OE2DMolDisplayOptions¶

class OE2DMolDisplayOptions

This class represents the OE2DMolDisplayOptions class that encapsulates properties that determine how a molecule is depicted.

The OE2DMolDisplayOptions class stores the following properties:

Property	Get method	Set method	Corresponding namespace / class / type
aromatic style	`GetAromaticStyle`	`SetAromaticStyle`	`OEAromaticStyle`
atomic number colors	`GetAtomColor`	`SetAtomColor`	OEColor
atom color style	`GetAtomColorStyle`	`SetAtomColorStyle`	`OEAtomColorStyle`
atom label font	`GetAtomLabelFont`	`SetAtomLabelFont`	OEFont
atom label font scale	`GetAtomLabelFontScale`	`SetAtomLabelFontScale`	positive floating point number in the range of `[0.5, 3.0]` or `0.0`
atom property font	`GetAtomPropLabelFont`	`SetAtomPropLabelFont`	OEFont
atom property label font scale	`GetAtomPropLabelFontScale`	`SetAtomPropLabelFontScale`	positive floating point number in the range of `[0.5, 2.0]`
atom property initializer	`GetAtomPropertyFunctor`	`SetAtomPropertyFunctor`	OEDisplayAtomPropBase
atom stereo style	`GetAtomStereoStyle`	`SetAtomStereoStyle`	`OEAtomStereoStyle`
atom SVG markup	`GetAtomSVGMarkupFunctor`	`SetAtomSVGMarkupFunctor`	OEAtomSVGMarkupBase
atom visibility initializer	`GetAtomVisibilityFunctor`	`SetAtomVisibilityFunctor`	`OEUnaryAtomPred`
background color	`GetBackgroundColor`	`SetBackgroundColor`	OEColor
bond color style	`GetBondColorStyle`	`SetBondColorStyle`	`OEBondColorStyle`
bond line gap scale	`GetBondLineGapScale`	`SetBondLineGapScale`	positive floating point number in the range of `[0.5, 2.0]`
bond line atom label gap scale	`GetBondLineAtomLabelGapScale`	`SetBondLineAtomLabelGapScale`	positive floating point number in the range of `[0.5, 2.0]`
bond property font	`GetBondPropLabelFont`	`SetBondPropLabelFont`	OEFont
bond property label font scale	`GetBondPropLabelFontScale`	`SetBondPropLabelFontScale`	positive floating point number in the range of `[0.5, 2.0]`
bond property initializer	`GetBondPropertyFunctor`	`SetBondPropertyFunctor`	OEDisplayBondPropBase
bond stereo style	`GetBondStereoStyle`	`SetBondStereoStyle`	`OEBondStereoStyle`
bond pen	`GetDefaultBondPen`	`SetDefaultBondPen`	OEPen
bond width scaling	`GetBondWidthScaling`	`SetBondWidthScaling`	boolean
bond SVG markup	`GetBondSVGMarkupFunctor`	`SetBondSVGMarkupFunctor`	OEBondSVGMarkupBase
explicit atom label angle	`GetExplicitAtomLabelAngle`	`SetExplicitAtomLabelAngle`	positive floating point number in the range of `[120.0, 180.0]`
height	`GetHeight`	`SetHeight`	positive floating point number
hydrogen style	`GetHydrogenStyle`	`SetHydrogenStyle`	`OEHydrogenStyle`
margin(s)	`GetMargin`	`SetMargin`, `SetMargins`	positive floating point number in the range of `[2.5, 25.0]`
scale	`GetScale`	`SetScale`	positive floating point number
super atom label font	`GetSuperAtomLabelFont`	`SetSuperAtomLabelFont`	OEFont
super atom display style	`GetSuperAtomStyle`	`SetSuperAtomStyle`	`OESuperAtomStyle`
protective group label font	`GetProtectiveGroupLabelFont`	`SetProtectiveGroupLabelFont`	OEFont
protective group display style	`HasProtectiveGroupStyle`	`SetProtectiveGroupStyle`	`OEProtectiveGroupStyle`
title font	`GetTitleFont`	`SetTitleFont`	OEFont
title font scale	`GetTitleFontScale`	`SetTitleFontScale`	positive floating point number in the range of `[0.5, 2.0]` or `0.0`
title height	`GetTitleHeight`	`SetTitleHeight`	`OETitleLocation`
title location	`GetTitleLocation`	`SetTitleLocation`	`OETitleLocation`
width	`GetWidth`	`SetWidth`	positive floating point number

The images below illustrate the three possible molecule display layouts depending on the position of the title. These layouts can be controlled by the following parameters:

The width and the height can be set either by the constructor of the OE2DMolDisplayOptions class, by calling the OE2DMolDisplayOptions.SetDimensions method or by the SetWidth and SetHeight methods, respectively.
The location of the title area (blue box) can be set by the SetTitleLocation method. The height of the title area (blue arrows) can be modified by invoking the SetTitleHeight method.
The padding around the molecule (red arrows) can be changed by calling either the SetMargin or the SetMargins methods.

**Example of molecule display layouts depending on position of the title**¶
title hidden	title at the top	title at the bottom

See also

OE2DMolDisplay class
Controlling the Size of Depicted Molecules section

Hint

Even though OEDepict TK provides access to manipulate the properties of the atom and bond displays after the OE2DMolDisplay object is constructed, it is highly recommended to determine the style of the depiction by using the OE2DMolDisplayOptions class. Only by knowing all properties (such as labels, font styles and sizes etc.) in advance can ensure the best depiction layout i.e. that the molecule diagram is rendered without any label clippings and the labels are displayed with the minimum number of overlaps.

Constructors¶

OE2DMolDisplayOptions()

Default constructor that initializes an OE2DMolDisplayOptions object with the following properties:

See example in Molecule depiction with default options)

**Default parameters of OE2DMolDisplayOptions**¶
Property	Default value
aromatic style	`OEAromaticStyle.Default`
atomic number colors	initialized based on `OEAtomColorStyle.Default`
atom color style	`OEAtomColorStyle.Default`
atom label font	`OEDepict.OEDefaultFont`
atom label font scale	1.0
atom property font	OEFont(OEColor(75, 75, 75))
atom property label font scale	1.0
atom property initializer	OEDisplayNoAtomProp
atom stereo style	`OEAtomStereoStyle.Default`
atom SVG markup	OEAtomSVGNoMarkup
atom visibility initializer	`OEIsTrueAtom`
background color	`OEDepict.OELightBackgroundColor` initialized based on `OEAtomColorStyle.Default`
bond color style	`OEBondColorStyle.Default`
bond line gap scale	1.0
bond line atom label gap scale	1.0
bond property font	OEFont(OEColor(75, 75, 75))
bond property label font scale	1.0
bond property initializer	OEDisplayNoBondProp
bond stereo style	`OEBondStereoStyle.Default`
bond pen	`OEDepict.OEBlackPen`
bond width scaling	false
bond SVG markup	OEBondSVGNoMarkup
explicit atom label angle	170.0 (degree)
height	0.0 (initialized based on scale)
hydrogen style	`OEHydrogenStyle.Default`
margins	left and right margin 5.0% of the width; top and bottom margin 5.0% of the height of the molecule display
scale	`OEScale.AutoScale`
super atom label font	OEFont(OEPink)
super atom display style	`OESuperAtomStyle.Default`
protective group label font	OEFont(OEPink)
protective group display style	`OEProtectiveGroupStyle.Default`
title font	`OEDepict.OEDefaultFont`
title font scale	1.0
title location	`OETitleLocation.Default`
title height	10% of the height of the molecule display
width	0.0 (initialized based on scale)

../../_images/OE2DMolDisplayOptions_Default.png

Molecule depiction with default options¶

OE2DMolDisplayOptions(double scale)

Creates an OE2DMolDisplayOptions object with the specified scaling.

scale: A non-negative number that controls the magnification of the depicted molecule.

OE2DMolDisplayOptions(double width, double height, double scale)

Creates an OE2DMolDisplayOptions object with the specified dimension and scaling.

OE2DMolDisplayOptions(const OE2DMolDisplayOptions &rhs)

Copy constructor.

operator=¶

OE2DMolDisplayOptions &operator=(const OE2DMolDisplayOptions &rhs)

Assignment operator.

GetAromaticStyle¶

unsigned int GetAromaticStyle() const

Returns the style that controls how aromatic rings are displayed. The return value is taken from the OEAromaticStyle namespace.

See also

OE2DMolDisplayOptions.SetAromaticStyle method
OEAromaticStyle namespace

GetAtomSVGMarkupFunctor¶

const OEAtomSVGMarkupBase &GetAtomSVGMarkupFunctor() const

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

See also

OE2DMolDisplayOptions.SetAtomSVGMarkupFunctor method

GetAtomColor¶

const OESystem::OEColor &GetAtomColor(unsigned int atomic) const

Returns the color associated with a specific atomic number.

See also

OE2DMolDisplayOptions.SetAtomColor method
OEColor class
Appendix: Element coloring (CPK) section

GetAtomColorStyle¶

unsigned int GetAtomColorStyle() const

Returns the style that is used to define the color of the background and the default color of atom labels. The return value is taken from the OEAtomColorStyle namespace.

See also

OE2DMolDisplayOptions.SetAtomColorStyle method
OEAtomColorStyle namespace

GetAtomLabelFont¶

const OEFont &GetAtomLabelFont() const

Returns the font that is used to initialize the depiction style of the atom labels (OE2DAtomDisplay.GetLabelFont).

See also

OE2DMolDisplayOptions.SetAtomLabelFont method
OE2DMolDisplayOptions.SetAtomLabelFontScale method
OEFont class

GetAtomLabelFontScale¶

double GetAtomLabelFontScale() const

Returns the multiplier that can be used to increase or decrease the size of the atom label fonts.

See also

OE2DMolDisplayOptions.SetAtomLabelFont method
OE2DMolDisplayOptions.SetAtomLabelFontScale method

GetAtomPropLabelFont¶

const OEFont &GetAtomPropLabelFont() const

Returns the font that is used to initialize the depiction style of the atom property labels (OE2DAtomDisplay.GetPropertyFont).

See also

OE2DMolDisplayOptions.SetAtomPropLabelFont method
OEFont class

GetAtomPropLabelFontScale¶

double GetAtomPropLabelFontScale() const

Returns the multiplier that can be used to increase or decrease the size of the atom property label fonts.

See also

OE2DMolDisplayOptions.SetAtomPropLabelFont method
OE2DMolDisplayOptions.SetAtomPropLabelFontScale method

GetAtomPropertyFunctor¶

const OEDisplayAtomPropBase &GetAtomPropertyFunctor() const

Returns the functor that is used to initialize the atom property labels (OE2DAtomDisplay.GetProperty).

See also

OE2DMolDisplayOptions.SetAtomPropertyFunctor method
OEDisplayAtomPropBase class
OEDisplayAtomIdx class
OEDisplayAtomMapIdx class
OEDisplayNoAtomProp class

GetAtomVisibilityFunctor¶

const OESystem::OEUnaryPredicate<OEChem::OEAtomBase> &GetAtomVisibilityFunctor() const

Returns the functor that is used to identify visible atoms. The default functor is the OEIsTrueAtom class which results in all atoms being displayed.

See also

OE2DMolDisplayOptions.SetAtomVisibilityFunctor method
OEUnaryAtomPred

GetAtomStereoStyle¶

unsigned int GetAtomStereoStyle() const

Returns the style that controls what atom stereo information is displayed. The return value is taken from the OEAtomStereoStyle namespace.

See also

OE2DMolDisplayOptions.SetAtomStereoStyle method
OEAtomStereoStyle namespace

GetBackgroundColor¶

const OESystem::OEColor &GetBackgroundColor() const

Returns the color that is used to clear the background of an image (by calling OEImageBase.Clear method) before rendering the molecule.

See also

OE2DMolDisplayOptions.SetBackgroundColor method
OEColor class
OERenderMolecule function

GetBondColorStyle¶

unsigned int GetBondColorStyle() const

Returns the style that controls how bonds are colored. The return value is taken from the OEBondColorStyle namespace.

See also

OE2DMolDisplayOptions.SetBondColorStyle method
OEBondColorStyle namespace

GetBondLineGapScale¶

double GetBondLineGapScale() const

Returns the multiplier that can be used to increase or decrease the gap between the lines of double and triple bonds.

See also

OE2DMolDisplayOptions.SetBondLineGapScale method

GetBondLineAtomLabelGapScale¶

double GetBondLineAtomLabelGapScale() constant

Returns the multiplier that can be used to increase or decrease the gap between the line(s) of bonds and the adjacent atom labels.

See also

OE2DMolDisplayOptions.SetBondLineAtomLabelGapScale method

GetBondPropLabelFont¶

const OEFont &GetBondPropLabelFont() const

Returns the font that is used to initialize the depiction style of the bond property labels (OE2DBondDisplay.GetPropertyFont).

See also

OE2DMolDisplayOptions.SetBondPropLabelFont method
OEFont class

GetBondPropLabelFontScale¶

double GetBondPropLabelFontScale() const

Returns the multiplier that can be used to increase or decrease the size of the bond property label fonts.

See also

OE2DMolDisplayOptions.SetBondPropLabelFont method
OE2DMolDisplayOptions.SetBondPropLabelFontScale method

GetBondPropertyFunctor¶

const OEDisplayBondPropBase &GetBondPropertyFunctor() const

Returns the functor that is used to initialize the bond property labels (OE2DBondDisplay.GetProperty).

See also

OE2DMolDisplayOptions.SetBondPropertyFunctor method
OEDisplayBondPropBase class
OEDisplayBondIdx class
OEDisplayNoBondProp class

GetBondStereoStyle¶

unsigned int GetBondStereoStyle() const

Returns the style that controls what bond stereo information is displayed. The return value is taken from the OEBondStereoStyle namespace.

See also

OE2DMolDisplayOptions.SetBondStereoStyle method
OEBondStereoStyle namespace

GetBondSVGMarkupFunctor¶

const OEBondSVGMarkupBase &GetBondSVGMarkupFunctor() const

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

See also

OE2DMolDisplayOptions.SetBondSVGMarkupFunctor method

GetBondWidthScaling¶

bool GetBondWidthScaling() const

Returns whether the line width of the bond are increase or decreased based on the molecule scaling factor (OE2DMolDisplayOptions.GetScale)

See also

OE2DMolDisplayOptions.SetBondWidthScaling method

GetDefaultBondPen¶

const OEPen &GetDefaultBondPen() const

Returns the pen that is used to initialize the bond pens (OE2DBondDisplay.GetBgnPen and OE2DBondDisplay.GetBgnPen).

See also

OE2DMolDisplayOptions.SetDefaultBondPen method
OEPen class

GetExplicitAtomLabelAngle¶

double GetExplicitAtomLabelAngle() const

In the case of an almost linear X-C-X bond, an explicit “C” label will be drawn if the angle is more that the returned value of this function. 180.0 degree means that the “C” label will never be drawn.

See also

OE2DMolDisplayOptions.SetExplicitAtomLabelAngle method

GetHeight¶

double GetHeight() const

Returns the vertical limit into which the molecule has to be fitted.

See also

OE2DMolDisplayOptions.SetDimensions method
OE2DMolDisplayOptions.SetHeight method

GetHydrogenStyle¶

unsigned int GetHydrogenStyle() const

Returns the style that controls of how implicit and explicit hydrogens are displayed. The return value is taken from the OEHydrogenStyle namespace.

See also

OE2DMolDisplayOptions.SetHydrogenStyle method
OEHydrogenStyle namespace

GetMargin¶

double GetMargin(unsigned int margin) const

Returns the ratio of a specific margin of the OE2DMolDisplayOptions object.

margin: This value has to be from the OEMargin namespace.

See also

OE2DMolDisplayOptions.SetMargin method
OE2DMolDisplayOptions.SetMargins method
OEMargin namespace

GetProtectiveGroupLabelFont¶

const OEFont &GetProtectiveGroupLabelFont() const

Returns the font that is used to display the protective group labels.

See also

OE2DMolDisplayOptions.SetProtectiveGroupLabelFont method
OE2DMolDisplayOptions.SetProtectiveGroupStyle method
OE2DMolDisplayOptions.SetSuperAtomStyle method
OEFont class

GetProtectiveGroupStyle¶

unsigned int GetProtectiveGroupStyle() const

Returns the style that controls whether or not specific pre-defined protective group are contracted and labeled with corresponding abbreviations. The return value is taken from the OEProtectiveGroupStyle namespace.

See also

OE2DMolDisplayOptions.HasProtectiveGroupStyle method
OE2DMolDisplayOptions.SetProtectiveGroupStyle method
OE2DMolDisplayOptions.SetProtectiveGroupLabelFont method
OE2DMolDisplayOptions.SetSuperAtomStyle method
OESuperAtomStyle namespace

Warning

This is a deprecated API. Please use OE2DMolDisplayOptions.HasProtectiveGroupStyle to determine which protective groups are set.

GetScale¶

double GetScale() const

Returns the scaling factor used to magnify a molecule.

See also

OE2DMolDisplayOptions.SetDimensions method
OE2DMolDisplayOptions.SetScale method

GetSuperAtomLabelFont¶

const OEFont &GetSuperAtomLabelFont() const

Returns the font that is used to display the abbreviations of contracted functional groups.

See also

OE2DMolDisplayOptions.SetSuperAtomLabelFont method
OE2DMolDisplayOptions.SetSuperAtomStyle method
OE2DMolDisplayOptions.SetProtectiveGroupStyle method
OEFont class

GetSuperAtomStyle¶

unsigned int GetSuperAtomStyle() const

Returns the style that controls whether or not specific pre-defined functional groups are contracted and labeled with corresponding abbreviations. The return value is taken from the OESuperAtomStyle namespace.

See also

OE2DMolDisplayOptions.SetSuperAtomStyle method
OE2DMolDisplayOptions.SetSuperAtomLabelFont method
OE2DMolDisplayOptions.SetProtectiveGroupStyle method
OESuperAtomStyle namespace

GetTitleFont¶

Returns the font that is used to display the title of the molecule (i.e. the string returned by the OEMolBase.GetTitle method).

const OEFont &GetTitleFont() const

See also

OE2DMolDisplayOptions.SetTitleFont method
OE2DMolDisplayOptions.SetTitleFontScale method
OEFont class

GetTitleFontScale¶

Returns the multiplier that can be used to increase or decrease the size of the title font.

double GetTitleFontScale() const

See also

OE2DMolDisplayOptions.SetTitleFontScale method
OE2DMolDisplayOptions.SetTitleFont method

GetTitleLocation¶

unsigned int GetTitleLocation() const

Returns the position of the molecule title. The return value is taken from the OETitleLocation namespace.

See also

OE2DMolDisplayOptions.SetTitleLocation method
OETitleLocation namespace

GetTitleHeight¶

double GetTitleHeight() const

Returns the height of the title area.

See also

OE2DMolDisplayOptions.SetTitleHeight method

GetWidth¶

double GetWidth() const

Returns the horizontal limit into which the molecule has to be fitted.

See also

OE2DMolDisplayOptions.SetDimensions method
OE2DMolDisplayOptions.SetWidth method

HasProtectiveGroupStyle¶

bool HasProtectiveGroupStyle(unsigned int style)

Returns true if the specific pre-defined protective group style is contracted and labeled with corresponding abbreviations.

style: This value has to be from the OEProtectiveGroupStyle namespace.

SetAromaticStyle¶

void SetAromaticStyle(unsigned int style)

Sets the style that controls how aromatic rings are displayed.

style: This value has to be from the OEAromaticStyle namespace.

Example: (Figure: Example of using the SetAromaticStyle method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetAromaticStyle(OEAromaticStyle.Circle);

../../_images/OE2DMolDisplayOptions_SetAromaticStyle.png

Example of using the SetAromaticStyle method¶

See also

OE2DMolDisplayOptions.GetAromaticStyle method
OEAromaticStyle namespace

SetAtomColor¶

void SetAtomColor(unsigned int atomic, const OESystem::OEColor &color)

Sets the color associated with a specific atomic number.

atomic: This value has to be from the OEElemNo namespace of OEChem TK.
color: The color being associated with the given atomic number.

Example: (Figure: Example of using the SetAtomColor method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetAtomColor(OEElemNo.O, new OEColor(80, 0, 0)); // very dark red
opts.SetAtomColor(OEElemNo.N, new OEColor(0, 0, 80)); // very dark blue

../../_images/OE2DMolDisplayOptions_SetAtomColor.png

Example of using the SetAtomColor method¶

See also

OE2DMolDisplayOptions.GetAtomColor method
OEColor class
Appendix: Element coloring (CPK) section

Note

The color of the atom also depends on the atom color style (OE2DMolDisplayOptions.GetAtomColorStyle).
Setting atom color style (OE2DMolDisplayOptions.SetAtomColorStyle) to WhiteMonochrome sets white background and black color for all atoms. Likewise, setting atom color style to BlackMonochrome sets black background and white color for all atoms. But, user can choose to have another color for all atoms (in monochrome atom color style) by setting another atom color (OE2DMolDisplayOptions.SetAtomColor) for Carbon atoms. The example in Listing 4 demonstrates setting non-default atom colors in monochrome mode. Setting atom color for other than Carbon atoms sets color of only specified atom types, not for all atoms.

SetAtomColorStyle¶

void SetAtomColorStyle(unsigned int style)

Sets the style that is used to define the color of the background and the default color of atom labels.

style: This value has to be from the OEAtomColorStyle namespace.

Example: (Figure: Example of using the SetAtomColorStyle method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetAtomColorStyle(OEAtomColorStyle.BlackMonochrome);

../../_images/OE2DMolDisplayOptions_SetAtomColorStyle.png

Example of using the SetAtomColorStyle method¶

See also

OE2DMolDisplayOptions.GetAtomColorStyle method
OEAtomColorStyle namespace

SetAtomLabelFont¶

void SetAtomLabelFont(const OEFont &font)

Sets the font that is used to initialize the depiction style of the atom labels (OE2DAtomDisplay.GetLabelFont).

Example: (Figure: Example of using the SetAtomLabelFont method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
OEFont font = new OEFont();
font.SetFamily(OEFontFamily.Courier);
font.SetStyle(OEFontStyle.Bold);
opts.SetAtomLabelFont(font);

../../_images/OE2DMolDisplayOptions_SetAtomLabelFont.png

Example of using the SetAtomLabelFont method¶

Note

The color of the atom label fonts also depends on the atom color style (OE2DMolDisplayOptions.GetAtomColorStyle).
The size of fonts of the atom labels also depends on:
- the scaling factor used to fit a molecule to a given dimension (OE2DMolDisplayOptions.GetScale)
- the multiplier set by the OE2DMolDisplayOptions.SetAtomLabelFontScale method
See example in Figure: Example of scaling the font of the atom label along with the molecule

Example of scaling the font of the atom label along with the molecule¶

See also

OE2DMolDisplayOptions.GetAtomLabelFont method
OEFont class

SetAtomLabelFontScale¶

void SetAtomLabelFontScale(double scale)

Sets the multiplier that can be used increase or decrease the size of the fonts of the atom labels.

scale

This value has to be either 0.0 or in a range of [0.5, 3.0]. See examples in Figure: Examples of scaling the font of the atom label relative to the molecule

In case of 0.0, the atom labels are not scaled with the molecule but rather fixed font size are used regardless of the size of the molecule. See example in Figure: Example of atom labels with fixed font size

../../_images/AtomLabelFontScalingFactor.png

Examples of scaling the font of the atom label relative to the molecule¶

../../_images/NoAtomLabelFontScaling.png

Example of atom labels with fixed font size¶

Example: (Figure: Example of using the SetAtomLabelFontScale method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetAtomLabelFontScale(1.5);

../../_images/OE2DMolDisplayOptions_SetAtomLabelFontScale.png

Example of using the SetAtomLabelFontScale method¶

See also

OE2DMolDisplayOptions.GetAtomLabelFontScale method

SetAtomPropLabelFont¶

void SetAtomPropLabelFont(const OEFont &font)

Sets the font that is used to initialize the depiction style of the atom property labels (OE2DAtomDisplay.GetPropertyFont).

Example: (Figure: Example of using the SetAtomPropLabelFont method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
OEFont font = new OEFont();
font.SetStyle(OEFontStyle.Bold);
font.SetColor(oechem.getOEDarkGreen());
opts.SetAtomPropLabelFont(font);
opts.SetAtomPropertyFunctor(new OEDisplayAtomIdx());

../../_images/OE2DMolDisplayOptions_SetAtomPropLabelFont.png

Example of using the SetAtomPropLabelFont method¶

Note

The size of the atom property label fonts also depends on the scaling factor used to fit a molecule to a given dimension (OE2DMolDisplayOptions.GetScale) and the multiplier set by the OE2DMolDisplayOptions.SetAtomPropLabelFontScale method. See example in Figure: Example of scaling the font of the atom property labels along with the molecule

../../_images/AtomPropLabelFontScaling.png

Example of scaling the font of the atom property labels along with the molecule¶

See also

OE2DMolDisplayOptions.GetAtomPropLabelFont method
OEFont class

SetAtomPropLabelFontScale¶

void SetAtomPropLabelFontScale(double scale)

Sets the multiplier that can be used increase or decrease the size of the fonts of the atom property labels.

scale: This value has to be in the range of [0.5, 2.0]. See examples in Figure: Examples of scaling the font of the atom property labels relative to the molecule

../../_images/AtomPropLabelFontScalingFactor.png

Examples of scaling the font of the atom property labels relative to the molecule¶

Example: (Figure: Example of using the SetAtomPropLabelFontScale method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetAtomPropLabelFontScale(1.5);
opts.SetAtomPropertyFunctor(new OEDisplayAtomIdx());

../../_images/OE2DMolDisplayOptions_SetAtomPropLabelFontScale.png

Example of using the SetAtomPropLabelFontScale method¶

See also

OE2DMolDisplayOptions.GetAtomPropLabelFontScale method

SetAtomPropertyFunctor¶

void SetAtomPropertyFunctor(const OEDisplayAtomPropBase &func)

Sets the functor that is used to initialize the atom property labels (OE2DAtomDisplay.GetProperty)

Example: (Figure: Example of using the SetAtomPropertyFunctor method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetAtomPropertyFunctor(new OEDisplayAtomIdx());

../../_images/OE2DMolDisplayOptions_SetAtomPropertyFunctor.png

Example of using the SetAtomPropertyFunctor method¶

Hint

It is recommended to use the OE2DMolDisplayOptions.SetAtomPropertyFunctor method to define the atom property labels when the OE2DMolDisplay object is constructed. All labels displayed on the molecule diagram have to be known in advance in order to be able to minimize the number of label clashes and clippings when calculating the positions of the bond property labels.

See example of user-defined atom properties in Displaying Atom Properties section.

See also

OE2DMolDisplayOptions.GetAtomPropertyFunctor method
OEDisplayAtomPropBase class
OEDisplayAtomIdx class
OEDisplayAtomMapIdx class
OEDisplayNoAtomProp class

SetAtomStereoStyle¶

void SetAtomStereoStyle(unsigned int style)

Sets the style that controls what atom stereo information is displayed.

style: This value has to be from the OEAtomStereoStyle namespace.

Example: (Figure: Example of using the SetAtomStereoStyle method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetAtomStereoStyle(OEAtomStereoStyle.Display.All|OEAtomStereoStyle.HashWedgeStyle.Standard);

../../_images/OE2DMolDisplayOptions_SetAtomStereoStyle.png

Example of using the SetAtomStereoStyle method¶

See also

OE2DMolDisplayOptions.GetAtomStereoStyle method
OEAtomStereoStyle namespace

SetAtomSVGMarkupFunctor¶

void SetAtomSVGMarkupFunctor(const OEAtomSVGMarkupBase &func)

Sets the functor that defines how atoms are marked in svg image. Drawing elements representing atoms 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.

See also

OEAtomSVGMarkupBase abstract base class
OEAtomSVGNoMarkup class
OEAtomSVGAtomIdxMarkup class
OEAtomSVGResidueMarkup class
OE2DMolDisplayOptions.GetAtomSVGMarkupFunctor method

SetAtomVisibilityFunctor¶

void SetAtomVisibilityFunctor(const OESystem::OEUnaryPredicate<OEChem::OEAtomBase> &func)

Sets the functor that is used to identify visible atoms.

Example: (Figure: Example of using the SetAtomVisibilityFunctor method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetAtomVisibilityFunctor(new OEAtomIsInRing());

../../_images/OE2DMolDisplayOptions_SetAtomVisibilityFunctor.png

Example of using the SetAtomVisibilityFunctor method to only display rings¶

Hint

It is recommended to use the OE2DMolDisplayOptions.SetAtomVisibilityFunctor method to identify the visible atoms when the OE2DMolDisplay object is constructed. All objects displayed in the molecule diagram have to be known in advance in order to be able to correctly size and scale the molecule.

See additional examples of atom visibility control in the Displaying Atom Properties section.

See also

OE2DMolDisplayOptions.GetAtomVisibilityFunctor method
OEUnaryAtomPred

SetBackgroundColor¶

void SetBackgroundColor(const OESystem::OEColor &color)

Sets the color that is used to clear the background of an image (by calling OEImageBase.Clear method) before rendering the molecule.

Example: (Figure: Example of using the SetBackgroundColor method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetBackgroundColor(oechem.getOEYellowTint());

../../_images/OE2DMolDisplayOptions_SetBackgroundColor.png

Example of using the SetBackgroundColor method¶

See also

OE2DMolDisplayOptions.GetBackgroundColor method
OEColor class

SetBondColorStyle¶

void SetBondColorStyle(unsigned int style)

Sets the style that controls how bonds are colored.

style: This value has to be from the OEBondColorStyle namespace.

Example: (Figure: Example of using the SetBondColorStyle method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetBondColorStyle(OEBondColorStyle.Monochrome);

../../_images/OE2DMolDisplayOptions_SetBondColorStyle.png

Example of using the SetBondColorStyle method¶

See also

OE2DMolDisplayOptions.GetBondColorStyle method
OEBondColorStyle namespace

SetBondLineGapScale¶

void SetBondLineGapScale(double scale)

Sets the multiplier that can be used increase or decrease the gap between the lines of double and triple bonds.

scale: This value has to be in the range of [0.5, 2.0]. See examples in Figure: Examples of altering the gap between the lines of double and triple bonds

Examples of altering the gap between the lines of double and triple bonds¶

Example: (Figure: Example of using the SetBondLineGapScale method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetBondLineGapScale(0.5);

../../_images/OE2DMolDisplayOptions_SetBondLineGapScale.png

Example of using the SetBondLineGapScale method¶

See also

OE2DMolDisplayOptions.GetBondLineGapScale method

SetBondLineAtomLabelGapScale¶

void SetBondLineAtomLabelGapScale(double scale)

Sets the multiplier that can be used to increase or decrease the gap between the line(s) of bonds and the adjacent atom labels.

scale: This value has to be in the range of [0.5, 2.0]. See examples in Figure: Examples of altering the gap between the line(s) of bonds and adjacent atom labels

../../_images/BondLineAtomLabelGapScale.png

Examples of altering the gap between the line(s) of bonds and adjacent atom labels¶

Example: (Figure: Example of using the SetBondLineAtomLabelGapScale method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetBondLineAtomLabelGapScale(2.0);

../../_images/OE2DMolDisplayOptions_SetBondLineAtomLabelGapScale.png

Example of using the SetBondLineAtomLabelGapScale method¶

See also

OE2DMolDisplayOptions.GetBondLineAtomLabelGapScale method

SetBondPropLabelFont¶

void SetBondPropLabelFont(const OEFont &color)

Sets the font that is used to initialize the depiction style of the bond property labels (OE2DBondDisplay.GetPropertyFont).

Example: (Figure: Example of using the SetBondPropLabelFont method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
OEFont font = new OEFont();
font.SetStyle(OEFontStyle.Bold);
font.SetColor(oechem.getOEDarkGreen());
opts.SetBondPropLabelFont(font);
opts.SetBondPropertyFunctor(new OEDisplayBondIdx());

../../_images/OE2DMolDisplayOptions_SetBondPropLabelFont.png

Example of using the SetBondPropLabelFont method¶

Note

The size of the bond property label fonts also depends on the scaling factor used to fit a molecule to a given dimension (OE2DMolDisplayOptions.GetScale) and the multiplier set by the OE2DMolDisplayOptions.SetBondPropLabelFontScale method. See example in Figure: Example of scaling the font of the bond property labels along with the molecule

../../_images/BondPropLabelFontScaling.png

Example of scaling the font of the bond property labels along with the molecule¶

See also

OE2DMolDisplayOptions.GetBondPropLabelFont method
OEFont class

SetBondPropLabelFontScale¶

void SetBondPropLabelFontScale(double scale)

Sets the multiplier that can be used increase or decrease the size of the fonts of the bond property labels.

scale: This value has to be in the range of [0.5, 2.0]. See examples in Figure:*Examples of scaling the font of the bond property labels relative to the molecule SetBondPropLabelFontScale method

../../_images/BondPropLabelFontScalingFactor.png

Examples of scaling the font of the bond property labels relative to the molecule¶

Example: (Figure: Example of using the SetBondPropLabelFontScale method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetBondPropLabelFontScale(1.5);
opts.SetBondPropertyFunctor(new OEDisplayBondIdx());

../../_images/OE2DMolDisplayOptions_SetBondPropLabelFontScale.png

Example of using the SetBondPropLabelFontScale method¶

See also

OE2DMolDisplayOptions.GetBondPropLabelFontScale method

SetBondPropertyFunctor¶

void SetBondPropertyFunctor(const OEDisplayBondPropBase &func)

Sets the functor that is used to initialize the bond property labels (OE2DBondDisplay.GetProperty)

Example: (Figure: Example of using the SetBondPropertyFunctor method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetBondPropertyFunctor(new OEDisplayBondIdx());

../../_images/OE2DMolDisplayOptions_SetBondPropertyFunctor.png

Example of using the SetBondPropertyFunctor method¶

Hint

It is recommended to use the OE2DMolDisplayOptions.SetBondPropertyFunctor method to define the bond property labels when the OE2DMolDisplay object is constructed. All labels displayed on the molecule diagram have to be known in advance in order to be able to minimize the number of label clashes and clippings when calculating the positions of the bond property labels.

See example of user-defined bond properties in Displaying Bond Properties section.

See also

OE2DMolDisplayOptions.GetBondPropertyFunctor method
OEDisplayBondPropBase class
OEDisplayBondIdx class
OEDisplayNoBondProp class

SetBondStereoStyle¶

void SetBondStereoStyle(unsigned int style)

Sets the style that controls what bond stereo information is displayed.

style: This value has to be from the OEBondStereoStyle namespace.

Example: (Figure: Example of using the SetBondStereoStyle method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetBondStereoStyle(OEBondStereoStyle.Display.All);

../../_images/OE2DMolDisplayOptions_SetBondStereoStyle.png

Example of using the SetBondStereoStyle method¶

See also

OE2DMolDisplayOptions.GetBondStereoStyle method
OEBondStereoStyle namespace

SetBondSVGMarkupFunctor¶

void SetBondSVGMarkupFunctor(const OEBondSVGMarkupBase &func)

Sets the functor that defines how bonds are marked in svg image. Drawing elements representing bonds 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.

See also

OEBondSVGMarkupBase abstract base class
OEBondSVGNoMarkup class
OEBondSVGBondIdxMarkup class
OE2DMolDisplayOptions.GetBondSVGMarkupFunctor method

SetBondWidthScaling¶

void SetBondWidthScaling(bool scale)

Sets whether the line width of the bond are increase or decreased based on the molecule scaling factor (OE2DMolDisplayOptions.GetScale). See examples in Figure: Examples of bond line width.

Note

The line width of the bonds also depends on the default bond pen that can be set by using the OE2DMolDisplayOptions.SetDefaultBondPen method.

Examples of bond line width: (A) scaling the line width of the bonds relative to the molecule; (B) using constant line width that does not depend on the molecule scaling¶

Example: (Figure: Example of using the SetBondWithScaling method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetBondWidthScaling(true);

../../_images/OE2DMolDisplayOptions_SetBondWidthScaling.png

Example of using the SetBondWidthScaling method¶

See also

OE2DMolDisplayOptions.GetBondWidthScaling method

SetDefaultBondPen¶

void SetDefaultBondPen(const OEPen &pen)

Sets the pen that is used to initialize the bond pens (OE2DBondDisplay.GetBgnPen and OE2DBondDisplay.GetEndPen)

Example: (Figure: Example of using the SetDefaultBondPen method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
OEPen pen = new OEPen(oechem.getOEBlack(), oechem.getOEBlack(), OEFill.On, 5.0);
opts.SetDefaultBondPen(pen);

../../_images/OE2DMolDisplayOptions_SetDefaultBondPen.png

Example of using the SetDefaultBondPen method¶

Note

The style of the pens being used to draw bonds also depends on the bond display style (OE2DBondDisplay)
The color of the pens being used to draw bonds also depends on the given atom and bond color styles (OE2DMolDisplayOptions.SetAtomColorStyle and OE2DMolDisplayOptions.SetBondColorStyle, respectively)

See also

OE2DMolDisplayOptions.GetDefaultBondPen method
OEPen class

SetDimensions¶

void SetDimensions(double width, double height, double scale)

Sets parameters that control the size of the depicted molecule.

width: A non-negative number that controls the horizontal limit.
height: A non-negative number that controls the vertical limit.
scale: A non-negative number that controls the magnification of the depicted molecule. OEScale.AutoScale scaling means that the molecule is scaled to maximally fit the given dimensions.

Example: (Figure: Example of using the SetDimensions method)

OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions();
double width  = 180.0;
double height = 180.0;
double scale  = 20.0;
opts.SetDimensions(width, height, scale);

../../_images/OE2DMolDisplayOptions_SetDimensions.png

Example of using the SetDimensions method¶

See also

OE2DMolDisplayOptions.GetHeight and OE2DMolDisplayOptions.SetHeight method
OE2DMolDisplayOptions.GetScale and OE2DMolDisplayOptions.SetScale method
OE2DMolDisplayOptions.GetWidth and OE2DMolDisplayOptions.SetWidth method
Controlling the Size of Depicted Molecules section

SetExplicitAtomLabelAngle¶

void SetExplicitAtomLabelAngle(const double angle)

In the case of an almost linear X-C-X bond, an explicit “C” label will be drawn if the angle is more that the given angle. 180.0 degree means that the “C” label will never be drawn.

../../_images/OE2DMolDisplay_SetExplicitAtomLabelAngle.png

Example of using the SetExplicitAtomLabelAngle method¶

See also

OE2DMolDisplayOptions.GetExplicitAtomLabelAngle method

SetHeight¶

void SetHeight(double height)

Sets the vertical limit into which the molecule has to be fitted.

height: This number has to be non-negative number.

Example: (Figure: Example of using the SetHeight method)

OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions();
opts.SetHeight(150.0);
opts.SetBackgroundColor(oechem.getOELightGrey());

../../_images/OE2DMolDisplayOptions_SetHeight.png

Example of using the SetHeight method¶

See also

OE2DMolDisplayOptions.GetHeight method
OE2DMolDisplayOptions.SetDimensions method
Controlling the Size of Depicted Molecules section

SetHydrogenStyle¶

void SetHydrogenStyle(unsigned int style)

Sets the style that controls how implicit and explicit hydrogens are displayed.

style: This value has to be from the OEHydrogenStyle namespace.

Example: (Figure: Example of using the SetHydrogenStyle method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetHydrogenStyle(OEHydrogenStyle.ImplicitTerminal);

../../_images/OE2DMolDisplayOptions_SetHydrogenStyle.png

Example of using the SetHydrogenStyle method¶

See also

OE2DMolDisplayOptions.GetHydrogenStyle method
OEHydrogenStyle namespace

SetMargin¶

void SetMargin(unsigned int marginloc, double margin)

Sets the size of a specific margin of the OE2DMolDisplayOptions object.

marginloc

This value has to be from the OEMargin namespace.

margin

This number is considered as a percentage of either the width or the height of the molecule display and has to be in the range of [2.5%, 25.0%]. See example in Table: Example of setting specific margins to 5% (default), 15% and 25%. For example, when setting a margin to 15.0%:

in case of the top or the bottom margins, it means that the margin will be 15% of the total height of the molecule display
in case of the left or the right margins, it means that the margin will be 15% of the total width of the molecule display

**Example of setting specific margins to 5% (default), 15% and 25%**¶
top margin	bottom margin

left margin	right margin

Example: (Figure: Example of using the SetMargin method)

double width = 240.0;
double height = 180.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetMargin(OEMargin.Bottom, 25.0);

../../_images/OE2DMolDisplayOptions_SetMargin.png

Example of using the SetMargin method¶

See also

OE2DMolDisplayOptions.GetMargin method
OEMargin namespace

SetMargins¶

void SetMargins(double margin)

Sets the size of all margins of the OE2DMolDisplayOptions object.

margin: This number is considered as a percentage of either the width or the height of the molecule display and has to be in the range of [2.5%, 25.0%]. For example, 15.0% means, that the left and right margin are 15% of the total width of the molecule display, and the top and bottom margins are 15% of the total height of the molecule display. See example in Figure: Example of setting all margins to 5% (default), 15% and 25%.

../../_images/OE2DMolDisplayLayout_SetMargins.png

Example of setting all margins to 5% (default), 15% and 25%¶

Example: (Figure: Example of using the SetMargin method)

double width = 240.0;
double height = 180.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetMargins(25.0);

../../_images/OE2DMolDisplayOptions_SetMargins.png

Example of using the SetMargins method¶

See also

OE2DMolDisplayOptions.GetMargin method
OEMargin namespace

SetProtectiveGroupLabelFont¶

void SetProtectiveGroupLabelFont(const OEFont &font)

Sets the font that is used to display the abbreviations of contracted functional groups.

Example: (Figure: Example of using the ProtectiveGroupLabelFont method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
OEFont font = new OEFont();
font.SetColor(oechem.getOEDarkRed());
opts.SetProtectiveGroupLabelFont(font);
opts.SetProtectiveGroupStyle(OEProtectiveGroupStyle.All);

../../_images/OE2DMolDisplayOptions_SetProtectiveGroupLabelFont.png

Example of using the SetProtectiveGroupLabelFont method¶

See also

OE2DMolDisplayOptions.GetProtectiveGroupLabelFont method
OE2DMolDisplayOptions.GetProtectiveGroupStyle method
OE2DMolDisplayOptions.GetSuperAtomStyle method
OEFont class

Note

The size of the protective group fonts also depends on the scaling factor used to fit a molecule to a given dimension (OE2DMolDisplayOptions.SetScale).

SetProtectiveGroupStyle¶

void SetProtectiveGroupStyle(unsigned int style)

Sets the style that controls whether or not specific pre-defined protective group are contracted and labeled with corresponding abbreviations.

style: This value has to be from the OEProtectiveGroupStyle namespace.

Example: (Figure: Example of using the SetProtectiveGroupStyle method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetProtectiveGroupStyle(OEProtectiveGroupStyle.All);

../../_images/OE2DMolDisplayOptions_SetProtectiveGroupStyle.png

Example of using the SetProtectiveGroupStyle method¶

See also

OE2DMolDisplayOptions.HasProtectiveGroupStyle method
OE2DMolDisplayOptions.GetProtectiveGroupLabelFont method
OE2DMolDisplayOptions.GetSuperAtomStyle method
OEProtectiveGroupStyle namespace

SetScale¶

void SetScale(double scale)

Sets the scaling factor used to magnify a molecule.

scale: This number has to be non-negative number.

Example: (Figure: Example of using the SetScale method)

OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions();
opts.SetScale(20.0);
opts.SetBackgroundColor(oechem.getOELightGrey());

../../_images/OE2DMolDisplayOptions_SetScale.png

Example of using the SetScale method¶

See also

OE2DMolDisplayOptions.GetScale method
OE2DMolDisplayOptions.SetDimensions method
Controlling the Size of Depicted Molecules section

SetSuperAtomLabelFont¶

void SetSuperAtomLabelFont(const OEFont &font)

Sets the font that is used to display the abbreviations of contracted functional groups.

Example: (Figure: Example of using the SetSuperAtomLabelFont method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
OEFont font = new OEFont();
font.SetColor(oechem.getOEDarkRed());
opts.SetSuperAtomLabelFont(font);
opts.SetSuperAtomStyle(OESuperAtomStyle.All);

../../_images/OE2DMolDisplayOptions_SetSuperAtomLabelFont.png

Example of using the SetSuperAtomLabelFont method¶

See also

OE2DMolDisplayOptions.GetSuperAtomLabelFont method
OE2DMolDisplayOptions.GetSuperAtomStyle method
OEFont class

Note

The size of the super atom fonts also depends on the scaling factor used to fit a molecule to a given dimension (OE2DMolDisplayOptions.SetScale).

SetSuperAtomStyle¶

void SetSuperAtomStyle(unsigned int style)

Sets the style that controls whether or not specific pre-defined functional groups are contracted and labeled with corresponding abbreviations.

style: This value has to be from the OESuperAtomStyle namespace.

Example: (Figure: Example of using the SetSuperAtomStyle method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetSuperAtomStyle(OESuperAtomStyle.All);

../../_images/OE2DMolDisplayOptions_SetSuperAtomStyle.png

Example of using the SetSuperAtomStyle method¶

See also

OE2DMolDisplayOptions.GetSuperAtomStyle method
OE2DMolDisplayOptions.GetSuperAtomLabelFont method
OESuperAtomStyle namespace

SetTitleFont¶

void SetTitleFont(const OEFont &font)

Sets the font that is used to display the title of the molecule (i.e. the string returned by the OEMolBase.GetTitle method).

Example: (Figure: Example of using the SetTitleFont method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
OEFont font = new OEFont();
font.SetStyle(OEFontStyle.Bold);
font.SetColor(oechem.getOEDarkBrown());
opts.SetTitleFont(font);

../../_images/OE2DMolDisplayOptions_SetTitleFont.png

Example of using the SetTitleFont method¶

Note

The size of the title font also depends on:

the width and height of the molecule display
the height of the title area that can be set by OE2DMolDisplayOptions.SetTitleHeight method
the multiplier that can be set by the OE2DMolDisplayOptions.SetTitleFontScale method

See example in Figure: Example of scaling the title along with the molecule

Example of scaling the title along with molecule¶

See also

OE2DMolDisplayOptions.GetTitleFont method
OE2DMolDisplayOptions.SetTitleFontScale method
OE2DMolDisplayOptions.SetTitleHeight method
OEFont class

SetTitleFontScale¶

void SetTitleFontScale(double scale)

Sets the multiplier that can be used increase or decrease the size of the fonts of the atom labels.

scale: This value has to be either 0.0 or in a range of [0.5, 2.0]. See examples in Examples of scaling the font of title relative to the molecule In case of 0.0, the title is not scaled with the molecule but rather fixed font size is used regardless of dimensions of the image. See example in Figure: Example of titles with fixed font size

../../_images/TitleFontScalingFactor.png

Examples of scaling the font of title relative to the molecule¶

Example of titles with fixed font size¶

Example: (Figure: Example of using the SetTitleFontScale method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetTitleFontScale(0.5);

../../_images/OE2DMolDisplayOptions_SetTitleFontScale.png

Example of using the SetTitleFontScale method¶

See also

OE2DMolDisplayOptions.GetTitleFontScale method

SetTitleLocation¶

void SetTitleLocation(unsigned int loc)

Sets the position of the molecule title.

loc: This value has to be from the OETitleLocation namespace.

Example: (Figure: Example of using the SetTitleLocation method)

double width = 300.0;
double height = 200.0;
double scale = OEScale.AutoScale;
OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions(width, height, scale);
opts.SetTitleLocation(OETitleLocation.Bottom);

../../_images/OE2DMolDisplayOptions_SetTitleLocation.png

Example of using the SetTitleLocation method¶

See also

OE2DMolDisplayOptions.GetTitleLocation method
OETitleLocation namespace

SetTitleHeight¶

void SetTitleHeight(double height)

Sets the height of the title area of the OE2DMolDisplayOptions object.

height: This number is considered as a percentage of the height of the molecule display and has to be in the range of [5.0%, 25.0%]. See example in Figure: Example of setting height of the title area to 5%, 10% (default) and 25%.

../../_images/OE2DMolDisplayLayout_SetTitleHeight.png

Example of setting height of the title area to 5%, 10% (default) and 25%¶

Note

A molecule display has a title area only if the title location is not hidden. See also OETitleLocation namespace.

Example: (Figure: Example of using the SetTitleHeight method)

../../_images/OE2DMolDisplayOptions_SetTitleHeight.png

Example of using the SetTitleHeight method¶

See also

OE2DMolDisplayOptions.GetTitleHeight method

SetWidth¶

void SetWidth(double width)

Sets the horizontal limit into which the molecule has to be fitted.

width: This number has to be non-negative number.

Example: (Figure: Example of using the SetWidth method)

OE2DMolDisplayOptions opts = new OE2DMolDisplayOptions();
opts.SetWidth(150.0);
opts.SetBackgroundColor(oechem.getOELightGrey());

../../_images/OE2DMolDisplayOptions_SetWidth.png

Example of using the SetWidth method¶

See also

OE2DMolDisplayOptions.GetWidth method
OE2DMolDisplayOptions.SetDimensions method
Controlling the Size of Depicted Molecules section