improve docstrings

examples/fundamentals/commands_and_state.ipynb

@@ -893,7 +893,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

examples/fundamentals/frame.ipynb

@@ -772,7 +772,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,

examples/fundamentals/servers.ipynb

@@ -146,7 +146,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -808,7 +808,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -822,9 +822,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.6"
+   "version": "3.12.0"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

python-libraries/nanover-omni/src/nanover/omni/omni.py

@@ -107,17 +107,26 @@ def print_basic_info_and_wait(self):
 
     @property
     def app_server(self):
+        """
+        The NanoVer application server used by this runner.
+        """
         return self._app_server
 
     @property
     def simulation(self):
+        """
+        The currently selected simulation.
+        """
         try:
             return self.simulations[self._simulation_index]
         except IndexError:
             return None
 
     @property
     def is_paused(self):
+        """
+        Is the currently selected simulation paused?
+        """
         return self._runner.is_paused if self._runner is not None else None
 
     @property

python-libraries/nanover-omni/src/nanover/omni/openmm.py

@@ -18,6 +18,9 @@
 class OpenMMSimulation:
     """
     A wrapper for OpenMM simulations so they can be run inside the OmniRunner.
+
+    The following attributes can be configured after construction: :attr:`frame_interval`, :attr:`include_velocities`,
+    :attr:`include_forces`
     """
 
     @classmethod
@@ -56,9 +59,13 @@ def __init__(self, name: Optional[str] = None):
         self.app_server: Optional[NanoverImdApplication] = None
 
         self.frame_interval = 5
+        """Number of simulation steps to advance between frames."""
         self.include_velocities = False
+        """Include particle velocities in frames."""
         self.include_forces = False
-        self.platform: Optional[str] = None
+        """Include particle forces in frames."""
+        self.platform_name: Optional[str] = None
+        """Name of OpenMM platform to use at the time the system is loaded from XML."""
 
         self.imd_force = create_imd_force()
         self.simulation: Optional[Simulation] = None
@@ -78,7 +85,7 @@ def load(self):
         with open(self.xml_path) as infile:
             self.imd_force = create_imd_force()
             self.simulation = serializer.deserialize_simulation(
-                infile, imd_force=self.imd_force, platform_name=self.platform
+                infile, imd_force=self.imd_force, platform_name=self.platform_name
             )
 
         self.checkpoint = self.simulation.context.createCheckpoint()