state docs

docs/state/readme.md

@@ -8,6 +8,8 @@ interface Snapshot {
     data?: State.Snapshot,
     // Snapshot of behavior state tree
     behaviour?: State.Snapshot,
+    // Snapshot for current animation,
+    animation?: PluginAnimationManager.Snapshot,
     // Saved camera positions
     cameraSnapshots?: CameraSnapshotManager.StateSnapshot,
     canvas3d?: {
@@ -69,6 +71,10 @@ interface Transform.Props {
 
 "Built-in" data state transforms and description of their parameters are defined in ``mol-plugin/state/transforms``. Behavior transforms are defined in ``mol-plugin/behavior``. Auto-generated documentation for the transforms is also [available](transforms.md).
 
+# Animation State
+
+Defined by ``CameraSnapshotManager.StateSnapshot`` in ``mol-plugin/state/animation/manager.ts``.
+
 # Canvas3D State
 
 Defined by ``Canvas3DParams`` in ``mol-canvas3d/canvas3d.ts``.

docs/state/transforms.md

@@ -7,9 +7,11 @@
 * [ms-plugin.parse-ccp4](#ms-plugin-parse-ccp4)
 * [ms-plugin.parse-dsn6](#ms-plugin-parse-dsn6)
 * [ms-plugin.trajectory-from-mmcif](#ms-plugin-trajectory-from-mmcif)
+* [ms-plugin.trajectory-from-pdb](#ms-plugin-trajectory-from-pdb)
 * [ms-plugin.model-from-trajectory](#ms-plugin-model-from-trajectory)
 * [ms-plugin.structure-from-model](#ms-plugin-structure-from-model)
 * [ms-plugin.structure-assembly-from-model](#ms-plugin-structure-assembly-from-model)
+* [ms-plugin.structure-symmetry-from-model](#ms-plugin-structure-symmetry-from-model)
 * [ms-plugin.structure-selection](#ms-plugin-structure-selection)
 * [ms-plugin.structure-complex-element](#ms-plugin-structure-complex-element)
 * [ms-plugin.custom-model-properties](#ms-plugin-custom-model-properties)
@@ -65,7 +67,7 @@
 
 ----------------------------
 ## <a name="ms-plugin-parse-ccp4"></a>ms-plugin.parse-ccp4 :: Binary -> Ccp4
-*Parse CCP4/MRC from Binary data*
+*Parse CCP4/MRC/MAP from Binary data*
 
 ----------------------------
 ## <a name="ms-plugin-parse-dsn6"></a>ms-plugin.parse-dsn6 :: Binary -> Dsn6
@@ -82,6 +84,9 @@
 ```js
 {}
 ```
+----------------------------
+## <a name="ms-plugin-trajectory-from-pdb"></a>ms-plugin.trajectory-from-pdb :: String -> Trajectory
+
 ----------------------------
 ## <a name="ms-plugin-model-from-trajectory"></a>ms-plugin.model-from-trajectory :: Trajectory -> Model
 *Create a molecular structure from the specified model.*
@@ -104,13 +109,36 @@
 *Create a molecular structure assembly.*
 
 ### Parameters
-- **id**?: String *(Assembly Id. If none specified (undefined or empty string), the asymmetric unit is used.)*
+- **id**?: String *(Assembly Id. Value 'deposited' can be used to specify deposited asymmetric unit.)*
 
 ### Default Parameters
 ```js
 {}
 ```
 ----------------------------
+## <a name="ms-plugin-structure-symmetry-from-model"></a>ms-plugin.structure-symmetry-from-model :: Model -> Structure
+*Create a molecular structure symmetry.*
+
+### Parameters
+- **ijkMin**: 3D vector [x, y, z]
+- **ijkMax**: 3D vector [x, y, z]
+
+### Default Parameters
+```js
+{
+  "ijkMin": [
+    -1,
+    -1,
+    -1
+  ],
+  "ijkMax": [
+    1,
+    1,
+    1
+  ]
+}
+```
+----------------------------
 ## <a name="ms-plugin-structure-selection"></a>ms-plugin.structure-selection :: Structure -> Structure
 *Create a molecular structure from the specified query expression.*
 
@@ -149,7 +177,7 @@
 ```
 ----------------------------
 ## <a name="ms-plugin-volume-from-ccp4"></a>ms-plugin.volume-from-ccp4 :: Ccp4 -> Data
-*Create Volume from CCP4/MRC data*
+*Create Volume from CCP4/MRC/MAP data*
 
 ### Parameters
 - **voxelSize**: 3D vector [x, y, z]
@@ -294,7 +322,7 @@ Object with:
       - **highlightColor**: Color as 0xrrggbb
       - **selectColor**: Color as 0xrrggbb
       - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **isoValue**: Numeric value
+      - **isoValueNorm**: Numeric value *(Normalized Isolevel Value)*
       - **renderMode**: One of 'isosurface', 'volume'
       - **controlPoints**: A list of 2d vectors [xi, yi][]
       - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'
@@ -480,7 +508,7 @@ Object with:
       - **highlightColor**: Color as 0xrrggbb
       - **selectColor**: Color as 0xrrggbb
       - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
-      - **isoValue**: Numeric value
+      - **isoValueNorm**: Numeric value *(Normalized Isolevel Value)*
       - **renderMode**: One of 'isosurface', 'volume'
       - **controlPoints**: A list of 2d vectors [xi, yi][]
       - **list**: One of 'OrangeRed', 'PurpleBlue', 'BluePurple', 'Oranges', 'BlueGreen', 'YellowOrangeBrown', 'YellowGreen', 'Reds', 'RedPurple', 'Greens', 'YellowGreenBlue', 'Purples', 'GreenBlue', 'Greys', 'YellowOrangeRed', 'PurpleRed', 'Blues', 'PurpleBlueGreen', 'Spectral', 'RedYellowGreen', 'RedBlue', 'PinkYellowGreen', 'PurpleGreen', 'RedYellowBlue', 'BrownWhiteGreen', 'RedGrey', 'PurpleOrange', 'Set2', 'Accent', 'Set1', 'Set3', 'Dark2', 'Paired', 'Pastel2', 'Pastel1', 'Magma', 'Inferno', 'Plasma', 'Viridis', 'Cividis', 'Twilight', 'Rainbow', 'RedWhiteBlue'