OE2DActiveSiteDisplayOptions

class OE2DActiveSiteDisplayOptions: public OEDepict::OE2DMolDisplayOptions

This class represents the OE2DActiveSiteDisplayOptions class that encapsulates properties that determine how an active site is depicted.

The following methods are publicly inherited from OE2DMolDisplayOptions:

`operator=`	`GetDefaultBondPen`	`SetBondColorStyle`
`GetAromaticStyle`	`GetHeight`	`SetBondLineAtomLabelGapScale`
`GetAtomColor`	`GetHydrogenStyle`	`SetBondLineGapScale`
`GetAtomColorStyle`	`GetScale`	`SetBondPropLabelFont`
`GetAtomLabelFont`	`GetSuperAtomLabelFont`	`SetBondPropLabelFontScale`
`GetAtomLabelFontScale`	`GetSuperAtomStyle`	`SetBondPropertyFunctor`
`GetAtomPropLabelFont`	`GetTitleFont`	`SetBondStereoStyle`
`GetAtomPropLabelFontScale`	`GetTitleLocation`	`SetBondWidthScaling`
`GetAtomPropertyFunctor`	`GetWidth`	`SetDefaultBondPen`
`GetAtomStereoStyle`	`SetAromaticStyle`	`SetDimensions`
`GetBackgroundColor`	`SetAtomColor`	`SetHeight`
`GetBondColorStyle`	`SetAtomColorStyle`	`SetHydrogenStyle`
`GetBondLineAtomLabelGapScale`	`SetAtomLabelFont`	`SetScale`
`GetBondLineGapScale`	`SetAtomLabelFontScale`	`SetSuperAtomLabelFont`
`GetBondPropLabelFont`	`SetAtomPropLabelFont`	`SetSuperAtomStyle`
`GetBondPropLabelFontScale`	`SetAtomPropLabelFontScale`	`SetTitleFont`
`GetBondPropertyFunctor`	`SetAtomPropertyFunctor`	`SetTitleLocation`
`GetBondStereoStyle`	`SetAtomStereoStyle`	`SetWidth`
`GetBondWidthScaling`	`SetBackgroundColor`

Code Example

Depicting Active Site Interactions example
Visualizing Protein-Ligand Interactions OpenEye Python Cookbook recipe

Constructors

OE2DActiveSiteDisplayOptions(width: float, height: float) -> OE2DActiveSiteDisplayOptions

Creates an OE2DActiveSiteDisplayOptions object with the specified dimension.

width, height: The width and height of the active site display. Both numbers have to be at least 200.0.

OE2DActiveSiteDisplayOptions(rhs: OE2DActiveSiteDisplayOptions) -> OE2DActiveSiteDisplayOptions

Copy constructor.

GetLigandAlignerFunctor

GetLigandAlignerFunctor() -> OELigandAlignerBase

Returns the functor that is used to align ligands in the active site display. By default, the functor is set to OENoOpLigandAligner.

See also

OE2DActiveSiteDisplayOptions.SetLigandAlignerFunctor method

GetOptimizeLigandOrientation

GetOptimizeLigandOrientation() -> bool

Returns whether the ligand orientation is optimized after generated the 2D layout. The default value is true.

See also

OE2DActiveSiteDisplayOptions.SetOptimizeLigandOrientation method

GetRenderInteractiveLegend

GetRenderInteractiveLegend() -> bool

Returns whether and interactive legend is rendered only when mouse is hovered over the “Legend” button depicted on the right top corner on the active site depiction.

See also

OE2DActiveSiteDisplayOptions.SetRenderInteractiveLegend method

GetResidueSVGMarkupFunctor

GetResidueSVGMarkupFunctor() -> OEResidueSVGMarkupBase

Returns the functor that defines how the residues are marked in svg image. By default, residues are not marked (OEResidueSVGNoMarkup).

See also

OE2DActiveSiteDisplayOptions.SetResidueSVGMarkupFunctor method

GetSVGMagnifyResidueInHover

GetSVGMagnifyResidueInHover() -> float

Returns the scaling factor that is used to magnify residue glyphs when mouse is hover over them.

See also

OE2DActiveSiteDisplayOptions.SetSVGMagnifyResidueInHover method

SetBackgroundColor

SetBackgroundColor(arg2: OEColor) -> None

This is a no-op method. The background of the active site display is always OEWhite

SetDimensions

SetDimensions(arg2: float, arg3: float, arg4: float) -> None

This is a no-op method. The dimension of the active site display only be specified with the OE2DActiveSiteDisplayOptions constructor.

SetHeight

SetHeight(arg2: float) -> None

This is a no-op method. The height of the active site display can only be specified with the OE2DActiveSiteDisplayOptions constructor.

SetLigandAlignerFunctor

SetLigandAlignerFunctor(func: OELigandAlignerBase) -> None

Sets the functor that can be used to custom align ligands in the active site display.

Hint

Turning off optimization of ligand orientation is also recommended for custom alignments with OE2DActiveSiteDisplayOptions.SetOptimizeLigandOrientation method.

See also

OELigandAlignerBase abstract base class

SetOptimizeLigandOrientation

SetOptimizeLigandOrientation(optimize: bool) -> None

Sets whether the ligand orientation is optimized after generated the 2D layout to maximize scaling for the depiction.

Hint

Its is recommended to disable this feature when using custom ligand alignment.

SetRenderInteractiveLegend

SetRenderInteractiveLegend(render: bool) -> None

Sets whether and interactive legend is rendered only when mouse is hovered over the “Legend” button depicted on the right top corner on the active site depiction.

Note

This functionality is only available for .svg image format. In other image formats it has no effect.

SetResidueSVGMarkupFunctor

SetResidueSVGMarkupFunctor(func: OEResidueSVGMarkupBase) -> None

Sets the functor that defines how the residues are marked in svg image. Drawing elements representing residues in svg image are grouped together in the following format in which the <group id> and <class name> strings are defined by the given functor:

<g id='<group id>' class='<class name>'>
..
list of drawing elements
..
</g>

Note

This setting has only effect when generating .svg images.

Example:

asite = oechem.OEInteractionHintContainer(protein, ligand)
oechem.OEPerceiveInteractionHints(asite)
oegrapheme.OEPrepareActiveSiteDepiction(asite)


opts = oegrapheme.OE2DActiveSiteDisplayOptions(800.0, 600.0)
opts.SetResidueSVGMarkupFunctor(oegrapheme.OEResidueSVGStandardMarkup())
adisp = oegrapheme.OE2DActiveSiteDisplay(asite, opts)

oegrapheme.OERenderActiveSite("SVGMarkResidues.svg", adisp)

See also

OEResidueSVGMarkupBase abstract base class
OEResidueSVGNoMarkup class
OEResidueSVGStandardMarkup class
OE2DActiveSiteDisplayOptions.GetResidueSVGMarkupFunctor method

SetSVGMagnifyResidueInHover

SetSVGMagnifyResidueInHover(scale: float) -> None

Sets the scaling factor that is used to magnify residue glyphs when mouse is hover over them.

scale: This value has to be in a range of [1.00, 3.00]. The default value is 1.00 which has has no effect.

Hint

This is a very useful feature when generating an active site image with residue labels that are too small to read.

Note

This functionality is only available for .svg image format. In other image formats it has no effect.

SetScale

SetScale(arg2: float) -> None

This is a no-op method. The active site display can not be scaled.

SetSuperAtomStyle

SetSuperAtomStyle(arg2: int) -> None

This is a no-op method. The super atom style can not be used when depicting an active site.

SetWidth

SetWidth(arg2: float) -> None

This is a no-op method. The width of the active site display can only be specified with the OE2DActiveSiteDisplayOptions constructor.