Add chemiscope test.

tests/databases/conftest.py

@@ -17,10 +17,10 @@
                 stk.BuildingBlock(smiles="CNC"),
             ],
             property_dicts=[
-                {"1": 2},
-                {"1": 2},
-                {"1": 2},
-                {"1": 3, "2": {"h": "w"}},
+                {"1": 2, "3": "astr"},
+                {"1": 2, "3": "bstr"},
+                {"1": 2, "3": "cstr"},
+                {"1": 3, "3": "cstr", "2": {"h": "w"}},
             ],
             expected_count=3,
             name=name,

tests/databases/test_chemiscope.py

@@ -0,0 +1,170 @@
+import json
+import pathlib
+
+import numpy as np
+import pytest
+
+from cgexplore.utilities import write_chemiscope_json
+
+from .case_data import CaseData
+
+
+def test_chemiscope(molecule: CaseData) -> None:
+    """Test :function:`.write_chemiscope_json`."""
+    path = pathlib.Path(__file__).resolve().parent / "test.json"
+
+    if path.exists():
+        path.unlink()
+
+    properties = {}
+    for propm in molecule.property_dicts:
+        for prop in propm:
+            if prop not in properties:
+                properties[prop] = []
+            properties[prop].append(propm[prop])
+
+    # Run a test with the provided dicts, which do not work because one
+    # property is too long.
+    with pytest.raises(
+        ValueError,
+        match=(
+            "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 = 40, n_structures = 4, the length of property values"
+            " is 1, for the '2' property"
+        ),
+    ):
+        write_chemiscope_json(
+            json_file=path,
+            structures=molecule.molecules,
+            properties=properties,
+            bonds_as_shapes=True,
+            meta_dict={
+                "name": "a test!",
+                "description": "testing this",
+                "authors": ["Andrew Tarzia"],
+                "references": ["Testing code"],
+            },
+            x_axis_dict={"property": "1"},
+            y_axis_dict={"property": "3"},
+            z_axis_dict={"property": ""},
+            color_dict={"property": ""},
+            bond_hex_colour="#ffffff",
+        )
+
+    # Then test with the filter.
+    to_delete = [
+        prop
+        for prop in properties
+        if len(properties[prop]) != len(molecule.molecules)
+    ]
+    for prop in to_delete:
+        properties.pop(prop, None)
+
+    write_chemiscope_json(
+        json_file=path,
+        structures=molecule.molecules,
+        properties=properties,
+        bonds_as_shapes=True,
+        meta_dict={
+            "name": "a test!",
+            "description": "testing this",
+            "authors": ["Andrew Tarzia"],
+            "references": ["Testing code"],
+        },
+        x_axis_dict={"property": "1"},
+        y_axis_dict={"property": "3"},
+        z_axis_dict={"property": ""},
+        color_dict={"property": ""},
+        bond_hex_colour="#ffffff",
+    )
+
+    with path.open("r") as f:
+        test_data = json.load(f)
+
+    assert test_data["properties"] == {
+        "1": {"target": "structure", "values": [2.0, 2.0, 2.0, 3.0]},
+        "3": {
+            "target": "structure",
+            "values": ["astr", "bstr", "cstr", "cstr"],
+        },
+    }
+    assert test_data["settings"]["structure"][0]["shape"] == (
+        "bond_0,bond_1,bond_2,bond_3,bond_4,bond_5,bond_6,bond_7,bond_8,"
+        "bond_9,bond_10"
+    )
+    assert len(test_data["structures"]) == len(molecule.molecules)
+
+    for test_molecule, json_molecule in zip(
+        molecule.molecules, test_data["structures"], strict=True
+    ):
+        pos_mat = test_molecule.get_position_matrix()
+        assert test_molecule.get_num_atoms() == json_molecule["size"]
+        for i, atom in enumerate(test_molecule.get_atoms()):
+            assert json_molecule["names"][i] == atom.__class__.__name__
+
+            posx, posy, posz = pos_mat[i]
+
+            assert np.isclose(posx, json_molecule["x"][i], rtol=0, atol=1e-6)
+            assert np.isclose(posy, json_molecule["y"][i], rtol=0, atol=1e-6)
+            assert np.isclose(posz, json_molecule["z"][i], rtol=0, atol=1e-6)
+
+    # Just test one.
+    assert test_data["shapes"]["bond_4"] == {
+        "kind": "cylinder",
+        "parameters": {
+            "global": {"radius": 0.1, "color": "#ffffff"},
+            "structure": [
+                {
+                    "vector": [
+                        0.21965005986273756,
+                        0.053109715994766646,
+                        -1.097856276168836,
+                    ],
+                    "position": [
+                        0.7597449018275233,
+                        -0.01803664139520529,
+                        -0.0343380685713224,
+                    ],
+                },
+                {
+                    "vector": [
+                        -0.5233967307595824,
+                        0.8111426230221287,
+                        0.5661924393326146,
+                    ],
+                    "position": [
+                        -1.1964536175356193,
+                        -0.07971778664788749,
+                        -0.056452517830615785,
+                    ],
+                },
+                {
+                    "vector": [
+                        -0.01425198400365102,
+                        0.9614121228603414,
+                        -0.5657493874400913,
+                    ],
+                    "position": [
+                        -1.7244190203314924,
+                        -0.31510088950566123,
+                        -0.07183607003687872,
+                    ],
+                },
+                {
+                    "vector": [
+                        -0.5233967307595824,
+                        0.8111426230221287,
+                        0.5661924393326146,
+                    ],
+                    "position": [
+                        -1.1964536175356193,
+                        -0.07971778664788749,
+                        -0.056452517830615785,
+                    ],
+                },
+            ],
+        },
+    }
+
+    path.unlink()

tests/databases/test_databasing.py

@@ -42,6 +42,10 @@ def test_databasing(molecule: CaseData) -> None:
             database.get_property(key, property_key="1", property_type=int)
             == prop["1"]
         )
+        assert (
+            database.get_property(key, property_key="3", property_type=str)
+            == prop["3"]
+        )
         if "2" in prop:
             assert (
                 database.get_property(