SBVisualPreset#

This class is a base class for visual presets.

Create and apply a visual preset#

# get an indexer of all structural models
structuralModelIndexer = SAMSON.getNodes("n.t sm")

# create a visual preset
visualPresetGroup = SBVisualPresetStep("Receptor-ligand interaction",
  [
    SBVisualPresetStep(
      selectionFilterString = "n.c receptor", selectionFilterName = "Receptor",
      visualModelName = "Ribbons",
      colorSchemeName = "Constant",
      color = SBColor.white),
    SBVisualPresetStep(
      selectionFilterString = "n.c ligand", selectionFilterName = "Ligand",
      visualModelName = "Licorice"),
    SBVisualPresetStep(
      selectionFilterString = "a.s C in (n.t r within 5A of n.c ligand)",
      selectionFilterName = "Carbons in residues with at least one atom within 5A of ligands",
      visualModelName = "",
      colorSchemeName = "Constant",
      color = SBColor.white),
    SBVisualPresetStep(
      selectionFilterString = "n.c heavyAtomsWithLinkingBonds in (n.t r within 5A of n.c ligand)",
      selectionFilterName = "Residues (heavy atoms) with at least one atom within 5A of ligands",
      visualModelName = "Licorice"),
    SBVisualPresetStep(
      selectionFilterString = "n.c water",
      selectionFilterName = "Water",
      hideStructureFlag = True),
    SBVisualPresetStep(
      selectionFilterString = "a.s O in n.c water",
      selectionFilterName = "Water oxygen",
      visualModelName = "Licorice"),
    SBVisualPresetStep(
      selectionFilterString = "n.c monatomicIon",
      selectionFilterName = "Monatomic ions",
      visualModelName = "Van der Waals")
  ]
)

# apply the visual preset
visualPresetGroup.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 describes a visual preset.

Overloaded function.

__init__(self: samson.SBVisualPreset, name: str, visualPresetSteps: list[samson.SBVisualPresetStep] = []) -> None

Constructs a visual preset with the given name and provided visual preset steps.

Parameters:

name (str) – A name for the visual preset
visualPresetSteps (list of samson.SBVisualPresetStep objects) – A list of visual preset steps

__init__(self: samson.SBVisualPreset, visualPreset: samson.SBVisualPreset) -> None

Constructs a visual preset based on the provided visual preset.

Parameters:: visualPreset (samson.SBVisualPreset) – Another visual preset

addVisualPresetStep(self: samson.SBVisualPreset, visualPresetStep: samson.SBVisualPresetStep) → None#

Adds a clone of the visual preset step visualPresetStep to the visual preset.

Parameters:: visualPresetStep (samson.SBVisualPresetStep) – A visual preset step to be added to the visual preset. A clone of the visual preset step is added to the visual preset, since it takes ownership of the visual preset step.

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

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

Parameters:

nodeIndexer (samson.SBNodeIndexer) – An indexer of nodes to which the visual preset should be applied
preferredFolder (samson.SBFolder) – A folder for the created visual models. If None, then a folder will be created based on the visual preset name and it will be added to the active document.

clone(self: samson.SBVisualPreset) → samson.SBVisualPreset#: Returns a copy of the visual preset

deleteVisualPresetStep(self: samson.SBVisualPreset, index: int) → None#

Deletes the visual preset with index index from the visual preset.

Parameters:: index (int) – An index of a visual preset step to be removed from the visual preset.

static getDefaultVisualPresets() → list[samson.SBVisualPreset]#: Returns a list of the default visual presets

getNumberOfVisualPresetSteps(self: samson.SBVisualPreset) → int#: Returns the number of visual preset steps

getVisualPresetSteps(self: samson.SBVisualPreset) → list[samson.SBVisualPresetStep]#: Returns a list of visual preset steps

swap(self: samson.SBVisualPreset, i: int, j: int) → None#

Swaps visual preset steps i and j.

Parameters:

i (int) – An index of a visual preset step.
j (int) – An index of a visual preset step.

property name#: The name of the visual preset

SBVisualPreset

Contents

SBVisualPreset#