SBVisualPreset#

This class is a base class for visual presets.

A visual preset gets several arguments depending on the constructor:

  • A selection: a Node Specification Language (NSL) expression and an arbitrary name for the selection which will be used for naming the visual model if one should be created.

  • A visual model: a name of the visual model or a name of the visual model class and a UUID of its extension.

  • A color scheme: a name of the color scheme or a name of the color scheme class and a UUID of its extension.

  • A color (SBColor) for a constant color scheme or a color palette (SBPalette) for a per-attribute color scheme.

  • A boolean flag indicating whether structural nodes corresponding to the selection should be hidden or shown.

Create and apply a visual preset#
# get an indexer of all structural models
structuralModelIndexer = SAMSON.getNodes("n.t sm")

# create a visual preset
visualPreset = SBVisualPreset(
    # selection
    selectionFilterString = "n.c receptor", selectionFilterName = "Receptor",
    # visual model: Ribbons
    visualModelName = "Ribbons",
    # color scheme
    colorSchemeName = "Constant",
    color = SBColor.white,
    # hiding structural nodes
    hideStructureFlag = False)

# apply the visual preset
visualPreset.apply(structuralModelIndexer)

Please refer to the Applying visual presets page for more information on how to create and apply visual presets.

See also

SAMSON SDK: SBDVisualPreset

class samson.SBVisualPreset(*args, **kwargs)#

Bases: pybind11_object

This class is a base class for visual presets.

Overloaded function.

  1. __init__(self: samson.SBVisualPreset) -> None

Default constructor

  1. __init__(self: samson.SBVisualPreset, selectionFilterString: str, selectionFilterName: str, visualModelName: str = ‘’, hideStructureFlag: bool = True) -> None

Constructs a visual preset based on the given parameters.

Parameters:

  • selectionFilterString (str) – A selection filter - Node Specification Language (NSL) expression string (SAMSON API: Node Specification Language)

  • selectionFilterName (str) – A selection filter name

  • visualModelName (str, default='') – A visual model name. If empty, then no visual model will be applied.

  • hideStructureFlag (bool, default=True) – Whether to hide the structure corresponding to the selection filter

Examples

Create a visual preset for receptors depicted as ribbons

>>> visualPreset = SBVisualPreset(selectionFilterString = "n.c receptor", selectionFilterName = "Receptor", visualModelName = "Ribbons")

  1. __init__(self: samson.SBVisualPreset, selectionFilterString: str, selectionFilterName: str, visualModelClassName: str, visualModelExtensionUUID: samson.SBUUID, hideStructureFlag: bool = True) -> None

Constructs a visual preset based on the given parameters.

Parameters:

  • selectionFilterString (str) – A selection filter - Node Specification Language (NSL) expression string (SAMSON API: Node Specification Language)

  • selectionFilterName (str) – A selection filter name

  • visualModelClassName (str) – A visual model class name

  • visualModelExtensionUUID (samson.SBUUID) – A visual model extension UUID

  • hideStructureFlag (bool, default=True) – Whether to hide the structure corresponding to the selection filter

  1. __init__(self: samson.SBVisualPreset, selectionFilterString: str, selectionFilterName: str, visualModelName: str, colorSchemeName: str, color: samson.SBColor, hideStructureFlag: bool = True) -> None

Constructs a visual preset based on the given parameters.

Parameters:

  • selectionFilterString (str) – A selection filter - Node Specification Language (NSL) expression string (SAMSON API: Node Specification Language)

  • selectionFilterName (str) – A selection filter name

  • visualModelName (str) – A visual model name

  • colorSchemeName (str) – A name of a constant color scheme: Constant, ConstantIllustrate, CPK

  • color (samson.SBColor) – A color for the color scheme

  • hideStructureFlag (bool, default=True) – Whether to hide the structure corresponding to the selection filter

Examples

Create a visual preset for receptors depicted as van der Waals

>>> visualPreset = SBVisualPreset(selectionFilterString = "n.c receptor", selectionFilterName = "Receptor", visualModelName = "Van der Waals", colorSchemeName = "ConstantIllustrate", color = SBColor(255, 255, 255))

  1. __init__(self: samson.SBVisualPreset, selectionFilterString: str, selectionFilterName: str, visualModelClassName: str, visualModelExtensionUUID: samson.SBUUID, colorSchemeClassName: str, colorSchemeExtensionUUID: samson.SBUUID, color: samson.SBColor, hideStructureFlag: bool = True) -> None

Constructs a visual preset based on the given parameters.

Parameters:

  • selectionFilterString (str) – A selection filter - Node Specification Language (NSL) expression string (SAMSON API: Node Specification Language)

  • selectionFilterName (str) – A selection filter name

  • visualModelClassName (str) – A visual model class name

  • visualModelExtensionUUID (samson.SBUUID) – A visual model extension UUID

  • colorSchemeClassName (str) – A class name of a constant color scheme: SBDColorSchemeConstant, SBDColorSchemeConstantIllustrate, SBDColorSchemeCPK

  • colorSchemeExtensionUUID (samson.SBUUID) – A color scheme extension UUID

  • color (samson.SBColor) – A color for the color scheme

  • hideStructureFlag (bool, default=True) – Whether to hide the structure corresponding to the selection filter

  1. __init__(self: samson.SBVisualPreset, selectionFilterString: str, selectionFilterName: str, visualModelName: str, colorSchemeName: str, colorPalette: samson.SBPalette = None, hideStructureFlag: bool = True) -> None

Constructs a visual preset based on the given parameters.

Parameters:

  • selectionFilterString (str) – A selection filter - Node Specification Language (NSL) expression string (SAMSON API: Node Specification Language)

  • selectionFilterName (str) – A selection filter name

  • visualModelName (str) – A visual model name

  • colorSchemeName (str) – A name of a color scheme that uses a color palette (e.g. PerChainIllustrate, PerFormalCharge, etc.)

  • colorPalette (samson.SBPalette, default=None) – A color palette for the color scheme. If None, then the default color palette associated with this color scheme will be used.

  • hideStructureFlag (bool, default=True) – Whether to hide the structure corresponding to the selection filter

Examples

Create a visual preset for receptors depicted as ribbons

>>> visualPreset = SBVisualPreset(selectionFilterString = "n.c receptor", selectionFilterName = "Receptor", visualModelName = "Ribbons", colorSchemeName = "PerSecondaryStructureType", colorPalette = SBPaletteDefaultPalette.qualitativeHCLDynamic)

  1. __init__(self: samson.SBVisualPreset, selectionFilterString: str, selectionFilterName: str, visualModelClassName: str, visualModelExtensionUUID: samson.SBUUID, colorSchemeClassName: str, colorSchemeExtensionUUID: samson.SBUUID, colorPalette: samson.SBPalette = None, hideStructureFlag: bool = True) -> None

Constructs a visual preset based on the given parameters.

Parameters:

  • selectionFilterString (str) – A selection filter - Node Specification Language (NSL) expression string (SAMSON API: Node Specification Language)

  • selectionFilterName (str) – A selection filter name

  • visualModelClassName (str) – A visual model class name

  • visualModelExtensionUUID (samson.SBUUID) – A visual model extension UUID

  • colorSchemeClassName (str) – A class name of a color scheme that uses a color palette (e.g. SBDColorSchemePerChainIllustrate, SBDColorSchemePerFormalCharge, etc.)

  • colorSchemeExtensionUUID (samson.SBUUID) – A color scheme extension UUID

  • colorPalette (samson.SBPalette, default=None) – A color palette for the color scheme. If None, then the default color palette associated with this color scheme will be used.

  • hideStructureFlag (bool, default=True) – Whether to hide the structure corresponding to the selection filter

apply(self: samson.SBVisualPreset, nodeIndexer: samson.SBNodeIndexer, preferredFolder: samson.SBFolder = None) → None#

Applies the visual preset to nodes in nodeIndexer and adds the visual models (if any) to preferredFolder.

Parameters:

  • nodeIndexer (samson.SBNodeIndexer) – An indexer of nodes to which the visual preset group should be applied

  • preferredFolder (samson.SBFolder, default=None) – A folder for the created visual models. If None, then the visual model will be added to the active document.

clearColor(self: samson.SBVisualPreset) → None#

Clears the color

clearColorScheme(self: samson.SBVisualPreset) → None#

Clears the color scheme

clearSelectionFilter(self: samson.SBVisualPreset) → None#

Clears the selection filter

clearSelector(self: samson.SBVisualPreset) → None#

Clears the selector

clearVisualModel(self: samson.SBVisualPreset) → None#

Clears the visual model

clone(self: samson.SBVisualPreset) → samson.SBVisualPreset#

Returns a copy of the visual preset

static createColorScheme(colorSchemeClassName: str, nodeIndexer: samson.SBNodeIndexer, colorPalette: samson.SBPalette) → samson.SBNodeColorScheme#

Creates a color scheme colorSchemeClassName

getColor(self: samson.SBVisualPreset) → samson.SBColor#

Returns the color

getColorSchemeProxy(self: samson.SBVisualPreset) → samson.SBProxy#

Returns a proxy to the color scheme

getDefaultColorPaletteForCurrentColorScheme(self: samson.SBVisualPreset) → samson.SBPalette#

Returns the default color palette of the color scheme

getPalette(self: samson.SBVisualPreset) → samson.SBPalette#

Returns the color palette

getSelectorProxy(self: samson.SBVisualPreset) → samson.SBProxy#

Returns a proxy to the selector

getVisualModelProxy(self: samson.SBVisualPreset) → samson.SBProxy#

Returns a proxy to the visual model

static isPerAttributeColorScheme(colorSchemeClassName: str) → bool#

Returns True if the color scheme colorSchemeClassName is a per-attribute color scheme

resetPalette(self: samson.SBVisualPreset) → None#

Sets the color palette to the default color palette for this color scheme

setColor(self: samson.SBVisualPreset, color: samson.SBColor) → None#

Sets the color

setColorSchemeProxy(self: samson.SBVisualPreset, colorSchemeProxy: samson.SBProxy) → None#

Sets the color scheme by proxy

setPalette(self: samson.SBVisualPreset, colorPalette: samson.SBPalette) → None#

Sets the color palette

setSelectionFilter(self: samson.SBVisualPreset, arg0: str, arg1: str) → None#

Sets the selection filter string and name

setSelectorProxy(self: samson.SBVisualPreset, selectorProxy: samson.SBProxy) → None#

Sets the selector by proxy

setVisualModelProxy(self: samson.SBVisualPreset, visualModelProxy: samson.SBProxy) → None#

Sets the visual model by proxy

property colorSchemeClassName#

Returns the color scheme’s class name

property colorSchemeExtensionUUID#

Returns the color scheme’s extension UUID

property hasColor#

Returns True if the visual preset has a color

property hasColorScheme#

Returns True if the visual preset has a color scheme

property hasDefaultPalette#

Returns True if the color scheme has a default color palette

property hasSelector#

Returns True if the visual preset has a selector

property hasVisualModel#

Returns True if the visual preset has a visual model

property hideStructureFlag#

The hide structure flag

property selectionFilterName#

Returns the selection filter name

property selectionFilterString#

Returns the selection filter string

property selectorClassName#

Returns the selector’s class name

property selectorExtensionUUID#

Returns the selector’s extension UUID

property visualModelClassName#

Returns the visual model’s class name

property visualModelExtensionUUID#

Returns the visual model’s extension UUID