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andrewtarzia · Oct 10, 2024 · b70743d · b70743d
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diff --git a/docs/source/_autosummary/cgexplore.rst b/docs/source/_autosummary/cgexplore.rst
@@ -35,5 +35,6 @@
    optimisation
    systems_optimisation
    terms
+   topologies
    utilities
 
diff --git a/docs/source/_autosummary/cgexplore.topologies.CGM12L24.rst b/docs/source/_autosummary/cgexplore.topologies.CGM12L24.rst
@@ -0,0 +1,26 @@
+cgexplore.topologies.CGM12L24
+=============================
+
+.. currentmodule:: cgexplore.topologies
+
+.. autoclass:: CGM12L24
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+      ~CGM12L24.get_vertex_alignments
+
+
+
+
+
+
diff --git a/docs/source/_autosummary/cgexplore.topologies.CGM4L8.rst b/docs/source/_autosummary/cgexplore.topologies.CGM4L8.rst
@@ -0,0 +1,25 @@
+cgexplore.topologies.CGM4L8
+===========================
+
+.. currentmodule:: cgexplore.topologies
+
+.. autoclass:: CGM4L8
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+
diff --git a/docs/source/_autosummary/cgexplore.topologies.M4L82.rst b/docs/source/_autosummary/cgexplore.topologies.M4L82.rst
@@ -0,0 +1,34 @@
+cgexplore.topologies.M4L82
+==========================
+
+.. currentmodule:: cgexplore.topologies
+
+.. autoclass:: M4L82
+   :members:
+   :inherited-members:
+   :undoc-members:
+   :show-inheritance:
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :nosignatures:
+
+
+
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+
+      ~M4L82.paired_wall_1_coord
+      ~M4L82.paired_wall_2_coord
+      ~M4L82.wall_1_shift
+      ~M4L82.wall_2_shift
+
+
diff --git a/docs/source/_autosummary/cgexplore.topologies.rst b/docs/source/_autosummary/cgexplore.topologies.rst
@@ -0,0 +1,35 @@
+cgexplore.topologies
+====================
+
+.. automodule:: cgexplore.topologies
+
+
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+      :toctree:
+      :template: class.rst
+      :nosignatures:
+
+      CGM12L24
+      CGM4L8
+      M4L82
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/source/_autosummary/cgexplore.utilities.AtomliteDatabase.rst b/docs/source/_autosummary/cgexplore.utilities.AtomliteDatabase.rst
@@ -20,6 +20,7 @@ cgexplore.utilities.AtomliteDatabase
       ~AtomliteDatabase.add_entries
       ~AtomliteDatabase.add_molecule
       ~AtomliteDatabase.add_properties
+      ~AtomliteDatabase.get_database
       ~AtomliteDatabase.get_entries
       ~AtomliteDatabase.get_entry
       ~AtomliteDatabase.get_molecule

diff --git a/docs/source/_autosummary/cgexplore.utilities.extract_property.rst b/docs/source/_autosummary/cgexplore.utilities.extract_property.rst
@@ -0,0 +1,6 @@
+cgexplore.utilities.extract\_property
+=====================================
+
+.. currentmodule:: cgexplore.utilities
+
+.. autofunction:: extract_property
diff --git a/docs/source/_autosummary/cgexplore.utilities.rst b/docs/source/_autosummary/cgexplore.utilities.rst
@@ -35,6 +35,7 @@ cgexplore.utilities
       check_directory
       convert_pyramid_angle
       draw_pie
+      extract_property
       get_supramolecule
       get_unforced_supramolecule
       optimise_ligand
@@ -43,6 +44,7 @@ cgexplore.utilities
       run_soft_md_cycle
       shift_beads
       soften_forcefield
+      write_chemiscope_json
       yield_near_models
       yield_shifted_models
 

diff --git a/docs/source/_autosummary/cgexplore.utilities.write_chemiscope_json.rst b/docs/source/_autosummary/cgexplore.utilities.write_chemiscope_json.rst
@@ -0,0 +1,6 @@
+cgexplore.utilities.write\_chemiscope\_json
+===========================================
+
+.. currentmodule:: cgexplore.utilities
+
+.. autofunction:: write_chemiscope_json
diff --git a/docs/source/databasing.rst b/docs/source/databasing.rst
@@ -1,5 +1,8 @@
-Databasing
-==========
+Sharing with collaborators
+==========================
+
+Databasing with atomlite
+------------------------
 
 .. seealso::
 
@@ -9,3 +12,17 @@ Databasing
   :maxdepth: 1
 
   AtomliteDatabase <_autosummary/cgexplore.utilities.AtomliteDatabase>
+
+
+Mapping with chemiscope
+-----------------------
+
+.. seealso::
+
+    chemiscope: https://chemiscope.org/
+
+.. toctree::
+  :maxdepth: 1
+
+  write_chemiscope_json <_autosummary/cgexplore.utilities.write_chemiscope_json>
+  extract_property <_autosummary/cgexplore.utilities.extract_property>
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -4,16 +4,16 @@
    :maxdepth: 2
 
    Analysis <analysis>
-   Databasing <databasing>
+   Sharing with collaborators <databasing>
    Forcefields <forcefields>
    Molecular <molecular>
    Optimisation <optimisation>
-   Systems Optimisation <systems_optimisation>
+   Systems optimisation <systems_optimisation>
    Terms <terms>
    Utilities <utilities>
    Executables <executables>
    Topologies <topologies>
-   First Paper Example <first_paper_example>
+   First paper example <first_paper_example>
 
 .. toctree::
   :hidden:

diff --git a/src/cgexplore/_internal/scripts/get_values.py b/src/cgexplore/_internal/scripts/get_values.py
@@ -65,7 +65,8 @@ def main() -> None:
         entry = database.get_entry(key=args.name)
         try:
             value = extract_property(
-                path=args.path, properties=entry.properties
+                path=args.path,
+                properties=entry.properties,
             )
 
         except KeyError as ex:

diff --git a/src/cgexplore/_internal/utilities/utilities.py b/src/cgexplore/_internal/utilities/utilities.py
@@ -90,16 +90,19 @@ def draw_pie(
             ax.scatter(xpos, ypos, **marker)
 
 
-def extract_property(path: list[str], properties: dict) -> atomlite.Json:
+def extract_property(
+    path: list[str],
+    properties: dict[str, atomlite.Json],
+) -> atomlite.Json:
     """Extract property from nested dict."""
     if len(path) == 1:
         value = properties[path[0]]
     elif len(path) == 2:  # noqa: PLR2004
-        value = properties[path[0]][path[1]]
+        value = properties[path[0]][path[1]]  # type: ignore[index,call-overload]
     elif len(path) == 3:  # noqa: PLR2004
-        value = properties[path[0]][path[1]][path[2]]
+        value = properties[path[0]][path[1]][path[2]]  # type: ignore[index,call-overload]
     elif len(path) == 4:  # noqa: PLR2004
-        value = properties[path[0]][path[1]][path[2]][path[3]]
+        value = properties[path[0]][path[1]][path[2]][path[3]]  # type: ignore[index,call-overload]
     else:
         msg = f"{path} is too deep ({len(path)})."
         raise RuntimeError(msg)