e4de38b5c090099 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Thu, 26 Sep 2024 14:10:16 +0200
Subject: [PATCH 25/35] WIP: Move docs to python 3.11.

---
 .github/workflows/website.yml | 2 +-
 docs/requirements.txt         | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/website.yml b/.github/workflows/website.yml
index d1c8c008b..7f9f6023b 100644
--- a/.github/workflows/website.yml
+++ b/.github/workflows/website.yml
@@ -21,7 +21,7 @@ jobs:
           cache: 'npm'
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - name: configure access to git repositories in package-lock.json
         run: git config --global url."https://github.com/".insteadOf ssh://git@github.com
       - name: install npm dependencies
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 61167e156..55e755647 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -8,9 +8,9 @@ numpy
 ipywidgets
 matplotlib
 ase==3.22.1
-rdkit==2023.9.4
-stk==2022.6.17.0
-stko==0.0.40
+rdkit==2023.9.5
+stk==2024.9.23.1
+stko==2024.8.29.1
 
 # required for the examples of chemiscope.explore
 mace-torch

From 6761b5f05bf817ff2c912636dc7762a6f087cff9 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Fri, 27 Sep 2024 13:41:12 +0200
Subject: [PATCH 26/35] Rename file with new number.

---
 .../{8-showing_custom_bonds.py => 9-showing_custom_bonds.py}      | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename python/examples/{8-showing_custom_bonds.py => 9-showing_custom_bonds.py} (100%)

diff --git a/python/examples/8-showing_custom_bonds.py b/python/examples/9-showing_custom_bonds.py
similarity index 100%
rename from python/examples/8-showing_custom_bonds.py
rename to python/examples/9-showing_custom_bonds.py

From f16914bbede8e26de4ddcab3bc25a431d48aa9f3 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Fri, 27 Sep 2024 13:45:54 +0200
Subject: [PATCH 27/35] Back to Python 3.11.

---
 python/examples/data/stk_3.mol | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/python/examples/data/stk_3.mol b/python/examples/data/stk_3.mol
index babf6d638..e6f366ee0 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 2.1870 0.0000 0.0000 0
-M  V30 170 Br -0.1870 0.0000 0.0000 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 END ATOM
 M  V30 BEGIN BOND
 M  V30 1 1 1 2

From f132c4a341aac4fc4e622eb39da7b95ff676890c Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Fri, 27 Sep 2024 13:52:33 +0200
Subject: [PATCH 28/35] Add to autofunction.

---
 docs/src/python/reference.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/src/python/reference.rst b/docs/src/python/reference.rst
index a65851ea3..63b6af907 100644
--- a/docs/src/python/reference.rst
+++ b/docs/src/python/reference.rst
@@ -28,3 +28,5 @@
 .. autofunction:: chemiscope.explore
 
 .. autofunction:: chemiscope.metatensor_featurizer
+
+.. autofunction:: chemiscope.convert_stk_bonds_as_shapes

From 5694ede281f276c3a957d0b910c751c053f2ad16 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Fri, 27 Sep 2024 13:57:03 +0200
Subject: [PATCH 29/35] Update example comments.

---
 python/examples/9-showing_custom_bonds.py | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/python/examples/9-showing_custom_bonds.py b/python/examples/9-showing_custom_bonds.py
index 3cfa5d62a..d5c1beb35 100644
--- a/python/examples/9-showing_custom_bonds.py
+++ b/python/examples/9-showing_custom_bonds.py
@@ -158,19 +158,14 @@
 
 # %%
 #
-# A chemiscope widget can be used to visualize structures and properties.
-# This generates a Chemiscope object that is rendered to an interactive
-# widget when executed in a Jupyter notebook.
+# A chemiscope widget showing the result without the added bonding.
 
 chemiscope.show(frames=structures, properties=properties)
 
 
 # %%
 #
-# For sharing with collaborators, or when one does not want to use an interactive
-# notebook, one can also write a JSON (or compressed JSON) file that contains all
-# information about structures and properties, and can be viewed at chemiscope.org
-# Save as a file that can be viewed at chemiscope.org
+# Writing to a json.gz file, again without added bonding.
 
 chemiscope.write_input(
     path="noshape_example.json.gz",
@@ -193,7 +188,8 @@
 
 # %%
 #
-# Write to json file with added shapes and note are present.
+# Write to json file with added shapes.
+
 chemiscope.write_input(
     path="shape_example.json.gz",
     frames=structures,

From 59b19668342802e6ca391fbc82d09a7dfe5e67fc Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Thu, 3 Oct 2024 17:01:56 +0200
Subject: [PATCH 30/35] Add comment about pins.

---
 docs/requirements.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/docs/requirements.txt b/docs/requirements.txt
index 55e755647..3a43f19d4 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -8,6 +8,9 @@ numpy
 ipywidgets
 matplotlib
 ase==3.22.1
+# These three pins are to avoid rdkit version 2024.3.5. Once a later version
+# is available, the latest version (assuming Python >= 3.11) of all three
+# should be ok.
 rdkit==2023.9.5
 stk==2024.9.23.1
 stko==2024.8.29.1

From c9191b68fff9312d12b30c2dc6c7f76005330777 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Thu, 3 Oct 2024 17:04:09 +0200
Subject: [PATCH 31/35] Update README.

---
 python/README.md | 36 ++++--------------------------------
 1 file changed, 4 insertions(+), 32 deletions(-)

diff --git a/python/README.md b/python/README.md
index ddd6ae200..acc9b97fd 100644
--- a/python/README.md
+++ b/python/README.md
@@ -24,6 +24,8 @@ import chemiscope
 import ase.io
 
 # read frames using ase
+# frames can also be stk objets, e.g.
+# frames = [stk.BuildingBlock(smiles="NCCN")]
 frames = ase.io.read("structures.xyz", ":")
 
 # add additional properties to display
@@ -44,6 +46,8 @@ import chemiscope
 import ase.io
 
 # read frames using ase
+# frames can also be stk objets, e.g.
+# frames = [stk.BuildingBlock(smiles="NCCN")]
 frames = ase.io.read("structures.xyz", ":")
 
 # add additional properties to display
@@ -53,35 +57,3 @@ properties = {
 
 chemiscope.show(frames=frames, properties=properties)
 ```
-
-To create a new chemiscope input file using `stk`_:
-
-.. _`stk`: https://github.com/lukasturcani/stk
-
-`stk` is an optional dependancy:
-
-```bash
-pip install stk
-```
-
-```python
-import chemiscope
-import stk
-
-# read frames using ase
-frames = [stk.BuildingBlock(smiles="NCCN")]
-
-# add additional properties to display
-properties = {
-    "<property name>": {
-        target: "atom",
-        values: [3, 4, 2, 8, 9, 10],
-    }
-}
-
-chemiscope.write_input(
-    "my-input.json.gz",
-    frames=frames,
-    properties=properties,
-)
-```
\ No newline at end of file

From 4fa814d98046ca555b44c50ad70c3cbc3deda4e2 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Thu, 3 Oct 2024 17:10:23 +0200
Subject: [PATCH 32/35] Clean up import.

---
 python/chemiscope/structures/__init__.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/python/chemiscope/structures/__init__.py b/python/chemiscope/structures/__init__.py
index 9aa8c6506..7141b3404 100644
--- a/python/chemiscope/structures/__init__.py
+++ b/python/chemiscope/structures/__init__.py
@@ -20,7 +20,7 @@
     ase_tensors_to_ellipsoids,
     ase_vectors_to_arrows,
 )
-from ._stk import (
+from ._stk import (  # noqa: F401
     _stk_valid_structures,
     _stk_to_json,
     convert_stk_bonds_as_shapes,
@@ -30,10 +30,6 @@
     _stk_list_structure_properties,
 )
 
-__all__ = [
-    "convert_stk_bonds_as_shapes",
-]
-
 
 def _guess_adapter(frames):
     """

From 850b2ca45d874e682d15823f79f317a9d21e677e Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Thu, 3 Oct 2024 17:17:34 +0200
Subject: [PATCH 33/35] Update example.

---
 python/examples/9-showing_custom_bonds.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/python/examples/9-showing_custom_bonds.py b/python/examples/9-showing_custom_bonds.py
index d5c1beb35..fab081951 100644
--- a/python/examples/9-showing_custom_bonds.py
+++ b/python/examples/9-showing_custom_bonds.py
@@ -3,7 +3,7 @@
 ==============================
 
 This example demonstrates how to add shapes into the chemiscope output such
-that custom bonds that would not normally be assigned by ASE can be rendered.
+that custom bonds that would not automatically be assigned can be rendered.
 
 This is done by using `stk <https://stk.readthedocs.io/en/stable/>`_ to
 generate and analyse molecules, which comes with topology/bonding information

From 995f6acacbdd563469ff8a38af92bf77ad82bbb8 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Thu, 3 Oct 2024 17:17:49 +0200
Subject: [PATCH 34/35] Move type check.

---
 python/chemiscope/structures/__init__.py | 19 ++++++-------------
 python/chemiscope/structures/_ase.py     |  6 +++++-
 2 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/python/chemiscope/structures/__init__.py b/python/chemiscope/structures/__init__.py
index 7141b3404..059e05b45 100644
--- a/python/chemiscope/structures/__init__.py
+++ b/python/chemiscope/structures/__init__.py
@@ -37,13 +37,10 @@ def _guess_adapter(frames):
     frames as a list and a string describing which adapter should be used.
     """
 
-    try:
-        ase_frames, use_ase = _ase_valid_structures(frames)
-        if use_ase:
-            return ase_frames, "ASE"
-    except TypeError:
-        # Error associated with it being an stk list.
-        pass
+    ase_frames, use_ase = _ase_valid_structures(frames)
+    if use_ase:
+        return ase_frames, "ASE"
+
     stk_frames, use_stk = _stk_valid_structures(frames)
     if use_stk:
         return stk_frames, "stk"
@@ -81,7 +78,6 @@ def _list_atom_properties(frames):
     if adapter == "ASE":
         return _ase_list_atom_properties(frames)
     elif adapter == "stk":
-        # stk does not contain properties inside the structure objects.
         return _stk_list_atom_properties(frames)
 
     else:
@@ -99,7 +95,6 @@ def _list_structure_properties(frames):
     if adapter == "ASE":
         return _ase_list_structure_properties(frames)
     elif adapter == "stk":
-        # stk does not contain properties inside the structure objects.
         return _stk_list_structure_properties(frames)
     else:
         raise Exception("reached unreachable code")
@@ -123,11 +118,9 @@ def extract_properties(frames, only=None, environments=None):
         return _ase_extract_properties(frames, only, environments)
 
     elif adapter == "stk":
-        msg = (
-            "stk molecules do not contain properties, you must write your "
-            "own dictionary as in example 8."
+        raise RuntimeError(
+            "stk molecules do not contain properties, you must manually provide them"
         )
-        raise RuntimeError(msg)
 
     else:
         raise Exception("reached unreachable code")
diff --git a/python/chemiscope/structures/_ase.py b/python/chemiscope/structures/_ase.py
index c597624b4..f10538e1f 100644
--- a/python/chemiscope/structures/_ase.py
+++ b/python/chemiscope/structures/_ase.py
@@ -15,7 +15,11 @@
 
 
 def _ase_valid_structures(frames):
-    frames_list = list(frames)
+    try:
+        frames_list = list(frames)
+    except TypeError:
+        return [], False
+
     if HAVE_ASE and isinstance(frames_list[0], ase.Atoms):
         for frame in frames_list:
             assert isinstance(frame, ase.Atoms)

From 859351f3b5e6816fa18f65a14191d4e55b261162 Mon Sep 17 00:00:00 2001
From: andrewtarzia <andrew.tarzia@gmail.com>
Date: Thu, 3 Oct 2024 17:19:06 +0200
Subject: [PATCH 35/35] Remove unnecessary files.

---
 python/examples/9-showing_custom_bonds.py |   3 -
 python/examples/data/stk_0.mol            |  37 ---
 python/examples/data/stk_1.mol            | 176 -----------
 python/examples/data/stk_2.mol            | 272 ----------------
 python/examples/data/stk_3.mol            | 365 ----------------------
 python/examples/data/stk_4.mol            |  44 ---
 6 files changed, 897 deletions(-)
 delete mode 100644 python/examples/data/stk_0.mol
 delete mode 100644 python/examples/data/stk_1.mol
 delete mode 100644 python/examples/data/stk_2.mol
 delete mode 100644 python/examples/data/stk_3.mol
 delete mode 100644 python/examples/data/stk_4.mol

diff --git a/python/examples/9-showing_custom_bonds.py b/python/examples/9-showing_custom_bonds.py
index fab081951..9c5af3658 100644
--- a/python/examples/9-showing_custom_bonds.py
+++ b/python/examples/9-showing_custom_bonds.py
@@ -124,9 +124,6 @@
     stk.BuildingBlock.init_from_rdkit_mol(rdkitmol),
 ]
 
-# Write to file for sanity checks.
-for i, struct in enumerate(structures):
-    struct.write(f"data/stk_{i}.mol")
 
 # %%
 #
diff --git a/python/examples/data/stk_0.mol b/python/examples/data/stk_0.mol
deleted file mode 100644
index cd294ed00..000000000
--- a/python/examples/data/stk_0.mol
+++ /dev/null
@@ -1,37 +0,0 @@
-
-     RDKit          3D
-
-  0  0  0  0  0  0  0  0  0  0999 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 12 11 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 N -1.3789 -0.7953 0.3238 0
-M  V30 2 C -0.6980 0.4411 0.5929 0
-M  V30 3 C 0.4802 0.6365 -0.3568 0
-M  V30 4 N 1.4531 -0.3716 -0.2778 0
-M  V30 5 H -1.8591 -0.7562 -0.6012 0
-M  V30 6 H -0.7320 -1.6254 0.3496 0
-M  V30 7 H -0.3501 0.4675 1.6463 0
-M  V30 8 H -1.4140 1.2621 0.3731 0
-M  V30 9 H 0.0242 0.6054 -1.3880 0
-M  V30 10 H 0.9168 1.6345 -0.1926 0
-M  V30 11 H 1.4680 -1.1058 -0.9708 0
-M  V30 12 H 2.0898 -0.3929 0.5016 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 1 1 2
-M  V30 2 1 2 3
-M  V30 3 1 3 4
-M  V30 4 1 1 5
-M  V30 5 1 1 6
-M  V30 6 1 2 7
-M  V30 7 1 2 8
-M  V30 8 1 3 9
-M  V30 9 1 3 10
-M  V30 10 1 4 11
-M  V30 11 1 4 12
-M  V30 END BOND
-M  V30 END CTAB
-M  END
-
-$$$$
diff --git a/python/examples/data/stk_1.mol b/python/examples/data/stk_1.mol
deleted file mode 100644
index 9b327414e..000000000
--- a/python/examples/data/stk_1.mol
+++ /dev/null
@@ -1,176 +0,0 @@
-
-     RDKit          3D
-
-  0  0  0  0  0  0  0  0  0  0999 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 80 82 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 C -1.2556 -0.4225 4.0772 0
-M  V30 2 C -0.0397 0.2975 4.5383 0
-M  V30 3 C 1.1868 -0.4347 4.0772 0
-M  V30 4 C -0.0576 1.6914 4.0772 0
-M  V30 5 H -1.4528 -0.5880 3.0318 0
-M  V30 6 H -0.0193 0.3109 5.6490 0
-M  V30 7 H 1.3357 -0.5727 3.0009 0
-M  V30 8 H 0.7275 2.4052 4.2944 0
-M  V30 9 C -3.7498 -1.7805 0.1839 0
-M  V30 10 C -3.7106 -1.7760 -1.3020 0
-M  V30 11 C -3.7569 -0.3623 -1.8045 0
-M  V30 12 C -2.5293 -2.4982 -1.7907 0
-M  V30 13 H -2.9918 -1.2913 0.7714 0
-M  V30 14 H -4.6098 -2.2967 -1.6952 0
-M  V30 15 H -2.9577 0.3230 -1.5023 0
-M  V30 16 H -2.2946 -2.6232 -2.8406 0
-M  V30 17 C 3.6233 -2.0364 -0.2630 0
-M  V30 18 C 3.5997 -2.0048 -1.7488 0
-M  V30 19 C 2.3985 -2.7516 -2.2514 0
-M  V30 20 C 3.6345 -0.6206 -2.2376 0
-M  V30 21 H 2.8205 -1.6246 0.3245 0
-M  V30 22 H 4.5003 -2.5231 -2.1420 0
-M  V30 23 H 1.4054 -2.4023 -1.9492 0
-M  V30 24 H 3.6254 -0.3549 -3.2875 0
-M  V30 25 C -0.1654 5.0154 -0.1294 0
-M  V30 26 C -0.1810 4.9791 -1.6153 0
-M  V30 27 C 1.0664 4.3124 -2.1178 0
-M  V30 28 C -1.3971 4.3173 -2.1040 0
-M  V30 29 H -0.1207 4.1143 0.4581 0
-M  V30 30 H -0.1824 6.0182 -2.0084 0
-M  V30 31 H 1.2603 3.2776 -1.8156 0
-M  V30 32 H -1.6227 4.1765 -3.1539 0
-M  V30 33 N -2.4870 -1.4284 4.1027 0
-M  V30 34 C -3.8743 -1.8020 4.1257 0
-M  V30 35 C -4.1982 -2.7786 2.9988 0
-M  V30 36 N -3.9500 -2.2731 1.7136 0
-M  V30 37 H -4.5169 -0.9007 4.0487 0
-M  V30 38 H -4.0476 -2.3537 5.0747 0
-M  V30 39 H -3.5080 -3.6538 3.1720 0
-M  V30 40 H -5.2394 -3.1223 3.1048 0
-M  V30 41 N 2.4914 -1.4606 3.6815 0
-M  V30 42 C 3.5084 -2.4755 3.7045 0
-M  V30 43 C 4.5162 -2.2677 2.5777 0
-M  V30 44 N 3.9544 -2.3053 1.2924 0
-M  V30 45 H 3.0489 -3.4825 3.6273 0
-M  V30 46 H 4.0728 -2.3500 4.6535 0
-M  V30 47 H 4.9293 -1.2325 2.7510 0
-M  V30 48 H 5.3343 -2.9978 2.6836 0
-M  V30 49 N -0.0432 3.5590 3.9060 0
-M  V30 50 C 0.3254 4.9476 3.9293 0
-M  V30 51 C -0.3584 5.7156 2.8019 0
-M  V30 52 N -0.0432 5.2483 1.5169 0
-M  V30 53 H 1.4272 5.0547 3.8532 0
-M  V30 54 H -0.0670 5.3731 4.8780 0
-M  V30 55 H -1.4614 5.5543 2.9742 0
-M  V30 56 H -0.1367 6.7895 2.9081 0
-M  V30 57 N -1.5947 -3.7958 -2.6583 0
-M  V30 58 C -0.8120 -4.5200 -3.6214 0
-M  V30 59 C 0.5519 -4.8952 -3.0492 0
-M  V30 60 N 1.3313 -3.7958 -2.6583 0
-M  V30 61 H -0.6881 -3.9197 -4.5463 0
-M  V30 62 H -1.3409 -5.4775 -3.8176 0
-M  V30 63 H 0.3181 -5.5054 -2.1299 0
-M  V30 64 H 1.0853 -5.5334 -3.7717 0
-M  V30 65 N -4.0129 0.8090 -2.7690 0
-M  V30 66 C -4.6181 2.0621 -3.1270 0
-M  V30 67 C -3.5788 3.0371 -3.6728 0
-M  V30 68 N -2.5499 3.3430 -2.7690 0
-M  V30 69 H -5.1355 2.5040 -2.2505 0
-M  V30 70 H -5.3215 1.8575 -3.9627 0
-M  V30 71 H -3.1237 2.5043 -4.5568 0
-M  V30 72 H -4.0872 3.9465 -4.0307 0
-M  V30 73 N 3.8995 1.1677 -2.7340 0
-M  V30 74 C 4.1353 2.2077 -3.6971 0
-M  V30 75 C 3.7783 3.5765 -3.1249 0
-M  V30 76 N 2.4365 3.7017 -2.7340 0
-M  V30 77 H 3.5534 2.0149 -4.6220 0
-M  V30 78 H 5.2290 2.2284 -3.8933 0
-M  V30 79 H 4.4236 3.6791 -2.2055 0
-M  V30 80 H 4.0643 4.3575 -3.8474 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 1 1 2
-M  V30 2 1 2 3
-M  V30 3 1 2 4
-M  V30 4 1 1 5
-M  V30 5 1 2 6
-M  V30 6 1 3 7
-M  V30 7 1 4 8
-M  V30 8 1 9 10
-M  V30 9 1 10 11
-M  V30 10 1 10 12
-M  V30 11 1 9 13
-M  V30 12 1 10 14
-M  V30 13 1 11 15
-M  V30 14 1 12 16
-M  V30 15 1 17 18
-M  V30 16 1 18 19
-M  V30 17 1 18 20
-M  V30 18 1 17 21
-M  V30 19 1 18 22
-M  V30 20 1 19 23
-M  V30 21 1 20 24
-M  V30 22 1 25 26
-M  V30 23 1 26 27
-M  V30 24 1 26 28
-M  V30 25 1 25 29
-M  V30 26 1 26 30
-M  V30 27 1 27 31
-M  V30 28 1 28 32
-M  V30 29 1 33 34
-M  V30 30 1 34 35
-M  V30 31 1 35 36
-M  V30 32 1 34 37
-M  V30 33 1 34 38
-M  V30 34 1 35 39
-M  V30 35 1 35 40
-M  V30 36 1 41 42
-M  V30 37 1 42 43
-M  V30 38 1 43 44
-M  V30 39 1 42 45
-M  V30 40 1 42 46
-M  V30 41 1 43 47
-M  V30 42 1 43 48
-M  V30 43 1 49 50
-M  V30 44 1 50 51
-M  V30 45 1 51 52
-M  V30 46 1 50 53
-M  V30 47 1 50 54
-M  V30 48 1 51 55
-M  V30 49 1 51 56
-M  V30 50 1 57 58
-M  V30 51 1 58 59
-M  V30 52 1 59 60
-M  V30 53 1 58 61
-M  V30 54 1 58 62
-M  V30 55 1 59 63
-M  V30 56 1 59 64
-M  V30 57 1 65 66
-M  V30 58 1 66 67
-M  V30 59 1 67 68
-M  V30 60 1 66 69
-M  V30 61 1 66 70
-M  V30 62 1 67 71
-M  V30 63 1 67 72
-M  V30 64 1 73 74
-M  V30 65 1 74 75
-M  V30 66 1 75 76
-M  V30 67 1 74 77
-M  V30 68 1 74 78
-M  V30 69 1 75 79
-M  V30 70 1 75 80
-M  V30 71 2 1 33
-M  V30 72 2 9 36
-M  V30 73 2 3 41
-M  V30 74 2 17 44
-M  V30 75 2 4 49
-M  V30 76 2 25 52
-M  V30 77 2 12 57
-M  V30 78 2 19 60
-M  V30 79 2 11 65
-M  V30 80 2 28 68
-M  V30 81 2 20 73
-M  V30 82 2 27 76
-M  V30 END BOND
-M  V30 END CTAB
-M  END
-
-$$$$
diff --git a/python/examples/data/stk_2.mol b/python/examples/data/stk_2.mol
deleted file mode 100644
index f0dfe7c02..000000000
--- a/python/examples/data/stk_2.mol
+++ /dev/null
@@ -1,272 +0,0 @@
-
-     RDKit          3D
-
-  0  0  0  0  0  0  0  0  0  0999 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 122 136 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 Pd 0.0000 6.7061 0.0000 0 CHG=2
-M  V30 2 Pd 0.0000 -6.7061 0.0000 0 CHG=2
-M  V30 3 C 14.6172 4.7881 -0.6066 0
-M  V30 4 N 13.4123 4.8933 -0.0000 0
-M  V30 5 C 12.9018 3.7993 0.5932 0
-M  V30 6 C 13.5659 2.5874 0.5996 0
-M  V30 7 C 14.7939 2.4749 -0.0171 0
-M  V30 8 C 15.4939 1.1926 -0.0090 0
-M  V30 9 C 16.8711 1.1292 -0.0077 0
-M  V30 10 C 17.5565 -0.0840 0.0004 0
-M  V30 11 C 16.8578 -1.2740 0.0075 0
-M  V30 12 C 15.4780 -1.2425 0.0064 0
-M  V30 13 C 14.7497 -2.4936 0.0146 0
-M  V30 14 C 13.5220 -2.5919 0.6235 0
-M  V30 15 C 12.8806 -3.8096 0.5967 0
-M  V30 16 N 13.4123 -4.8933 0.0000 0
-M  V30 17 C 14.6118 -4.8155 -0.6003 0
-M  V30 18 C 15.2647 -3.6219 -0.5866 0
-M  V30 19 C 14.8141 -0.0144 -0.0018 0
-M  V30 20 C 15.3148 3.5984 -0.6246 0
-M  V30 21 H 14.9944 5.6977 -1.0750 0
-M  V30 22 H 11.9249 3.8319 1.1009 0
-M  V30 23 H 13.1630 1.6997 1.0741 0
-M  V30 24 H 17.4342 2.0590 -0.0132 0
-M  V30 25 H 18.6349 -0.1061 0.0012 0
-M  V30 26 H 17.3723 -2.2363 0.0139 0
-M  V30 27 H 13.0431 -1.7455 1.1225 0
-M  V30 28 H 11.9020 -3.9029 1.0772 0
-M  V30 29 H 15.0316 -5.7081 -1.0820 0
-M  V30 30 H 16.2391 -3.5986 -1.0858 0
-M  V30 31 H 13.7460 0.0126 -0.0026 0
-M  V30 32 H 16.2634 3.5747 -1.1195 0
-M  V30 33 C 0.6066 4.7881 14.6172 0
-M  V30 34 N 0.0000 4.8933 13.4123 0
-M  V30 35 C -0.5932 3.7993 12.9018 0
-M  V30 36 C -0.5996 2.5874 13.5659 0
-M  V30 37 C 0.0171 2.4749 14.7939 0
-M  V30 38 C 0.0090 1.1926 15.4939 0
-M  V30 39 C 0.0077 1.1292 16.8711 0
-M  V30 40 C -0.0004 -0.0840 17.5565 0
-M  V30 41 C -0.0075 -1.2740 16.8578 0
-M  V30 42 C -0.0064 -1.2425 15.4780 0
-M  V30 43 C -0.0146 -2.4936 14.7497 0
-M  V30 44 C -0.6235 -2.5919 13.5220 0
-M  V30 45 C -0.5967 -3.8096 12.8806 0
-M  V30 46 N 0.0000 -4.8933 13.4123 0
-M  V30 47 C 0.6003 -4.8155 14.6118 0
-M  V30 48 C 0.5866 -3.6219 15.2647 0
-M  V30 49 C 0.0018 -0.0144 14.8141 0
-M  V30 50 C 0.6246 3.5984 15.3148 0
-M  V30 51 H 1.0750 5.6977 14.9944 0
-M  V30 52 H -1.1009 3.8319 11.9249 0
-M  V30 53 H -1.0741 1.6997 13.1630 0
-M  V30 54 H 0.0132 2.0590 17.4342 0
-M  V30 55 H -0.0012 -0.1061 18.6349 0
-M  V30 56 H -0.0139 -2.2363 17.3723 0
-M  V30 57 H -1.1225 -1.7455 13.0431 0
-M  V30 58 H -1.0772 -3.9029 11.9020 0
-M  V30 59 H 1.0820 -5.7081 15.0316 0
-M  V30 60 H 1.0858 -3.5986 16.2391 0
-M  V30 61 H 0.0026 0.0126 13.7460 0
-M  V30 62 H 1.1195 3.5747 16.2634 0
-M  V30 63 C -14.6172 4.7881 0.6066 0
-M  V30 64 N -13.4123 4.8933 0.0000 0
-M  V30 65 C -12.9018 3.7993 -0.5932 0
-M  V30 66 C -13.5659 2.5874 -0.5996 0
-M  V30 67 C -14.7939 2.4749 0.0171 0
-M  V30 68 C -15.4939 1.1926 0.0090 0
-M  V30 69 C -16.8711 1.1292 0.0077 0
-M  V30 70 C -17.5565 -0.0840 -0.0004 0
-M  V30 71 C -16.8578 -1.2740 -0.0075 0
-M  V30 72 C -15.4780 -1.2425 -0.0064 0
-M  V30 73 C -14.7497 -2.4936 -0.0146 0
-M  V30 74 C -13.5220 -2.5919 -0.6235 0
-M  V30 75 C -12.8806 -3.8096 -0.5967 0
-M  V30 76 N -13.4123 -4.8933 -0.0000 0
-M  V30 77 C -14.6118 -4.8155 0.6003 0
-M  V30 78 C -15.2647 -3.6219 0.5866 0
-M  V30 79 C -14.8141 -0.0144 0.0018 0
-M  V30 80 C -15.3148 3.5984 0.6246 0
-M  V30 81 H -14.9944 5.6977 1.0750 0
-M  V30 82 H -11.9249 3.8319 -1.1009 0
-M  V30 83 H -13.1630 1.6997 -1.0741 0
-M  V30 84 H -17.4342 2.0590 0.0132 0
-M  V30 85 H -18.6349 -0.1061 -0.0012 0
-M  V30 86 H -17.3723 -2.2363 -0.0139 0
-M  V30 87 H -13.0431 -1.7455 -1.1225 0
-M  V30 88 H -11.9020 -3.9029 -1.0772 0
-M  V30 89 H -15.0316 -5.7081 1.0820 0
-M  V30 90 H -16.2391 -3.5986 1.0858 0
-M  V30 91 H -13.7460 0.0126 0.0026 0
-M  V30 92 H -16.2634 3.5747 1.1195 0
-M  V30 93 C -0.6066 4.7881 -14.6172 0
-M  V30 94 N -0.0000 4.8933 -13.4123 0
-M  V30 95 C 0.5932 3.7993 -12.9018 0
-M  V30 96 C 0.5996 2.5874 -13.5659 0
-M  V30 97 C -0.0171 2.4749 -14.7939 0
-M  V30 98 C -0.0090 1.1926 -15.4939 0
-M  V30 99 C -0.0077 1.1292 -16.8711 0
-M  V30 100 C 0.0004 -0.0840 -17.5565 0
-M  V30 101 C 0.0075 -1.2740 -16.8578 0
-M  V30 102 C 0.0064 -1.2425 -15.4780 0
-M  V30 103 C 0.0146 -2.4936 -14.7497 0
-M  V30 104 C 0.6235 -2.5919 -13.5220 0
-M  V30 105 C 0.5967 -3.8096 -12.8806 0
-M  V30 106 N -0.0000 -4.8933 -13.4123 0
-M  V30 107 C -0.6003 -4.8155 -14.6118 0
-M  V30 108 C -0.5866 -3.6219 -15.2647 0
-M  V30 109 C -0.0018 -0.0144 -14.8141 0
-M  V30 110 C -0.6246 3.5984 -15.3148 0
-M  V30 111 H -1.0750 5.6977 -14.9944 0
-M  V30 112 H 1.1009 3.8319 -11.9249 0
-M  V30 113 H 1.0741 1.6997 -13.1630 0
-M  V30 114 H -0.0132 2.0590 -17.4342 0
-M  V30 115 H 0.0012 -0.1061 -18.6349 0
-M  V30 116 H 0.0139 -2.2363 -17.3723 0
-M  V30 117 H 1.1225 -1.7455 -13.0431 0
-M  V30 118 H 1.0772 -3.9029 -11.9020 0
-M  V30 119 H -1.0820 -5.7081 -15.0316 0
-M  V30 120 H -1.0858 -3.5986 -16.2391 0
-M  V30 121 H -0.0026 0.0126 -13.7460 0
-M  V30 122 H -1.1195 3.5747 -16.2634 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 2 3 4
-M  V30 2 1 4 5
-M  V30 3 2 5 6
-M  V30 4 1 6 7
-M  V30 5 1 7 8
-M  V30 6 2 8 9
-M  V30 7 1 9 10
-M  V30 8 2 10 11
-M  V30 9 1 11 12
-M  V30 10 1 12 13
-M  V30 11 2 13 14
-M  V30 12 1 14 15
-M  V30 13 2 15 16
-M  V30 14 1 16 17
-M  V30 15 2 17 18
-M  V30 16 2 12 19
-M  V30 17 2 7 20
-M  V30 18 1 20 3
-M  V30 19 1 19 8
-M  V30 20 1 18 13
-M  V30 21 1 3 21
-M  V30 22 1 5 22
-M  V30 23 1 6 23
-M  V30 24 1 9 24
-M  V30 25 1 10 25
-M  V30 26 1 11 26
-M  V30 27 1 14 27
-M  V30 28 1 15 28
-M  V30 29 1 17 29
-M  V30 30 1 18 30
-M  V30 31 1 19 31
-M  V30 32 1 20 32
-M  V30 33 2 33 34
-M  V30 34 1 34 35
-M  V30 35 2 35 36
-M  V30 36 1 36 37
-M  V30 37 1 37 38
-M  V30 38 2 38 39
-M  V30 39 1 39 40
-M  V30 40 2 40 41
-M  V30 41 1 41 42
-M  V30 42 1 42 43
-M  V30 43 2 43 44
-M  V30 44 1 44 45
-M  V30 45 2 45 46
-M  V30 46 1 46 47
-M  V30 47 2 47 48
-M  V30 48 2 42 49
-M  V30 49 2 37 50
-M  V30 50 1 50 33
-M  V30 51 1 49 38
-M  V30 52 1 48 43
-M  V30 53 1 33 51
-M  V30 54 1 35 52
-M  V30 55 1 36 53
-M  V30 56 1 39 54
-M  V30 57 1 40 55
-M  V30 58 1 41 56
-M  V30 59 1 44 57
-M  V30 60 1 45 58
-M  V30 61 1 47 59
-M  V30 62 1 48 60
-M  V30 63 1 49 61
-M  V30 64 1 50 62
-M  V30 65 2 63 64
-M  V30 66 1 64 65
-M  V30 67 2 65 66
-M  V30 68 1 66 67
-M  V30 69 1 67 68
-M  V30 70 2 68 69
-M  V30 71 1 69 70
-M  V30 72 2 70 71
-M  V30 73 1 71 72
-M  V30 74 1 72 73
-M  V30 75 2 73 74
-M  V30 76 1 74 75
-M  V30 77 2 75 76
-M  V30 78 1 76 77
-M  V30 79 2 77 78
-M  V30 80 2 72 79
-M  V30 81 2 67 80
-M  V30 82 1 80 63
-M  V30 83 1 79 68
-M  V30 84 1 78 73
-M  V30 85 1 63 81
-M  V30 86 1 65 82
-M  V30 87 1 66 83
-M  V30 88 1 69 84
-M  V30 89 1 70 85
-M  V30 90 1 71 86
-M  V30 91 1 74 87
-M  V30 92 1 75 88
-M  V30 93 1 77 89
-M  V30 94 1 78 90
-M  V30 95 1 79 91
-M  V30 96 1 80 92
-M  V30 97 2 93 94
-M  V30 98 1 94 95
-M  V30 99 2 95 96
-M  V30 100 1 96 97
-M  V30 101 1 97 98
-M  V30 102 2 98 99
-M  V30 103 1 99 100
-M  V30 104 2 100 101
-M  V30 105 1 101 102
-M  V30 106 1 102 103
-M  V30 107 2 103 104
-M  V30 108 1 104 105
-M  V30 109 2 105 106
-M  V30 110 1 106 107
-M  V30 111 2 107 108
-M  V30 112 2 102 109
-M  V30 113 2 97 110
-M  V30 114 1 110 93
-M  V30 115 1 109 98
-M  V30 116 1 108 103
-M  V30 117 1 93 111
-M  V30 118 1 95 112
-M  V30 119 1 96 113
-M  V30 120 1 99 114
-M  V30 121 1 100 115
-M  V30 122 1 101 116
-M  V30 123 1 104 117
-M  V30 124 1 105 118
-M  V30 125 1 107 119
-M  V30 126 1 108 120
-M  V30 127 1 109 121
-M  V30 128 1 110 122
-M  V30 129 9 4 1
-M  V30 130 9 34 1
-M  V30 131 9 64 1
-M  V30 132 9 94 1
-M  V30 133 9 16 2
-M  V30 134 9 46 2
-M  V30 135 9 76 2
-M  V30 136 9 106 2
-M  V30 END BOND
-M  V30 END CTAB
-M  END
-
-$$$$
diff --git a/python/examples/data/stk_3.mol b/python/examples/data/stk_3.mol
deleted file mode 100644
index e6f366ee0..000000000
--- a/python/examples/data/stk_3.mol
+++ /dev/null
@@ -1,365 +0,0 @@
-
-     RDKit          3D
-
-  0  0  0  0  0  0  0  0  0  0999 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 170 181 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 C -2.5393 -1.2587 5.2649 0
-M  V30 2 C -1.2725 -0.5338 5.2649 0
-M  V30 3 C -1.2400 0.8527 5.2649 0
-M  V30 4 C -0.0713 1.5643 5.2649 0
-M  V30 5 C -0.0571 3.0229 5.2649 0
-M  V30 6 C 1.0968 0.8497 5.2649 0
-M  V30 7 C 1.1356 -0.5436 5.2649 0
-M  V30 8 C 2.4110 -1.2491 5.2649 0
-M  V30 9 C -0.0685 -1.1963 5.2649 0
-M  V30 10 H -2.5200 -2.3313 5.2649 0
-M  V30 11 H -2.1982 1.3669 5.2649 0
-M  V30 12 H 0.8725 3.5663 5.2649 0
-M  V30 13 H 2.0496 1.3873 5.2649 0
-M  V30 14 H 3.3080 -0.6695 5.2649 0
-M  V30 15 H -0.0712 -2.2788 5.2649 0
-M  V30 16 C -5.3748 -3.1335 1.1212 0
-M  V30 17 C -4.9564 -2.8854 -0.2548 0
-M  V30 18 C -4.1559 -3.7909 -0.9350 0
-M  V30 19 C -3.7450 -3.5906 -2.2247 0
-M  V30 20 C -2.9029 -4.5548 -2.9239 0
-M  V30 21 C -4.1576 -2.4398 -2.8415 0
-M  V30 22 C -4.9620 -1.4885 -2.2165 0
-M  V30 23 C -5.3693 -0.2819 -2.9252 0
-M  V30 24 C -5.3388 -1.7486 -0.9256 0
-M  V30 25 H -5.9941 -2.4073 1.6110 0
-M  V30 26 H -3.8590 -4.6870 -0.3950 0
-M  V30 27 H -2.5892 -4.3804 -3.9390 0
-M  V30 28 H -3.8472 -2.2482 -3.8729 0
-M  V30 29 H -5.0347 -0.1503 -3.9308 0
-M  V30 30 H -5.9638 -1.0285 -0.4132 0
-M  V30 31 C 5.1527 -2.9337 0.9085 0
-M  V30 32 C 4.7285 -2.6954 -0.4675 0
-M  V30 33 C 5.1125 -1.5494 -1.1476 0
-M  V30 34 C 4.7336 -1.2937 -2.4373 0
-M  V30 35 C 5.1475 -0.0823 -3.1365 0
-M  V30 36 C 3.9433 -2.2264 -3.0541 0
-M  V30 37 C 3.5217 -3.3987 -2.4291 0
-M  V30 38 C 2.6803 -4.3547 -3.1378 0
-M  V30 39 C 3.9353 -3.5950 -1.1382 0
-M  V30 40 H 4.8334 -3.8332 1.3984 0
-M  V30 41 H 5.7401 -0.8442 -0.6076 0
-M  V30 42 H 4.8396 0.1022 -4.1517 0
-M  V30 43 H 3.6221 -2.0534 -4.0856 0
-M  V30 44 H 2.3991 -4.1307 -4.1435 0
-M  V30 45 H 3.6242 -4.4963 -0.6258 0
-M  V30 46 C 0.2771 5.8890 0.7434 0
-M  V30 47 C 0.2828 5.4025 -0.6326 0
-M  V30 48 C -0.9017 5.1620 -1.3128 0
-M  V30 49 C -0.9336 4.7060 -2.6025 0
-M  V30 50 C -2.1897 4.4588 -3.3017 0
-M  V30 51 C 0.2693 4.4879 -3.2193 0
-M  V30 52 C 1.4953 4.7089 -2.5943 0
-M  V30 53 C 2.7439 4.4584 -3.3030 0
-M  V30 54 C 1.4585 5.1653 -1.3034 0
-M  V30 55 H 1.2157 6.0622 1.2332 0
-M  V30 56 H -1.8262 5.3529 -0.7728 0
-M  V30 57 H -2.1955 4.0999 -4.3168 0
-M  V30 58 H 0.2800 4.1233 -4.2507 0
-M  V30 59 H 2.6906 4.1028 -4.3086 0
-M  V30 60 H 2.3946 5.3465 -0.7910 0
-M  V30 61 N -3.9995 -2.4253 5.2236 0
-M  V30 62 C -5.4158 -2.8155 5.1613 0
-M  V30 63 C -5.7872 -3.2781 6.5523 0
-M  V30 64 C -7.0619 -4.0595 6.5945 0
-M  V30 65 C -7.7087 -3.9302 5.2113 0
-M  V30 66 C -6.7934 -4.7174 4.2776 0
-M  V30 67 C -5.5256 -3.8946 4.1338 0
-M  V30 68 N -5.4752 -3.2773 2.8138 0
-M  V30 69 H -5.9636 -1.8840 4.8745 0
-M  V30 70 H -4.9665 -3.9451 6.8946 0
-M  V30 71 H -5.9109 -2.3910 7.1992 0
-M  V30 72 H -6.8650 -5.1557 6.7160 0
-M  V30 73 H -7.7332 -3.7367 7.3959 0
-M  V30 74 H -8.7057 -4.3809 5.2971 0
-M  V30 75 H -7.7738 -2.8742 4.9264 0
-M  V30 76 H -6.4844 -5.6625 4.7981 0
-M  V30 77 H -7.2653 -4.9642 3.3285 0
-M  V30 78 H -4.6072 -4.5426 4.1892 0
-M  V30 79 N 3.6993 -2.3691 5.2408 0
-M  V30 80 C 4.7456 -3.4002 5.1786 0
-M  V30 81 C 5.3321 -3.4902 6.5695 0
-M  V30 82 C 6.6464 -4.2031 6.6118 0
-M  V30 83 C 6.8578 -4.8281 5.2286 0
-M  V30 84 C 7.0815 -3.6419 4.2947 0
-M  V30 85 C 5.7348 -2.9557 4.1510 0
-M  V30 86 N 5.1750 -3.2210 2.8310 0
-M  V30 87 H 4.2131 -4.3406 4.8920 0
-M  V30 88 H 5.4991 -2.4458 6.9117 0
-M  V30 89 H 4.6259 -4.0410 7.2166 0
-M  V30 90 H 7.4971 -3.4842 6.7331 0
-M  V30 91 H 6.7028 -4.9457 7.4132 0
-M  V30 92 H 7.7469 -5.4658 5.3144 0
-M  V30 93 H 5.9760 -5.4127 4.9439 0
-M  V30 94 H 7.7453 -2.9015 4.8151 0
-M  V30 95 H 7.5312 -3.9272 3.3456 0
-M  V30 96 H 5.8365 -1.8363 4.2062 0
-M  V30 97 N -0.2313 4.7317 4.6410 0
-M  V30 98 C 0.1393 6.1533 4.5786 0
-M  V30 99 C -0.0754 6.7063 5.9696 0
-M  V30 100 C -0.1143 8.2010 6.0119 0
-M  V30 101 C 0.3210 8.6963 4.6286 0
-M  V30 102 C -0.8187 8.2975 3.6951 0
-M  V30 103 C -0.7404 6.7881 3.5513 0
-M  V30 104 N -0.2313 6.4357 2.2312 0
-M  V30 105 H 1.2198 6.1618 4.2916 0
-M  V30 106 H -1.0633 6.3292 6.3121 0
-M  V30 107 H 0.7548 6.3696 6.6164 0
-M  V30 108 H -1.1621 8.5787 6.1335 0
-M  V30 109 H 0.5011 8.6207 6.8131 0
-M  V30 110 H 0.4293 9.7851 4.7144 0
-M  V30 111 H 1.2678 8.2245 4.3435 0
-M  V30 112 H -1.7915 8.5026 4.2158 0
-M  V30 113 H -0.7965 8.8296 2.7460 0
-M  V30 114 H -1.7608 6.3169 3.6068 0
-M  V30 115 N -1.5219 -5.3789 -3.4557 0
-M  V30 116 C -0.6502 -6.0829 -4.4078 0
-M  V30 117 C -1.4667 -7.2310 -4.9573 0
-M  V30 118 C -0.6383 -8.2697 -5.6445 0
-M  V30 119 C 0.7772 -7.6965 -5.7721 0
-M  V30 120 C 1.3092 -7.6490 -4.3424 0
-M  V30 121 C 0.5551 -6.5299 -3.6465 0
-M  V30 122 N 1.4295 -5.3789 -3.4557 0
-M  V30 123 H -0.4110 -5.3291 -5.1981 0
-M  V30 124 H -1.9640 -7.7118 -4.0872 0
-M  V30 125 H -2.1892 -6.8320 -5.6919 0
-M  V30 126 H -0.5195 -9.1840 -5.0080 0
-M  V30 127 H -1.0501 -8.5716 -6.6120 0
-M  V30 128 H 1.3358 -8.4000 -6.4027 0
-M  V30 129 H 0.7376 -6.7007 -6.2275 0
-M  V30 130 H 1.0024 -8.5930 -3.8187 0
-M  V30 131 H 2.3913 -7.5435 -4.2950 0
-M  V30 132 H 0.2377 -6.8315 -2.6098 0
-M  V30 133 N -5.2458 1.4088 -3.6806 0
-M  V30 134 C -5.7902 2.7297 -4.0283 0
-M  V30 135 C -6.9776 2.4724 -4.9287 0
-M  V30 136 C -7.4236 3.6865 -5.6801 0
-M  V30 137 C -6.6552 4.8773 -5.0970 0
-M  V30 138 C -5.2077 4.6558 -5.5272 0
-M  V30 139 C -4.6944 3.4888 -4.7029 0
-M  V30 140 N -3.7701 3.9648 -3.6806 0
-M  V30 141 H -6.0994 3.1844 -3.0548 0
-M  V30 142 H -6.6539 1.7112 -5.6712 0
-M  V30 143 H -7.8241 2.1269 -4.3083 0
-M  V30 144 H -7.1073 3.6410 -6.7539 0
-M  V30 145 H -8.5067 3.8363 -5.6435 0
-M  V30 146 H -7.0934 5.7753 -5.5511 0
-M  V30 147 H -6.7605 4.8923 -4.0066 0
-M  V30 148 H -5.2049 4.3000 -6.5916 0
-M  V30 149 H -4.5975 5.5531 -5.4435 0
-M  V30 150 H -4.0930 2.7751 -5.3318 0
-M  V30 151 N 5.7193 1.4642 -4.0422 0
-M  V30 152 C 5.8932 2.5711 -4.9943 0
-M  V30 153 C 7.2958 2.4380 -5.5438 0
-M  V30 154 C 7.7810 3.6748 -6.2310 0
-M  V30 155 C 6.5769 4.6140 -6.3587 0
-M  V30 156 C 6.2698 5.0510 -4.9290 0
-M  V30 157 C 5.6777 3.8384 -4.2331 0
-M  V30 158 N 4.2436 4.0201 -4.0422 0
-M  V30 159 H 5.1208 2.4013 -5.7847 0
-M  V30 160 H 7.9608 2.2477 -4.6737 0
-M  V30 161 H 7.3114 1.6128 -6.2785 0
-M  V30 162 H 8.5135 4.2348 -5.5945 0
-M  V30 163 H 8.2484 3.4691 -7.1986 0
-M  V30 164 H 6.9069 5.4495 -6.9892 0
-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 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 1 1 2
-M  V30 2 2 2 3
-M  V30 3 1 3 4
-M  V30 4 1 4 5
-M  V30 5 2 4 6
-M  V30 6 1 6 7
-M  V30 7 1 7 8
-M  V30 8 2 7 9
-M  V30 9 1 9 2
-M  V30 10 1 1 10
-M  V30 11 1 3 11
-M  V30 12 1 5 12
-M  V30 13 1 6 13
-M  V30 14 1 8 14
-M  V30 15 1 9 15
-M  V30 16 1 16 17
-M  V30 17 2 17 18
-M  V30 18 1 18 19
-M  V30 19 1 19 20
-M  V30 20 2 19 21
-M  V30 21 1 21 22
-M  V30 22 1 22 23
-M  V30 23 2 22 24
-M  V30 24 1 24 17
-M  V30 25 1 16 25
-M  V30 26 1 18 26
-M  V30 27 1 20 27
-M  V30 28 1 21 28
-M  V30 29 1 23 29
-M  V30 30 1 24 30
-M  V30 31 1 31 32
-M  V30 32 2 32 33
-M  V30 33 1 33 34
-M  V30 34 1 34 35
-M  V30 35 2 34 36
-M  V30 36 1 36 37
-M  V30 37 1 37 38
-M  V30 38 2 37 39
-M  V30 39 1 39 32
-M  V30 40 1 31 40
-M  V30 41 1 33 41
-M  V30 42 1 35 42
-M  V30 43 1 36 43
-M  V30 44 1 38 44
-M  V30 45 1 39 45
-M  V30 46 1 46 47
-M  V30 47 2 47 48
-M  V30 48 1 48 49
-M  V30 49 1 49 50
-M  V30 50 2 49 51
-M  V30 51 1 51 52
-M  V30 52 1 52 53
-M  V30 53 2 52 54
-M  V30 54 1 54 47
-M  V30 55 1 46 55
-M  V30 56 1 48 56
-M  V30 57 1 50 57
-M  V30 58 1 51 58
-M  V30 59 1 53 59
-M  V30 60 1 54 60
-M  V30 61 1 61 62
-M  V30 62 1 62 63
-M  V30 63 1 63 64
-M  V30 64 1 64 65
-M  V30 65 1 65 66
-M  V30 66 1 66 67
-M  V30 67 1 67 68
-M  V30 68 1 67 62
-M  V30 69 1 62 69
-M  V30 70 1 63 70
-M  V30 71 1 63 71
-M  V30 72 1 64 72
-M  V30 73 1 64 73
-M  V30 74 1 65 74
-M  V30 75 1 65 75
-M  V30 76 1 66 76
-M  V30 77 1 66 77
-M  V30 78 1 67 78
-M  V30 79 1 79 80
-M  V30 80 1 80 81
-M  V30 81 1 81 82
-M  V30 82 1 82 83
-M  V30 83 1 83 84
-M  V30 84 1 84 85
-M  V30 85 1 85 86
-M  V30 86 1 85 80
-M  V30 87 1 80 87
-M  V30 88 1 81 88
-M  V30 89 1 81 89
-M  V30 90 1 82 90
-M  V30 91 1 82 91
-M  V30 92 1 83 92
-M  V30 93 1 83 93
-M  V30 94 1 84 94
-M  V30 95 1 84 95
-M  V30 96 1 85 96
-M  V30 97 1 97 98
-M  V30 98 1 98 99
-M  V30 99 1 99 100
-M  V30 100 1 100 101
-M  V30 101 1 101 102
-M  V30 102 1 102 103
-M  V30 103 1 103 104
-M  V30 104 1 103 98
-M  V30 105 1 98 105
-M  V30 106 1 99 106
-M  V30 107 1 99 107
-M  V30 108 1 100 108
-M  V30 109 1 100 109
-M  V30 110 1 101 110
-M  V30 111 1 101 111
-M  V30 112 1 102 112
-M  V30 113 1 102 113
-M  V30 114 1 103 114
-M  V30 115 1 115 116
-M  V30 116 1 116 117
-M  V30 117 1 117 118
-M  V30 118 1 118 119
-M  V30 119 1 119 120
-M  V30 120 1 120 121
-M  V30 121 1 121 122
-M  V30 122 1 121 116
-M  V30 123 1 116 123
-M  V30 124 1 117 124
-M  V30 125 1 117 125
-M  V30 126 1 118 126
-M  V30 127 1 118 127
-M  V30 128 1 119 128
-M  V30 129 1 119 129
-M  V30 130 1 120 130
-M  V30 131 1 120 131
-M  V30 132 1 121 132
-M  V30 133 1 133 134
-M  V30 134 1 134 135
-M  V30 135 1 135 136
-M  V30 136 1 136 137
-M  V30 137 1 137 138
-M  V30 138 1 138 139
-M  V30 139 1 139 140
-M  V30 140 1 139 134
-M  V30 141 1 134 141
-M  V30 142 1 135 142
-M  V30 143 1 135 143
-M  V30 144 1 136 144
-M  V30 145 1 136 145
-M  V30 146 1 137 146
-M  V30 147 1 137 147
-M  V30 148 1 138 148
-M  V30 149 1 138 149
-M  V30 150 1 139 150
-M  V30 151 1 151 152
-M  V30 152 1 152 153
-M  V30 153 1 153 154
-M  V30 154 1 154 155
-M  V30 155 1 155 156
-M  V30 156 1 156 157
-M  V30 157 1 157 158
-M  V30 158 1 157 152
-M  V30 159 1 152 159
-M  V30 160 1 153 160
-M  V30 161 1 153 161
-M  V30 162 1 154 162
-M  V30 163 1 154 163
-M  V30 164 1 155 164
-M  V30 165 1 155 165
-M  V30 166 1 156 166
-M  V30 167 1 156 167
-M  V30 168 1 157 168
-M  V30 169 2 1 61
-M  V30 170 2 16 68
-M  V30 171 2 8 79
-M  V30 172 2 31 86
-M  V30 173 2 5 97
-M  V30 174 2 46 104
-M  V30 175 2 20 115
-M  V30 176 2 38 122
-M  V30 177 2 23 133
-M  V30 178 2 50 140
-M  V30 179 2 35 151
-M  V30 180 2 53 158
-M  V30 181 1 169 170
-M  V30 END BOND
-M  V30 END CTAB
-M  END
-
-$$$$
diff --git a/python/examples/data/stk_4.mol b/python/examples/data/stk_4.mol
deleted file mode 100644
index 7195b102e..000000000
--- a/python/examples/data/stk_4.mol
+++ /dev/null
@@ -1,44 +0,0 @@
-
-     RDKit          3D
-
-  0  0  0  0  0  0  0  0  0  0999 V3000
-M  V30 BEGIN CTAB
-M  V30 COUNTS 15 15 0 0 0
-M  V30 BEGIN ATOM
-M  V30 1 C 2.2158 0.0324 -0.0218 0
-M  V30 2 C 0.7287 0.0297 -0.0118 0
-M  V30 3 C 0.0383 -1.1614 0.0667 0
-M  V30 4 C -1.3527 -1.1977 0.0782 0
-M  V30 5 C -2.0901 -0.0334 0.0108 0
-M  V30 6 C -1.3920 1.1548 -0.0676 0
-M  V30 7 C -0.0036 1.1972 -0.0794 0
-M  V30 8 H 2.6349 -0.0844 1.0025 0
-M  V30 9 H 2.5646 -0.8265 -0.6062 0
-M  V30 10 H 2.5418 1.0131 -0.3925 0
-M  V30 11 H 0.6086 -2.1021 0.1214 0
-M  V30 12 H -1.8853 -2.1304 0.1396 0
-M  V30 13 H -3.1787 -0.0848 0.0212 0
-M  V30 14 H -1.9686 2.0588 -0.1199 0
-M  V30 15 H 0.5383 2.1347 -0.1412 0
-M  V30 END ATOM
-M  V30 BEGIN BOND
-M  V30 1 1 1 2
-M  V30 2 2 2 3
-M  V30 3 1 3 4
-M  V30 4 2 4 5
-M  V30 5 1 5 6
-M  V30 6 2 6 7
-M  V30 7 1 7 2
-M  V30 8 1 1 8
-M  V30 9 1 1 9
-M  V30 10 1 1 10
-M  V30 11 1 3 11
-M  V30 12 1 4 12
-M  V30 13 1 5 13
-M  V30 14 1 6 14
-M  V30 15 1 7 15
-M  V30 END BOND
-M  V30 END CTAB
-M  END
-
-$$$$