Mol* Plugin State Transformer Reference

build-in.root
ms-plugin.download
ms-plugin.read-file
ms-plugin.parse-cif
ms-plugin.parse-ccp4
ms-plugin.parse-dsn6
ms-plugin.trajectory-from-mmcif
ms-plugin.trajectory-from-pdb
ms-plugin.model-from-trajectory
ms-plugin.structure-from-model
ms-plugin.structure-assembly-from-model
ms-plugin.structure-symmetry-from-model
ms-plugin.structure-selection
ms-plugin.structure-complex-element
ms-plugin.custom-model-properties
ms-plugin.volume-from-ccp4
ms-plugin.volume-from-dsn6
ms-plugin.representation-highlight-loci
ms-plugin.representation-select-loci
ms-plugin.default-loci-label-provider
ms-plugin.structure-representation-3d
ms-plugin.explode-structure-representation-3d
ms-plugin.volume-representation-3d
ms-plugin.focus-loci-on-select
ms-plugin.pdbe-structure-quality-report-prop
ms-plugin.rcsb-assembly-symmetry-prop
ms-plugin.structure-animation
ms-plugin.scene-labels

build-in.root :: () -> ()

For internal use.

ms-plugin.download :: Root -> String | Binary

Download string or binary data from the specified URL

Parameters

url: String (Resource URL. Must be the same domain or support CORS.)
label?: String
isBinary?: true/false (If true, download data as binary (string otherwise))

Default Parameters

{
  "url": "https://www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif"
}

ms-plugin.read-file :: Root -> String | Binary

Read string or binary data from the specified file

Parameters

file: JavaScript File Handle
label?: String
isBinary?: true/false (If true, open file as as binary (string otherwise))

Default Parameters

{}

ms-plugin.parse-cif :: String | Binary -> Cif

Parse CIF from String or Binary data

ms-plugin.parse-ccp4 :: Binary -> Ccp4

Parse CCP4/MRC/MAP from Binary data

ms-plugin.parse-dsn6 :: Binary -> Dsn6

Parse CCP4/BRIX from Binary data

ms-plugin.trajectory-from-mmcif :: Cif -> Trajectory

Identify and create all separate models in the specified CIF data block

Parameters

blockHeader?: String (Header of the block to parse. If none is specifed, the 1st data block in the file is used.)

Default Parameters

{}

ms-plugin.trajectory-from-pdb :: String -> Trajectory

ms-plugin.model-from-trajectory :: Trajectory -> Model

Create a molecular structure from the specified model.

Parameters

modelIndex: Numeric value (Zero-based index of the model)

Default Parameters

{
  "modelIndex": 0
}

ms-plugin.structure-from-model :: Model -> Structure

Create a molecular structure from the specified model.

ms-plugin.structure-assembly-from-model :: Model -> Structure

Create a molecular structure assembly.

Parameters

id?: String (Assembly Id. Value 'deposited' can be used to specify deposited asymmetric unit.)

Default Parameters

{}

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

{
  "ijkMin": [
    -1,
    -1,
    -1
  ],
  "ijkMax": [
    1,
    1,
    1
  ]
}

ms-plugin.structure-selection :: Structure -> Structure

Create a molecular structure from the specified query expression.

Parameters

query: Value
label?: String

Default Parameters

{}

ms-plugin.structure-complex-element :: Structure -> Structure

Create a molecular structure from the specified model.

Parameters

type: One of 'atomic-sequence', 'water', 'atomic-het', 'spheres'

Default Parameters

{
  "type": "atomic-sequence"
}

ms-plugin.custom-model-properties :: Model -> Model

Parameters

properties: Array of (A list of property descriptor ids.)

Default Parameters

{
  "properties": []
}

ms-plugin.volume-from-ccp4 :: Ccp4 -> Data

Create Volume from CCP4/MRC/MAP data

Parameters

voxelSize: 3D vector [x, y, z]

Default Parameters

{
  "voxelSize": [
    1,
    1,
    1
  ]
}

ms-plugin.volume-from-dsn6 :: Dsn6 -> Data

Create Volume from DSN6/BRIX data

Parameters

voxelSize: 3D vector [x, y, z]

Default Parameters

{
  "voxelSize": [
    1,
    1,
    1
  ]
}

ms-plugin.representation-highlight-loci :: Root -> Behavior

ms-plugin.representation-select-loci :: Root -> Behavior

ms-plugin.default-loci-label-provider :: Root -> Behavior

ms-plugin.structure-representation-3d :: Structure -> Representation3D

Parameters

type: Object { name: string, params: object } where name+params are:
- cartoon: 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
  - unitKinds: Array of 'atomic', 'spheres', 'gaussians'
  - sizeFactor: Numeric value
  - linearSegments: Numeric value
  - radialSegments: Numeric value
  - aspectRatio: Numeric value
  - arrowFactor: Numeric value
  - visuals: Array of 'polymer-trace', 'polymer-gap', 'nucleotide-block', 'direction-wedge'
- ball-and-stick: 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
  - unitKinds: Array of 'atomic', 'spheres', 'gaussians'
  - sizeFactor: Numeric value
  - detail: Numeric value
  - linkScale: Numeric value
  - linkSpacing: Numeric value
  - radialSegments: Numeric value
  - sizeAspectRatio: Numeric value
  - visuals: Array of 'element-sphere', 'intra-link', 'inter-link'
- carbohydrate: 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
  - unitKinds: Array of 'atomic', 'spheres', 'gaussians'
  - detail: Numeric value
  - sizeFactor: Numeric value
  - linkScale: Numeric value
  - linkSpacing: Numeric value
  - radialSegments: Numeric value
  - linkSizeFactor: Numeric value
  - visuals: Array of 'carbohydrate-symbol', 'carbohydrate-link', 'carbohydrate-terminal-link'
- distance-restraint: 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
  - unitKinds: Array of 'atomic', 'spheres', 'gaussians'
  - linkScale: Numeric value
  - linkSpacing: Numeric value
  - radialSegments: Numeric value
  - sizeFactor: Numeric value
- molecular-surface: 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
  - unitKinds: Array of 'atomic', 'spheres', 'gaussians'
  - resolution: Numeric value
  - radiusOffset: Numeric value
  - smoothness: Numeric value
  - useGpu: true/false
  - ignoreCache: true/false
  - sizeFactor: Numeric value
  - lineSizeAttenuation: true/false
  - visuals: Array of 'gaussian-surface', 'gaussian-wireframe'
- molecular-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'
  - 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'
  - unitKinds: Array of 'atomic', 'spheres', 'gaussians'
  - resolution: Numeric value
  - radiusOffset: Numeric value
  - smoothness: Numeric value
- point: 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'
  - sizeFactor: Numeric value
  - pointSizeAttenuation: true/false
  - pointFilledCircle: true/false
  - pointEdgeBleach: Numeric value
  - unitKinds: Array of 'atomic', 'spheres', 'gaussians'
- spacefill: 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
  - unitKinds: Array of 'atomic', 'spheres', 'gaussians'
  - sizeFactor: Numeric value
  - detail: Numeric value
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

{
  "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
    }
  }
}

ms-plugin.explode-structure-representation-3d :: Representation3D -> Obj

Parameters

t: Numeric value

Default Parameters

{
  "t": 0
}

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: - absolute: Numeric value
  - relative: Numeric value
  - sizeFactor: Numeric value
  - lineSizeAttenuation: true/false
  - visuals: Array of 'solid', 'wireframe'
- 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'
  - 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'
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

{
  "type": {
    "name": "isosurface",
    "params": {
      "alpha": 1,
      "useFog": true,
      "highlightColor": 16737945,
      "selectColor": 3407641,
      "quality": "auto",
      "doubleSided": false,
      "flipSided": false,
      "flatShaded": false,
      "isoValue": {
        "kind": "relative",
        "stats": {
          "min": 0,
          "max": 0,
          "mean": 0,
          "sigma": 0
        },
        "relativeValue": 2
      },
      "sizeFactor": 1,
      "lineSizeAttenuation": false,
      "visuals": [
        "solid"
      ]
    }
  },
  "colorTheme": {
    "name": "uniform",
    "params": {
      "value": 13421772
    }
  },
  "sizeTheme": {
    "name": "uniform",
    "params": {
      "value": 1
    }
  }
}

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

{
  "minRadius": 10,
  "extraRadius": 4
}

ms-plugin.pdbe-structure-quality-report-prop :: Root -> Behavior

Parameters

autoAttach: true/false

Default Parameters

{
  "autoAttach": false
}

ms-plugin.rcsb-assembly-symmetry-prop :: Root -> Behavior

Parameters

autoAttach: true/false

Default Parameters

{
  "autoAttach": false
}

ms-plugin.structure-animation :: Root -> Behavior

Parameters

rotate: true/false
rotateValue: Numeric value
explode: true/false
explodeValue: Numeric value

Default Parameters

{
  "rotate": false,
  "rotateValue": 0,
  "explode": false,
  "explodeValue": 0
}

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

{
  "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": []
}

transforms.md 29 KB تاريخچه خام

Mol* Plugin State Transformer Reference

build-in.root :: () -> ()

ms-plugin.download :: Root -> String | Binary

Parameters

Default Parameters

ms-plugin.read-file :: Root -> String | Binary

Parameters

Default Parameters

ms-plugin.parse-cif :: String | Binary -> Cif

ms-plugin.parse-ccp4 :: Binary -> Ccp4

ms-plugin.parse-dsn6 :: Binary -> Dsn6

ms-plugin.trajectory-from-mmcif :: Cif -> Trajectory

Parameters

Default Parameters

ms-plugin.trajectory-from-pdb :: String -> Trajectory

ms-plugin.model-from-trajectory :: Trajectory -> Model

Parameters

Default Parameters

ms-plugin.structure-from-model :: Model -> Structure

ms-plugin.structure-assembly-from-model :: Model -> Structure

Parameters

Default Parameters

ms-plugin.structure-symmetry-from-model :: Model -> Structure

Parameters

Default Parameters

ms-plugin.structure-selection :: Structure -> Structure

Parameters

Default Parameters

ms-plugin.structure-complex-element :: Structure -> Structure

Parameters

Default Parameters

ms-plugin.custom-model-properties :: Model -> Model

Parameters

Default Parameters

ms-plugin.volume-from-ccp4 :: Ccp4 -> Data

Parameters

Default Parameters

ms-plugin.volume-from-dsn6 :: Dsn6 -> Data

Parameters

Default Parameters

ms-plugin.representation-highlight-loci :: Root -> Behavior

ms-plugin.representation-select-loci :: Root -> Behavior

ms-plugin.default-loci-label-provider :: Root -> Behavior

ms-plugin.structure-representation-3d :: Structure -> Representation3D

Parameters

Default Parameters

ms-plugin.explode-structure-representation-3d :: Representation3D -> Obj

Parameters

Default Parameters

ms-plugin.volume-representation-3d :: Data -> Representation3D

Parameters

Default Parameters

ms-plugin.focus-loci-on-select :: Root -> Behavior

Parameters

Default Parameters

ms-plugin.pdbe-structure-quality-report-prop :: Root -> Behavior

Parameters

Default Parameters

ms-plugin.rcsb-assembly-symmetry-prop :: Root -> Behavior

Parameters

Default Parameters

ms-plugin.structure-animation :: Root -> Behavior

Parameters

Default Parameters

ms-plugin.scene-labels :: Root -> Behavior

Parameters

Default Parameters

transforms.md 29 KB

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