Public Member Functions
	RenderOptions ()
	The default constructor will create an object with reasonable properties. Various setters can then modify particular elements of the scene that will be rendered.

double	getReceptorLineWidth () const
	Get the receptor bond thickness.

double	getLigandLineWidth () const
	Get the ligand bond thickness.

double	getReceptorLightAtomSize () const
	Get the marker size to be used in depictions of light atoms in the receptor.

double	getReceptorHeavyAtomSize () const
	Get the marker size to be used in depictions of heavy atoms in the receptor.

double	getLigandLightAtomSize () const
	Get the marker size to be used in depictions of light atoms in the ligand.

double	getLigandHeavyAtomSize () const
	Get the marker size to be used in depictions of heavy atoms in the ligand.

double	getWaterLightAtomSize () const
	Get the water hydrogen and virtual site size to display.

double	getWaterHeavyAtomSize () const
	Get the water oxygen size to display.

double	getAddedPointSize () const
	Get the marker size to be used in depictions of added points.

const std::string &	getReceptorHighlight () const
	Get the atom mask string for highlighting selected atoms of the receptor.

const std::string &	getLigandHighlight () const
	Get the atom mask string for highlighting selected atoms of the ligand.

uchar4	getReceptorLineColor () const
	Get the line color to be used in depictions of the receptor.

std::string	getFormattedReceptorLineColor (GridFileSyntax syntax) const
	Get the color for depicting a line connecting atoms of the receptor in matrix package syntax, as a string stating a three-element row vector of reals on a scale of [0.0, 1.0]. The string will be preceded by "'color'," (the word being in single quotes) and followed by another comma, to present a compact way to express the color code as a cohesive keyword / parameter pair for a plotting command.

uchar4	getLigandLineColor () const
	Get the line color to be used in depictions of the ligand.

std::string	getFormattedLigandLineColor (GridFileSyntax syntax) const
	Get the color for depicting a line connecting atoms of the ligand in matrix package syntax. The methodology follows from getFormattedReceptorColor() above.

uchar4	getAddedPointColor () const
	Get the color to be used in placing arbitrary points in the scene.

std::string	getFormattedAddedPointColor (GridFileSyntax syntax) const
	Get the color for placing added points on the scene in matrix package syntax. The methodology follows from getFormattedReceptorColor() above.

bool	displayFieldBorders () const
	Get an indication of whether to display borders of the potential field in the scene.

double	getBorderLineWidth () const
	Get the line weight for plotting borders of a potential field in the scene.

LinePlotStyle	getBorderLineStyle () const
	Get the line style for plotting borders of a potential field in the scene.

uchar4	getBorderLineColor () const
	\rbief

std::string	getFormattedBorderColor (GridFileSyntax syntax) const
	Get the color for drawing borders around the region containing the potential field, formatted for a specific visualization package. The methodology follows from getFormattedReceptorColor() above.

const std::string &	getLightingMode () const
	Get the lighting mode.

const std::string &	getCamlightPosition () const
	Get the camlight position.

int	getIsosurfaceCount () const
	Get the number of isosurfaces to render.

double	getIsosurfaceValue (int index) const
	Get one of the requested isosurface values. This will be plotted using the matrix package's own isosurface() and patch() commands.

uchar4	getIsosurfaceColor (int index) const
	Get the color prescribed for depicting a requested isosurface.

SurfaceRender	getIsosurfaceDrawingMethod (int index) const
	Get the method of drawing one of the requested isosurfaces.

uchar4	getElementColor (int z_number) const
	Get the color for depicting a particular element. The R, G, and B colors will be given in the "x", "y", and "z" members of the tuple. The alpha channel ("w" member) is irrelevant, as markers, points, and lines cannot have transparency.

std::string	getFormattedElementColor (int z_number, GridFileSyntax syntax) const
	Get the color for depicting a particular element in matrix package syntax. The methodology follows from getFormattedReceptorLineColor() above.

const RenderOptions *	getSelfPointer () const
	Get a const pointer to the object itself.

void	setReceptorLineWidth (double width_in)
	Set the line width to be used in plotting receptor bonds.

void	setLigandLineWidth (double width_in)
	Set the line width to be used in plotting ligand bonds.

void	setReceptorLightAtomSize (double marker_size_in)
	Set the marker size to be used in plotting light atoms of the receptor.

void	setReceptorHeavyAtomSize (double marker_size_in)
	Set the marker size to be used in plotting heavy atoms of the receptor.

void	setLigandLightAtomSize (double marker_size_in)
	Set the marker size to be used in plotting light atoms of the ligand.

void	setLigandHeavyAtomSize (double marker_size_in)
	Set the marker size to be used in plotting heavy atoms of the ligand.

void	setWaterLightAtomSize (double marker_size_in)
	Set the marker size to be used in plotting hydrogen atoms and virtual sites of water.

void	setWaterHeavyAtomSize (double marker_size_in)
	Set the marker size to be used in plotting oxygen atoms of water.

void	setAddedPointSize (double marker_size_in)
	Set the marker size to be used in adding arbitrary points to the scene.

void	setPotentialFieldBorderDisplay (bool display_borders_in)
	Set whether to display borders on the potential field.

void	setFieldBorderLineWidth (double width_in)
	Set the line width for border lines on the potential field.

void	setFieldBorderStyle (LinePlotStyle style_in)
	Set the style for displaying border lines on the potential field in the scene.

void	setFieldBorderColor (const uchar4 color_in)
	Set the color for displaying borders to the potential field in the scene.

void	setReceptorHighlight (const std::string &highlight_in)
	Set the receptor atom selection mask string.

void	setLigandHighlight (const std::string &highlight_in)
	Set the ligand atom selection mask string.

void	setLightingMode (const std::string &mode_in)
	Set the lighting mode. The mode will be checked for validity. Allowed values include "none", "flat", and "gouraud".

void	setCamlightPosition (const std::string &position_in)
	Set the camlight position. Acceptable values include "left", "right", and "headlight".


	RenderOptions (const RenderOptions &original)=default
	With no pointers to repair and no const member variables, the default copy and move constructors as well as copy and move assignment operators are valid.

	RenderOptions (RenderOptions &&original)=default

RenderOptions &	operator= (const RenderOptions &original)=default

RenderOptions &	operator= (RenderOptions &&original)=default


void	setReceptorLineColor (const uchar4 color_in)
	Set the line color to be used in coloring the receptor's bonds.

void	setReceptorLineColor (double red_in, double green_in, double blue_in)


void	setLigandLineColor (const uchar4 color_in)
	Set the line color to be used in coloring the ligand's bonds. Overloading and descriptions of input parameters follow from setReceptorLineColor() above.

void	setLigandLineColor (double red_in, double green_in, double blue_in)


void	setAddedPointColor (const uchar4 color_in)
	Set the line color to be used in coloring poitns added to the scene. Overloading and descriptions of input parameters follow from setReceptorLineColor() above.

void	setAddedPointColor (double red_in, double green_in, double blue_in)


void	setAtomicElementColor (int z_number, const uchar4 color_in)
	Set the color of a specific element. Overloading and descriptions of input parameters follow from setReceptorLineColor() above, in addition to:

void	setAtomicElementColor (int z_number, double red_in, double green_in, double blue_in)


void	addIsosurface (double value_in, const uchar4 color_in, SurfaceRender material_in)
	Add an isosurface to the list of requests.

void	addIsosurface (double value_in, const double4 color_in, SurfaceRender material_in)

Constructor & Destructor Documentation

◆ RenderOptions()

stormm::review::RenderOptions::RenderOptions ( const RenderOptions & original )

default

With no pointers to repair and no const member variables, the default copy and move constructors as well as copy and move assignment operators are valid.

Parameters

original	The original object to copy or move
other	An existing object on the right hand side of the assignment statement

Member Function Documentation

◆ addIsosurface()

void stormm::review::RenderOptions::addIsosurface	(	double	value_in,
		const uchar4	color_in,
		SurfaceRender	material_in )

Add an isosurface to the list of requests.

Overloaded:

Provide the color and transparency for the surface as a uint_8 four-tuple (RGB/alpha)
Provide the color and transparency for the surface as a double four-tuple (RGB/alpha)

Parameters

value_in	The isosurface value
color_in	Color and transparency of the surface to create
material_in	The imaginary material from which to build the surface

◆ getBorderLineColor()

uchar4 stormm::review::RenderOptions::getBorderLineColor ( ) const

\rbief

Get the line color for plotting borders of a potential field in the scene.

◆ getElementColor()

uchar4 stormm::review::RenderOptions::getElementColor ( int z_number ) const

Get the color for depicting a particular element. The R, G, and B colors will be given in the "x", "y", and "z" members of the tuple. The alpha channel ("w" member) is irrelevant, as markers, points, and lines cannot have transparency.

Parameters

z_number The atomic number of the element in question (enter zero for virtual sites). This will be checked for validity.

◆ getFormattedAddedPointColor()

std::string stormm::review::RenderOptions::getFormattedAddedPointColor ( GridFileSyntax syntax ) const

Get the color for placing added points on the scene in matrix package syntax. The methodology follows from getFormattedReceptorColor() above.

Parameters

syntax Indicate the visualization package which will ultimately process the color details.

◆ getFormattedBorderColor()

std::string stormm::review::RenderOptions::getFormattedBorderColor ( GridFileSyntax syntax ) const

Get the color for drawing borders around the region containing the potential field, formatted for a specific visualization package. The methodology follows from getFormattedReceptorColor() above.

Parameters

syntax Indicate the visualization package which will ultimately process the color details.

◆ getFormattedElementColor()

std::string stormm::review::RenderOptions::getFormattedElementColor	(	int	z_number,
		GridFileSyntax	syntax ) const

Get the color for depicting a particular element in matrix package syntax. The methodology follows from getFormattedReceptorLineColor() above.

Parameters

z_number	The atomic number of the element in question (enter zero for virtual sites). This will be checked for validity.
syntax	Indicate the visualization package which will ultimately process the color details.

◆ getFormattedLigandLineColor()

std::string stormm::review::RenderOptions::getFormattedLigandLineColor ( GridFileSyntax syntax ) const

Get the color for depicting a line connecting atoms of the ligand in matrix package syntax. The methodology follows from getFormattedReceptorColor() above.

Parameters

syntax Indicate the visualization package which will ultimately process the color details.

◆ getFormattedReceptorLineColor()

std::string stormm::review::RenderOptions::getFormattedReceptorLineColor ( GridFileSyntax syntax ) const

Get the color for depicting a line connecting atoms of the receptor in matrix package syntax, as a string stating a three-element row vector of reals on a scale of [0.0, 1.0]. The string will be preceded by "'color'," (the word being in single quotes) and followed by another comma, to present a compact way to express the color code as a cohesive keyword / parameter pair for a plotting command.

Parameters

syntax Indicate the visualization package which will ultimately process the color details.

◆ getIsosurfaceColor()

uchar4 stormm::review::RenderOptions::getIsosurfaceColor ( int index ) const

Get the color prescribed for depicting a requested isosurface.

Parameters

index Index of the isosurface described in one of the member variable arrays

◆ getIsosurfaceDrawingMethod()

SurfaceRender stormm::review::RenderOptions::getIsosurfaceDrawingMethod ( int index ) const

Get the method of drawing one of the requested isosurfaces.

Parameters

index Index of the isosurface described in one of the member variable arrays

◆ getIsosurfaceValue()

double stormm::review::RenderOptions::getIsosurfaceValue ( int index ) const

Get one of the requested isosurface values. This will be plotted using the matrix package's own isosurface() and patch() commands.

Parameters

index Index of the isosurface described in one of the member variable arrays. This will be checked for validity.

◆ setAddedPointSize()

void stormm::review::RenderOptions::setAddedPointSize ( double marker_size_in )

Set the marker size to be used in adding arbitrary points to the scene.

Parameters

marker_size_in The marker weight to use

◆ setAtomicElementColor()

void stormm::review::RenderOptions::setAtomicElementColor	(	int	z_number,
		const uchar4	color_in )

Set the color of a specific element. Overloading and descriptions of input parameters follow from setReceptorLineColor() above, in addition to:

Parameters

z_number Atomic number of the atom of interest

◆ setCamlightPosition()

void stormm::review::RenderOptions::setCamlightPosition ( const std::string & position_in )

Set the camlight position. Acceptable values include "left", "right", and "headlight".

Parameters

position_in The position of the light relative to the camera.

◆ setFieldBorderColor()

void stormm::review::RenderOptions::setFieldBorderColor ( const uchar4 color_in )

Set the color for displaying borders to the potential field in the scene.

Parameters

color_in The color to set (the alpha channel is irrelevant for a line-based object)

◆ setFieldBorderLineWidth()

void stormm::review::RenderOptions::setFieldBorderLineWidth ( double width_in )

Set the line width for border lines on the potential field.

Parameters

width_in The border line width to set

◆ setFieldBorderStyle()

void stormm::review::RenderOptions::setFieldBorderStyle ( LinePlotStyle style_in )

Set the style for displaying border lines on the potential field in the scene.

Parameters

style_in The style (e.g. 'solid', 'dashed') to set

◆ setLigandHeavyAtomSize()

void stormm::review::RenderOptions::setLigandHeavyAtomSize ( double marker_size_in )

Set the marker size to be used in plotting heavy atoms of the ligand.

Parameters

marker_size_in The marker weight to use

◆ setLigandHighlight()

void stormm::review::RenderOptions::setLigandHighlight ( const std::string & highlight_in )

Set the ligand atom selection mask string.

Parameters

highlight_in String specifying an atom mask that will be applied to the ligand

◆ setLigandLightAtomSize()

void stormm::review::RenderOptions::setLigandLightAtomSize ( double marker_size_in )

Set the marker size to be used in plotting light atoms of the ligand.

Parameters

marker_size_in The marker weight to use

◆ setLigandLineWidth()

void stormm::review::RenderOptions::setLigandLineWidth ( double width_in )

Set the line width to be used in plotting ligand bonds.

Parameters

width_in The line weight to use

◆ setLightingMode()

void stormm::review::RenderOptions::setLightingMode ( const std::string & mode_in )

Set the lighting mode. The mode will be checked for validity. Allowed values include "none", "flat", and "gouraud".

Parameters

mode_in The lighting mode to set

◆ setPotentialFieldBorderDisplay()

void stormm::review::RenderOptions::setPotentialFieldBorderDisplay ( bool display_borders_in )

Set whether to display borders on the potential field.

Parameters

display_borders_in Indicate whether to display the borders

◆ setReceptorHeavyAtomSize()

void stormm::review::RenderOptions::setReceptorHeavyAtomSize ( double marker_size_in )

Set the marker size to be used in plotting heavy atoms of the receptor.

Parameters

marker_size_in The marker weight to use

◆ setReceptorHighlight()

void stormm::review::RenderOptions::setReceptorHighlight ( const std::string & highlight_in )

Set the receptor atom selection mask string.

Parameters

highlight_in String specifying an atom mask that will be applied to the receptor

◆ setReceptorLightAtomSize()

void stormm::review::RenderOptions::setReceptorLightAtomSize ( double marker_size_in )

Set the marker size to be used in plotting light atoms of the receptor.

Parameters

marker_size_in The marker weight to use

◆ setReceptorLineColor()

void stormm::review::RenderOptions::setReceptorLineColor ( const uchar4 color_in )

Set the line color to be used in coloring the receptor's bonds.

Overloaded:

Provide an unsigned four-character tuple (includes an alpha channel, which is ignored)
Provide three double precision numbers for red, green, and blue intensities on a scale of 0.0 (this will be translated to 0 in the unsigned 8-bit integer representation) to 1.0 (255 in the unsigned 8-bit integer representation).

Parameters

color_in	Tuple containing R/G/B values
red_in	The intensity of red in the color, in the range [0.0, 1.0].
green_in	The intensity of green in the color, in the range [0.0, 1.0].
blue_in	The intensity of blue in the color, in the range [0.0, 1.0].

◆ setReceptorLineWidth()

void stormm::review::RenderOptions::setReceptorLineWidth ( double width_in )

Set the line width to be used in plotting receptor bonds.

Parameters

width_in The line weight to use

◆ setWaterHeavyAtomSize()

void stormm::review::RenderOptions::setWaterHeavyAtomSize ( double marker_size_in )

Set the marker size to be used in plotting oxygen atoms of water.

Parameters

marker_size_in The marker weight to use

◆ setWaterLightAtomSize()

void stormm::review::RenderOptions::setWaterLightAtomSize ( double marker_size_in )

Set the marker size to be used in plotting hydrogen atoms and virtual sites of water.

Parameters

marker_size_in The marker weight to use

The documentation for this class was generated from the following files:

src/Reporting/render_options.h
src/Reporting/render_options.cpp

Public Member Functions

Constructor & Destructor Documentation

◆ RenderOptions()

Member Function Documentation

◆ addIsosurface()

◆ getBorderLineColor()

◆ getElementColor()

◆ getFormattedAddedPointColor()

◆ getFormattedBorderColor()

◆ getFormattedElementColor()

◆ getFormattedLigandLineColor()

◆ getFormattedReceptorLineColor()

◆ getIsosurfaceColor()

◆ getIsosurfaceDrawingMethod()

◆ getIsosurfaceValue()

◆ setAddedPointSize()

◆ setAtomicElementColor()

◆ setCamlightPosition()

◆ setFieldBorderColor()

◆ setFieldBorderLineWidth()

◆ setFieldBorderStyle()

◆ setLigandHeavyAtomSize()

◆ setLigandHighlight()

◆ setLigandLightAtomSize()

◆ setLigandLineWidth()

◆ setLightingMode()

◆ setPotentialFieldBorderDisplay()

◆ setReceptorHeavyAtomSize()

◆ setReceptorHighlight()

◆ setReceptorLightAtomSize()

◆ setReceptorLineColor()

◆ setReceptorLineWidth()

◆ setWaterHeavyAtomSize()

◆ setWaterLightAtomSize()