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+# Mol* Plugin State Transformer Reference
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+
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+* [build-in.root](#build-in-root)
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+* [ms-plugin.download](#ms-plugin-download)
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+* [ms-plugin.read-file](#ms-plugin-read-file)
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+* [ms-plugin.parse-cif](#ms-plugin-parse-cif)
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+* [ms-plugin.parse-ccp4](#ms-plugin-parse-ccp4)
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+* [ms-plugin.trajectory-from-mmcif](#ms-plugin-trajectory-from-mmcif)
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+* [ms-plugin.model-from-trajectory](#ms-plugin-model-from-trajectory)
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+* [ms-plugin.structure-from-model](#ms-plugin-structure-from-model)
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+* [ms-plugin.structure-assembly-from-model](#ms-plugin-structure-assembly-from-model)
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+* [ms-plugin.structure-selection](#ms-plugin-structure-selection)
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+* [ms-plugin.structure-complex-element](#ms-plugin-structure-complex-element)
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+* [ms-plugin.custom-model-properties](#ms-plugin-custom-model-properties)
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+* [ms-plugin.volume-from-ccp4](#ms-plugin-volume-from-ccp4)
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+* [ms-plugin.representation-highlight-loci](#ms-plugin-representation-highlight-loci)
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+* [ms-plugin.representation-select-loci](#ms-plugin-representation-select-loci)
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+* [ms-plugin.default-loci-label-provider](#ms-plugin-default-loci-label-provider)
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+* [ms-plugin.structure-representation-3d](#ms-plugin-structure-representation-3d)
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+* [ms-plugin.explode-structure-representation-3d](#ms-plugin-explode-structure-representation-3d)
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+* [ms-plugin.volume-representation-3d](#ms-plugin-volume-representation-3d)
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+* [ms-plugin.focus-loci-on-select](#ms-plugin-focus-loci-on-select)
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+* [ms-plugin.pdbe-structure-quality-report-prop](#ms-plugin-pdbe-structure-quality-report-prop)
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+* [ms-plugin.rcsb-assembly-symmetry-prop](#ms-plugin-rcsb-assembly-symmetry-prop)
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+* [ms-plugin.structure-animation](#ms-plugin-structure-animation)
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+* [ms-plugin.scene-labels](#ms-plugin-scene-labels)
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+
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+----------------------------
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+## <a name="build-in-root"></a>build-in.root :: () -> ()
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+*For internal use.*
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+
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+----------------------------
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+## <a name="ms-plugin-download"></a>ms-plugin.download :: Root -> String | Binary
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+*Download string or binary data from the specified URL*
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+
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+### Parameters
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+- **url**: String *(Resource URL. Must be the same domain or support CORS.)*
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+- **label**?: String
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+- **isBinary**?: true/false *(If true, download data as binary (string otherwise))*
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+
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+### Default Parameters
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+```js
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+{
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+ "url": "https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif"
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+}
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+```
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+----------------------------
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+## <a name="ms-plugin-read-file"></a>ms-plugin.read-file :: Root -> String | Binary
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+*Read string or binary data from the specified file*
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+
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+### Parameters
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+- **file**: JavaScript File Handle
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+- **label**?: String
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+- **isBinary**?: true/false *(If true, open file as as binary (string otherwise))*
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+
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+### Default Parameters
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+```js
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+{}
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+```
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+----------------------------
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+## <a name="ms-plugin-parse-cif"></a>ms-plugin.parse-cif :: String | Binary -> Cif
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+*Parse CIF from String or Binary data*
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+
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+----------------------------
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+## <a name="ms-plugin-parse-ccp4"></a>ms-plugin.parse-ccp4 :: Binary -> Ccp4
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+*Parse CCP4 from Binary data*
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+
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+----------------------------
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+## <a name="ms-plugin-trajectory-from-mmcif"></a>ms-plugin.trajectory-from-mmcif :: Cif -> Trajectory
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+*Identify and create all separate models in the specified CIF data block*
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+
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+### Parameters
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+- **blockHeader**?: String *(Header of the block to parse. If none is specifed, the 1st data block in the file is used.)*
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+
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+### Default Parameters
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+```js
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+{}
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+```
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+----------------------------
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+## <a name="ms-plugin-model-from-trajectory"></a>ms-plugin.model-from-trajectory :: Trajectory -> Model
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+*Create a molecular structure from the specified model.*
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+
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+### Parameters
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+- **modelIndex**: Numeric value *(Zero-based index of the model)*
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+
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+### Default Parameters
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+```js
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+{
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+ "modelIndex": 0
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+}
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+```
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+----------------------------
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+## <a name="ms-plugin-structure-from-model"></a>ms-plugin.structure-from-model :: Model -> Structure
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+*Create a molecular structure from the specified model.*
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+
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+----------------------------
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+## <a name="ms-plugin-structure-assembly-from-model"></a>ms-plugin.structure-assembly-from-model :: Model -> Structure
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+*Create a molecular structure assembly.*
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+
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+### Parameters
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+- **id**: String *(Assembly Id. If none specified (undefined or empty string), the asymmetric unit is used.)*
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+
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+### Default Parameters
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+```js
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+{
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+ "id": ""
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+}
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+```
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+----------------------------
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+## <a name="ms-plugin-structure-selection"></a>ms-plugin.structure-selection :: Structure -> Structure
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+*Create a molecular structure from the specified query expression.*
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+
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+### Parameters
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+- **query**: Value
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+- **label**?: String
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+
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+### Default Parameters
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+```js
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+{}
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+```
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+----------------------------
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+## <a name="ms-plugin-structure-complex-element"></a>ms-plugin.structure-complex-element :: Structure -> Structure
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+*Create a molecular structure from the specified model.*
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+
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+### Parameters
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+- **type**: One of 'atomic-sequence', 'water', 'atomic-het', 'spheres'
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+
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+### Default Parameters
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+```js
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+{
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+ "type": "atomic-sequence"
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+}
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+```
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+----------------------------
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+## <a name="ms-plugin-custom-model-properties"></a>ms-plugin.custom-model-properties :: Model -> Model
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+
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+### Parameters
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+- **properties**: Array of *(A list of property descriptor ids.)*
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+
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+### Default Parameters
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+```js
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+{
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+ "properties": []
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+}
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+```
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+----------------------------
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+## <a name="ms-plugin-volume-from-ccp4"></a>ms-plugin.volume-from-ccp4 :: Ccp4 -> Data
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+*Create Volume from CCP4/MRC data*
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+
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+### Parameters
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+- **voxelSize**: 3D vector [x, y, z]
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+
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+### Default Parameters
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+```js
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+{
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+ "voxelSize": [
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+ 1,
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+ 1,
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+ 1
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+ ]
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+}
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+```
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+----------------------------
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+## <a name="ms-plugin-representation-highlight-loci"></a>ms-plugin.representation-highlight-loci :: Root -> Behavior
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+
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+----------------------------
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+## <a name="ms-plugin-representation-select-loci"></a>ms-plugin.representation-select-loci :: Root -> Behavior
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+
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+----------------------------
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+## <a name="ms-plugin-default-loci-label-provider"></a>ms-plugin.default-loci-label-provider :: Root -> Behavior
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+
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+----------------------------
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+## <a name="ms-plugin-structure-representation-3d"></a>ms-plugin.structure-representation-3d :: Structure -> Representation3D
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+
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+### Parameters
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+- **type**: Object { name: string, params: object } where name+params are:
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+ - **cartoon**:
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+Object with:
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+ - **alpha**: Numeric value
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+ - **useFog**: true/false
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+ - **highlightColor**: Color as 0xrrggbb
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+ - **selectColor**: Color as 0xrrggbb
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+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
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+ - **doubleSided**: true/false
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+ - **flipSided**: true/false
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+ - **flatShaded**: true/false
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+ - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
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+ - **sizeFactor**: Numeric value
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+ - **linearSegments**: Numeric value
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+ - **radialSegments**: Numeric value
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+ - **aspectRatio**: Numeric value
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+ - **arrowFactor**: Numeric value
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+ - **visuals**: Array of 'polymer-trace', 'polymer-gap', 'nucleotide-block', 'direction-wedge'
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+
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+ - **ball-and-stick**:
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+Object with:
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+ - **alpha**: Numeric value
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+ - **useFog**: true/false
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+ - **highlightColor**: Color as 0xrrggbb
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+ - **selectColor**: Color as 0xrrggbb
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+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
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+ - **doubleSided**: true/false
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+ - **flipSided**: true/false
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+ - **flatShaded**: true/false
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+ - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
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+ - **sizeFactor**: Numeric value
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+ - **detail**: Numeric value
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+ - **linkScale**: Numeric value
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+ - **linkSpacing**: Numeric value
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+ - **radialSegments**: Numeric value
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+ - **sizeAspectRatio**: Numeric value
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+ - **visuals**: Array of 'element-sphere', 'intra-link', 'inter-link'
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+
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+ - **carbohydrate**:
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+Object with:
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+ - **alpha**: Numeric value
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+ - **useFog**: true/false
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+ - **highlightColor**: Color as 0xrrggbb
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+ - **selectColor**: Color as 0xrrggbb
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+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
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+ - **doubleSided**: true/false
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+ - **flipSided**: true/false
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+ - **flatShaded**: true/false
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+ - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
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+ - **detail**: Numeric value
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+ - **sizeFactor**: Numeric value
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+ - **linkScale**: Numeric value
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+ - **linkSpacing**: Numeric value
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+ - **radialSegments**: Numeric value
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+ - **linkSizeFactor**: Numeric value
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+ - **visuals**: Array of 'carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'
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+
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+ - **distance-restraint**:
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+Object with:
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+ - **alpha**: Numeric value
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+ - **useFog**: true/false
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+ - **highlightColor**: Color as 0xrrggbb
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+ - **selectColor**: Color as 0xrrggbb
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+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
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+ - **doubleSided**: true/false
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+ - **flipSided**: true/false
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+ - **flatShaded**: true/false
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+ - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
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+ - **linkScale**: Numeric value
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+ - **linkSpacing**: Numeric value
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+ - **radialSegments**: Numeric value
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+ - **sizeFactor**: Numeric value
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+
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+ - **molecular-surface**:
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+Object with:
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+ - **alpha**: Numeric value
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+ - **useFog**: true/false
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+ - **highlightColor**: Color as 0xrrggbb
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+ - **selectColor**: Color as 0xrrggbb
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+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
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+ - **doubleSided**: true/false
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+ - **flipSided**: true/false
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+ - **flatShaded**: true/false
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+ - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
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+ - **resolution**: Numeric value
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+ - **radiusOffset**: Numeric value
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+ - **smoothness**: Numeric value
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+ - **useGpu**: true/false
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+ - **ignoreCache**: true/false
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+ - **sizeFactor**: Numeric value
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+ - **lineSizeAttenuation**: true/false
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+ - **visuals**: Array of 'gaussian-surface', 'gaussian-wireframe'
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+
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+ - **molecular-volume**:
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+Object with:
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+ - **alpha**: Numeric value
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+ - **useFog**: true/false
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+ - **highlightColor**: Color as 0xrrggbb
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+ - **selectColor**: Color as 0xrrggbb
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+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
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+ - **isoValue**: Numeric value
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+ - **renderMode**: One of 'isosurface', 'volume'
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+ - **controlPoints**: A list of 2d vectors [xi, yi][]
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+ - **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'
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+ - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
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+ - **resolution**: Numeric value
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+ - **radiusOffset**: Numeric value
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+ - **smoothness**: Numeric value
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+
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+ - **point**:
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+Object with:
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+ - **alpha**: Numeric value
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+ - **useFog**: true/false
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+ - **highlightColor**: Color as 0xrrggbb
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+ - **selectColor**: Color as 0xrrggbb
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+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
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+ - **sizeFactor**: Numeric value
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+ - **pointSizeAttenuation**: true/false
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+ - **pointFilledCircle**: true/false
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+ - **pointEdgeBleach**: Numeric value
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+ - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
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+
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+ - **spacefill**:
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+Object with:
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+ - **alpha**: Numeric value
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+ - **useFog**: true/false
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+ - **highlightColor**: Color as 0xrrggbb
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+ - **selectColor**: Color as 0xrrggbb
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+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
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+ - **doubleSided**: true/false
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+ - **flipSided**: true/false
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+ - **flatShaded**: true/false
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+ - **unitKinds**: Array of 'atomic', 'spheres', 'gaussians'
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+ - **sizeFactor**: Numeric value
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+ - **detail**: Numeric value
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+
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+
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+- **colorTheme**: Object { name: string, params: object } where name+params are:
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+ - **carbohydrate-symbol**:
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+Object with:
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+
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+ - **chain-id**:
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+Object with:
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+ - **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'
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+
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+ - **cross-link**:
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+Object with:
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+ - **domain**: Interval [min, max]
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+ - **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'
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+
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+ - **element-index**:
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+Object with:
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+ - **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'
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+
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+ - **element-symbol**:
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+Object with:
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+
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+ - **molecule-type**:
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+Object with:
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+
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+ - **polymer-id**:
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+Object with:
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|
+ - **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'
|
|
|
+
|
|
|
+ - **polymer-index**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **residue-name**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **secondary-structure**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **sequence-id**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **shape-group**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **unit-index**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **uniform**:
|
|
|
+Object with:
|
|
|
+ - **value**: Color as 0xrrggbb
|
|
|
+
|
|
|
+
|
|
|
+- **sizeTheme**: Object { name: string, params: object } where name+params are:
|
|
|
+ - **physical**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **shape-group**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **uniform**:
|
|
|
+Object with:
|
|
|
+ - **value**: Numeric value
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+### Default Parameters
|
|
|
+```js
|
|
|
+{
|
|
|
+ "type": {
|
|
|
+ "name": "cartoon",
|
|
|
+ "params": {
|
|
|
+ "alpha": 1,
|
|
|
+ "useFog": true,
|
|
|
+ "highlightColor": 16737945,
|
|
|
+ "selectColor": 3407641,
|
|
|
+ "quality": "auto",
|
|
|
+ "doubleSided": false,
|
|
|
+ "flipSided": false,
|
|
|
+ "flatShaded": false,
|
|
|
+ "unitKinds": [
|
|
|
+ "atomic",
|
|
|
+ "spheres"
|
|
|
+ ],
|
|
|
+ "sizeFactor": 0.2,
|
|
|
+ "linearSegments": 8,
|
|
|
+ "radialSegments": 16,
|
|
|
+ "aspectRatio": 5,
|
|
|
+ "arrowFactor": 1.5,
|
|
|
+ "visuals": [
|
|
|
+ "polymer-trace"
|
|
|
+ ]
|
|
|
+ }
|
|
|
+ },
|
|
|
+ "colorTheme": {
|
|
|
+ "name": "polymer-id",
|
|
|
+ "params": {
|
|
|
+ "list": "RedYellowBlue"
|
|
|
+ }
|
|
|
+ },
|
|
|
+ "sizeTheme": {
|
|
|
+ "name": "uniform",
|
|
|
+ "params": {
|
|
|
+ "value": 1
|
|
|
+ }
|
|
|
+ }
|
|
|
+}
|
|
|
+```
|
|
|
+----------------------------
|
|
|
+## <a name="ms-plugin-explode-structure-representation-3d"></a>ms-plugin.explode-structure-representation-3d :: Representation3D -> Obj
|
|
|
+
|
|
|
+### Parameters
|
|
|
+- **t**: Numeric value
|
|
|
+
|
|
|
+### Default Parameters
|
|
|
+```js
|
|
|
+{
|
|
|
+ "t": 0
|
|
|
+}
|
|
|
+```
|
|
|
+----------------------------
|
|
|
+## <a name="ms-plugin-volume-representation-3d"></a>ms-plugin.volume-representation-3d :: Data -> Representation3D
|
|
|
+
|
|
|
+### Parameters
|
|
|
+- **type**: Object { name: string, params: object } where name+params are:
|
|
|
+ - **isosurface**:
|
|
|
+Object with:
|
|
|
+ - **alpha**: Numeric value
|
|
|
+ - **useFog**: true/false
|
|
|
+ - **highlightColor**: Color as 0xrrggbb
|
|
|
+ - **selectColor**: Color as 0xrrggbb
|
|
|
+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
|
|
|
+ - **doubleSided**: true/false
|
|
|
+ - **flipSided**: true/false
|
|
|
+ - **flatShaded**: true/false
|
|
|
+ - **isoValue**: Numeric value
|
|
|
+
|
|
|
+ - **direct-volume**:
|
|
|
+Object with:
|
|
|
+ - **alpha**: Numeric value
|
|
|
+ - **useFog**: true/false
|
|
|
+ - **highlightColor**: Color as 0xrrggbb
|
|
|
+ - **selectColor**: Color as 0xrrggbb
|
|
|
+ - **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
|
|
|
+ - **isoValue**: Numeric 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'
|
|
|
+
|
|
|
+
|
|
|
+- **colorTheme**: Object { name: string, params: object } where name+params are:
|
|
|
+ - **carbohydrate-symbol**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **chain-id**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **cross-link**:
|
|
|
+Object with:
|
|
|
+ - **domain**: Interval [min, max]
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **element-index**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **element-symbol**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **molecule-type**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **polymer-id**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **polymer-index**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **residue-name**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **secondary-structure**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **sequence-id**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **shape-group**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **unit-index**:
|
|
|
+Object with:
|
|
|
+ - **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'
|
|
|
+
|
|
|
+ - **uniform**:
|
|
|
+Object with:
|
|
|
+ - **value**: Color as 0xrrggbb
|
|
|
+
|
|
|
+
|
|
|
+- **sizeTheme**: Object { name: string, params: object } where name+params are:
|
|
|
+ - **physical**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **shape-group**:
|
|
|
+Object with:
|
|
|
+
|
|
|
+ - **uniform**:
|
|
|
+Object with:
|
|
|
+ - **value**: Numeric value
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+### Default Parameters
|
|
|
+```js
|
|
|
+{
|
|
|
+ "type": {
|
|
|
+ "name": "isosurface",
|
|
|
+ "params": {
|
|
|
+ "alpha": 1,
|
|
|
+ "useFog": true,
|
|
|
+ "highlightColor": 16737945,
|
|
|
+ "selectColor": 3407641,
|
|
|
+ "quality": "auto",
|
|
|
+ "doubleSided": false,
|
|
|
+ "flipSided": false,
|
|
|
+ "flatShaded": false,
|
|
|
+ "isoValue": 0.22
|
|
|
+ }
|
|
|
+ },
|
|
|
+ "colorTheme": {
|
|
|
+ "name": "uniform",
|
|
|
+ "params": {
|
|
|
+ "value": 13421772
|
|
|
+ }
|
|
|
+ },
|
|
|
+ "sizeTheme": {
|
|
|
+ "name": "uniform",
|
|
|
+ "params": {
|
|
|
+ "value": 1
|
|
|
+ }
|
|
|
+ }
|
|
|
+}
|
|
|
+```
|
|
|
+----------------------------
|
|
|
+## <a name="ms-plugin-focus-loci-on-select"></a>ms-plugin.focus-loci-on-select :: Root -> Behavior
|
|
|
+
|
|
|
+### Parameters
|
|
|
+- **minRadius**: Numeric value
|
|
|
+- **extraRadius**: Numeric value *(Value added to the boundning sphere radius of the Loci.)*
|
|
|
+
|
|
|
+### Default Parameters
|
|
|
+```js
|
|
|
+{
|
|
|
+ "minRadius": 10,
|
|
|
+ "extraRadius": 4
|
|
|
+}
|
|
|
+```
|
|
|
+----------------------------
|
|
|
+## <a name="ms-plugin-pdbe-structure-quality-report-prop"></a>ms-plugin.pdbe-structure-quality-report-prop :: Root -> Behavior
|
|
|
+
|
|
|
+### Parameters
|
|
|
+- **autoAttach**: true/false
|
|
|
+
|
|
|
+### Default Parameters
|
|
|
+```js
|
|
|
+{
|
|
|
+ "autoAttach": false
|
|
|
+}
|
|
|
+```
|
|
|
+----------------------------
|
|
|
+## <a name="ms-plugin-rcsb-assembly-symmetry-prop"></a>ms-plugin.rcsb-assembly-symmetry-prop :: Root -> Behavior
|
|
|
+
|
|
|
+### Parameters
|
|
|
+- **autoAttach**: true/false
|
|
|
+
|
|
|
+### Default Parameters
|
|
|
+```js
|
|
|
+{
|
|
|
+ "autoAttach": false
|
|
|
+}
|
|
|
+```
|
|
|
+----------------------------
|
|
|
+## <a name="ms-plugin-structure-animation"></a>ms-plugin.structure-animation :: Root -> Behavior
|
|
|
+
|
|
|
+### Parameters
|
|
|
+- **rotate**: true/false
|
|
|
+- **rotateValue**: Numeric value
|
|
|
+- **explode**: true/false
|
|
|
+- **explodeValue**: Numeric value
|
|
|
+
|
|
|
+### Default Parameters
|
|
|
+```js
|
|
|
+{
|
|
|
+ "rotate": false,
|
|
|
+ "rotateValue": 0,
|
|
|
+ "explode": false,
|
|
|
+ "explodeValue": 0
|
|
|
+}
|
|
|
+```
|
|
|
+----------------------------
|
|
|
+## <a name="ms-plugin-scene-labels"></a>ms-plugin.scene-labels :: Root -> Behavior
|
|
|
+
|
|
|
+### Parameters
|
|
|
+- **alpha**: Numeric value
|
|
|
+- **useFog**: true/false
|
|
|
+- **highlightColor**: Color as 0xrrggbb
|
|
|
+- **selectColor**: Color as 0xrrggbb
|
|
|
+- **quality**: One of 'custom', 'auto', 'highest', 'higher', 'high', 'medium', 'low', 'lower', 'lowest'
|
|
|
+- **fontFamily**: One of 'sans-serif', 'monospace', 'serif', 'cursive'
|
|
|
+- **fontQuality**: One of '0', '1', '2', '3', '4'
|
|
|
+- **fontStyle**: One of 'normal', 'italic', 'oblique'
|
|
|
+- **fontVariant**: One of 'normal', 'small-caps'
|
|
|
+- **fontWeight**: One of 'normal', 'bold'
|
|
|
+- **sizeFactor**: Numeric value
|
|
|
+- **borderWidth**: Numeric value
|
|
|
+- **borderColor**: Color as 0xrrggbb
|
|
|
+- **offsetX**: Numeric value
|
|
|
+- **offsetY**: Numeric value
|
|
|
+- **offsetZ**: Numeric value
|
|
|
+- **background**: true/false
|
|
|
+- **backgroundMargin**: Numeric value
|
|
|
+- **backgroundColor**: Color as 0xrrggbb
|
|
|
+- **backgroundOpacity**: Numeric value
|
|
|
+- **attachment**: One of 'bottom-left', 'bottom-center', 'bottom-right', 'middle-left', 'middle-center', 'middle-right', 'top-left', 'top-center', 'top-right'
|
|
|
+- **levels**: Array of 'structure', 'polymer', 'ligand'
|
|
|
+
|
|
|
+### Default Parameters
|
|
|
+```js
|
|
|
+{
|
|
|
+ "alpha": 1,
|
|
|
+ "useFog": true,
|
|
|
+ "highlightColor": 16737945,
|
|
|
+ "selectColor": 3407641,
|
|
|
+ "quality": "auto",
|
|
|
+ "fontFamily": "sans-serif",
|
|
|
+ "fontQuality": 3,
|
|
|
+ "fontStyle": "normal",
|
|
|
+ "fontVariant": "normal",
|
|
|
+ "fontWeight": "normal",
|
|
|
+ "sizeFactor": 1,
|
|
|
+ "borderWidth": 0,
|
|
|
+ "borderColor": 8421504,
|
|
|
+ "offsetX": 0,
|
|
|
+ "offsetY": 0,
|
|
|
+ "offsetZ": 0,
|
|
|
+ "background": true,
|
|
|
+ "backgroundMargin": 0.2,
|
|
|
+ "backgroundColor": 16775930,
|
|
|
+ "backgroundOpacity": 0.9,
|
|
|
+ "attachment": "middle-center",
|
|
|
+ "levels": []
|
|
|
+}
|
|
|
+```
|
|
|
+----------------------------
|
Alexander Rose