Display Functions

The functions detailed in this section enable the customization of how the application itself as well as the currently loaded objects are displayed.

AnnotationGet

std::string AnnotationGet(const OEPropDB::OEKey &key)

Returns the text annotation associated with the object specified by key.

AnnotationHas

bool AnnotationHas(const OEPropDB::OEKey &key)

Returns whether or not the object specified by key has a text annotation.

AnnotationSet

void AnnotationSet(const OEPropDB::OEKey &key, const std::string &txt,
                   bool notify=true)

Sets a text annotation on the object specified by key containing the text specified by txt. If notify is set to True, VIDA will be notified to update the user interface to reflect this change.

AtomClearColorScoped

void AtomClearColorScoped(unsigned int scope = BestScope)

This function restores the default atom coloring to those atoms within the specified scope.

AtomColorPaletteUpdate

void AtomColorPaletteUpdate()

This function updates the default atom coloring palette based on whether or not the application is using a dark or light colored background scheme. This function is called internally and should not be called by the user.

AtomColorReferenceScoped

void AtomColorReferenceScoped(unsigned int scope = BestScope)

This function provides a quick way to mark a molecule (or set of atoms) as a reference structure. The coloring function that is applied colors all carbon atoms the current application ‘reference’ color (default is green). The ‘reference’ color can be changed in the preferences.

AtomColorResidueScoped

void AtomColorResidueScoped(unsigned int scope = BestScope)

This function provides a quick way to color a molecule (or set of atoms) based on associated residue information. The default coloring that is applied uses the ‘Shapely’ color scheme for coloring residues. The residue colors can be changed in the preferences:

* ALA     Medium Green  [140,255,140]
* GLY     White         [255,255,255]
* LEU     Olive Green   [ 69, 94, 69]
* SER     Medium Orange [255,112, 66]
* VAL     Light Purple  [255,140,255]
* THR     Dark Orange   [184, 76,  0]
* LYS     Royal Blue    [ 71, 71,184]
* ASP     Dark Rose     [160,  0, 66]
* ILE     Dark Green    [  0, 76,  0]
* ASN     Light Salmon  [255,124,112]
* GLU     Dark Brown    [102,  0,  0]
* PRO     Dark Grey     [ 82, 82, 82]
* ARG     Dark Blue     [  0,  0,124]
* PHE     Olive Grey    [ 83, 76, 66]
* GLN     Dark Salmon   [255, 76, 76]
* TYR     Medium Brown  [140,112, 76]
* HIS     Medium Blue   [112,112,255]
* CYS     Medium Yellow [255,255,112]
* MET     Light Brown   [184,160, 66]
* TRP     Olive Brown   [ 79, 70,  0]
* ASX     Medium Purple [255,  0,255]
* GLX     Medium Purple [255,  0,255]
* PCA     Medium Purple [255,  0,255]
* HYP     Medium Purple [255,  0,255]
* A       Light Blue    [160,160,255]
* C       Light Orange  [255,140, 75]
* G       Medium Salmon [255,112,112]
* T       Light Green   [160,255,160]
* Default Medium Purple [255,  0,255]

AtomColorSetScoped

void AtomColorSetScoped(const OESystem::OEColor &color,
                        unsigned int scope = BestScope)
void AtomColorSetScoped(unsigned int element, const OESystem::OEColor &color,
                        unsigned int scope = BestScope)

This function sets the color of the atoms in the specified scope to be the specified color.

AtomDarkColorsGet

bool AtomDarkColorsGet()

Returns whether or not the application is using the atom color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.

AtomDarkColorsSet

void AtomDarkColorsSet(bool dark)

Sets whether or not the application is using the atom color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.

AtomDefaultColorGet

OESystem::OEColor AtomDefaultColorGet()
OESystem::OEColor AtomDefaultColorGet(unsigned int elem)

Returns the current default atom color. The default atom color is applied to every atom that does not have its own specific default color assigned. Calling this function with the elem parameter returns the specific default color associated with the passed element number (e.g. carbon = 6).

AtomDefaultColorSet

void AtomDefaultColorSet(const OESystem::OEColor &color)
void AtomDefaultColorSet(unsigned int elem, const OESystem::OEColor &color)

Sets the current default atom color. The default atom color is applied to every atom that does not have its own specific default color assigned. Calling this function with the elem parameter sets the specific default color associated with the passed element number (e.g. carbon = 6).

AtomHaloRadiusGet

float AtomHaloRadiusGet()

Returns the current radius of atom selection halo. The atom selection halo is a transparent white surface with the specified radius drawn around the current selected set of atoms. If the DistanceControlsVisibility property is set (see DistanceControlsVisibilitySet/Get functions), only atoms falling within this radius will be displayed.

AtomHaloRadiusSet

float AtomHaloRadiusSet(float radius, bool notify=true)

Sets the current radius of atom selection halo. The atom selection halo is a transparent white surface with the specified radius drawn around the current selected set of atoms. If the DistanceControlsVisibility property is set (see DistanceControlsVisibilitySet/Get functions), only atoms falling within this radius will be displayed.

AtomHydrogenStyleGet

unsigned int AtomHydrogenStyleGet()
unsigned int AtomHydrogenStyleGet(const OEPropDB::OEKey &key)

Returns the current default hydrogen display style - 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.

AtomHydrogenStyleSet

void AtomHydrogenStyleSet(unsigned int style)

Sets the current default hydrogen display style. Valid style parameter values are 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.

AtomHydrogenStyleSetScoped

void AtomHydrogenStyleSetScoped(unsigned int style,
                                unsigned int scope = BestScope)

Sets the hydrogen display style for all the molecules in the specified scope. Valid style parameter values are 0 for no hydrogens, 1 for polar hydrogens only, and 2 for all hydrogens.

AtomLabelDefaultGet

std::string AtomLabelDefaultGet()

Returns the default label displayed on atoms. The default is “None”. See the AtomLabelSetScoped function for more information about label types.

AtomLabelDefaultSet

void AtomLabelDefaultSet(const std::string &label)

Sets the default label displayed on atoms. The default is “None”. See the AtomLabelSetScoped function for more information about label types.

AtomLabelGet

std::string AtomLabelGet(const OEPropDB::OEKey &k)

Returns the current label set on the specified atom.

AtomLabelSet

bool AtomLabelSet(const OEPropDB::OEKey &k, const std::string &label)

Sets the label on the specified atom. The parameter label contains the text of the label and the parameter key specifies which atom this label should apply to. See the AtomLabelSetScoped function for more information about label types.

AtomLabelSetScoped

bool AtomLabelSetScoped(const std::string &label,
                        unsigned int scope = BestScope)

Sets the current label displayed on the atoms in the specified scope. Label types include:

* "none"               or ""
* "index"              or "%i"
* "element"            or "%e"
* "name"               or "%n"
* "type"               or "%t"
* "inttype"            or "%it"
* "implicit hcount"    or "%h"
* "formal charge"      or "%f"
* "partial charge"     or "%p"
* "residue info"       or "%r"
* "degree"             or "%d"
* "ischiral"           or "%c"
* "chirality"          or "%chi"
* "hasstereospecified" or "%sts"
* "symmetry class"     or "%sy"
* "isinring"           or "%rng"
* "oechem idx"         or "%oei"
* "map index"          or "%m"
* "read order"         or "%ro"
* "isotope"            or "%iso"
* "hcount"             or "%h"
* "residue info (ca)"  or "%car"
* "bfactor"            or "%cab"
* "degree"             or "%d"
* "hybrid"             or "%hyb"
* "comment"            or "%cm"
* "%gd(x)" - where x specifies the desired piece of generic data to use as the label

AtomStyleGet

std::string AtomStyleGet()

Returns the default atom style. The default is “small”. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleGetScoped

unsigned int AtomStyleGetScoped(unsigned int scope = BestScope)

Returns the style of the atoms in the specified scope. If there are multiple styles present, the return type is “mixed”. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleLargeGet

std::string AtomStyleLargeGet()

Returns the default atom style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is “none”. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleLargeSet

void AtomStyleLargeSet(unsigned int style)
void AtomStyleLargeSet(const std::string &atomStyle)

Sets the default atom style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. This function accepts either a string or an enumerated representation as its parameter. The default is “none”. For more information on this large molecule atom cutoff, see the MoleculeSizeCutoff function. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleNucleicGet

std::string AtomStyleNucleicGet()

Returns the default atom style for nucleic acids. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

AtomStyleNucleicSet

void AtomStyleNucleicSet(unsigned int style)
void AtomStyleNucleicSet(const std::string &atomStyle)

Sets the default atom style for nucleic acids. This function accepts either a string or an enumerated representation as its parameter. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

AtomStyleProteinGet

std::string AtomStyleProteinGet()

Returns the default atom style for proteins. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

AtomStyleProteinSet

void AtomStyleProteinSet(unsigned int style)
void AtomStyleProteinSet(const std::string &atomStyle)

Sets the default atom style for proteins. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

AtomStyleSet

void AtomStyleSet(unsigned int style)
void AtomStyleSet(const std::string &atomStyle)

Sets the default atom style. This function accepts either a string or an enumerated representation as its parameter. The default is “small”. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleSetScoped

void AtomStyleSetScoped(unsigned int style,
                        unsigned int scope = BestScope)
void AtomStyleSetScoped(const std::string &atomStyle,
                        unsigned int scope = BestScope)

Sets the display style for the specified atoms. This function accepts either a string or an enumerated representation as its parameter. Available atom styles include:

* "small"   atoms are drawn as small sized spheres
* "medium"  atoms are drawn as medium sized spheres
* "large"   atoms are drawn as large sized spheres
* "stars"   atoms are drawn as stars
* "radii"   atoms are drawn as spheres with radii equivalent to their VDW radii
* "none"    atoms are not drawn, but are still considered visible and thus selectable
* "hidden"  atoms are not drawn and are not considered visible and thus are not selectable

AtomStyleToEnum

unsigned int AtomStyleToEnum(const std::string &style)

This function returns the enumerated type associated the specified string atoms style representation. See the AtomStyleSetScoped function for more information about atom styles.

AtomStyleToText

std::string AtomStyleToText(unsigned int style)

This function returns the text string associated with the specified enumerated atom style representation. See the AtomStyleSetScoped function for more information about atom styles.

BondBallToStickRatioGet

float BondBallToStickRatioGet()

This function is currently a placeholder for future functionality.

BondBallToStickRatioSet

float BondBallToStickRatioSet(float ballStickRatio)

This function is currently a placeholder for future functionality.

BondClearColorScoped

void BondClearColorScoped(unsigned int scope = BestScope)

This function restores the default bond coloring to those bonds within the specified scope.

BondColorSetScoped

void BondColorSetScoped(const OESystem::OEColor &color,
                        unsigned int scope = BestScope)

This function sets the color of the bonds in the specified scope to be the specified color c.

BondDrawAromaticGet

bool BondDrawAromaticGet(unsigned int id)

Returns whether or not aromatic bonds should be drawn as aromatic or instead in Kekule format for the molecule with the specified id.

BondDrawAromaticSet

bool BondDrawAromaticSet(unsigned int id, bool aromatic)

Sets whether or not aromatic bonds should be drawn as aromatic or instead in kekule format for the molecule with the specified id.

BondHideHydrogenGet

bool BondHideHydrogenGet()

Returns the global property which specifies whether or not explicit hydrogens should be displayed.

BondHideHydrogenSet

bool BondHideHydrogenSet(bool hide)

Sets the global property which specifies whether or not explicit hydrogens should be displayed.

BondHideNonbondedGet

bool BondHideNonbondedGet()

Returns the global property which specifies whether or not explicit non-bonded atoms should be displayed.

BondHideNonbondedSet

bool BondHideNonbondedSet(bool hide)

Sets the global property which specifies whether or not explicit non-bonded atoms should be displayed.

BondLabelDefaultGet

std::string BondLabelDefaultGet()

Returns the default label displayed on bonds. The default is “None”. See the BondLabelSetScoped function for more information about label types.

BondLabelDefaultSet

void BondLabelDefaultSet(const std::string &label)

Sets the default label displayed on bonds. The default is “None”. See the BondLabelSetScoped function for more information about label types.

BondLabelGet

std::string BondLabelGet(const OEPropDB::OEKey &k)

Returns the current label on the specified bond.

BondLabelSet

bool BondLabelSet(const OEPropDB::OEKey &k, const std::string &label)

Sets the label on the specified bond. The parameter label contains the text of the label and the parameter key specifies which bond this label should apply to. See the BondLabelSetScoped function for more information about label types.

BondLabelSetScoped

bool BondLabelSetScoped(const std::string &label,
                        unsigned int scope = BestScope)

Sets the current label displayed on the bonds in the specified scope. Label types include:

* "none"               or ""
* "index"              or "%i"
* "order"              or "%o"
* "length"             or "%l"
* "type"               or "%t"
* "inttype"            or "%it"
* "ischiral"           or "%c"
* "chirality"          or "%chi"
* "hasstereospecified" or "%sts"
* "oechem idx"         or "%oei"
* "%gd(x)" - where x specifies the desired piece of generic data to use as the label

BondLineWidthGet

float BondLineWidthGet()

Returns the line width (in pixels) to be used when drawing bonds in “line” or “wireframe” styles.

BondLineWidthSet

float BondLineWidthSet(float width)
bool BondLineWidthSet(const OEPropDB::OEKey &k, float width)

Sets the line width (in pixels) to be used when drawing bonds in “line” or “wireframe” styles.

BondRadiusGet

float BondRadiusGet()

Returns the radius of the cylinders to be used when drawing bonds in “cylinder” style.

BondRadiusSet

float BondRadiusSet(float radius)
bool BondRadiusSet(const OEPropDB::OEKey &k, float radius)

Sets the radius of the cylinders to be used when drawing bonds in “cylinder” style.

BondShowAromaticGet

bool BondShowAromaticGet()

Returns the global property which specifies whether or not aromatic bonds should be drawn as aromatic or instead in kekule format.

BondShowAromaticSet

bool BondShowAromaticSet(bool show)

Sets the global property which specifies whether or not aromatic bonds should be drawn as aromatic or instead in kekule format.

BondShowDipolarGet

bool BondShowDipolarGet()

Returns the global property which specifies whether or not dipolar bonds should be drawn as directed bonds.

BondShowDipolarSet

bool BondShowDipolarSet(bool show)

Sets the global property which specifies whether or not dipolar bonds should be drawn as directed bonds.

BondShowOrdersGet

bool BondShowOrdersGet()

Returns the global property which specifies whether or not bond orders should be displayed.

BondShowOrdersSet

bool BondShowOrdersSet(bool show)

Sets the global property which specifies whether or not bond orders should be displayed.

BondStyleGet

std::string BondStyleGet()

Returns the default bond style. The default is “cylinders”. See the BondStyleSetScoped function for more information about bond styles.

BondStyleGetScoped

unsigned int BondStyleGetScoped(unsigned int scope = BestScope)

Returns the style of the bonds in the specified scope. If there are multiple styles present, the return type is “mixed”. See the BondStyleSetScoped function for more information about bond styles.

BondStyleLargeGet

std::string BondStyleLargeGet()

Returns the default bond style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is “lines”. See the BondStyleSetScoped function for more information about bond styles.

BondStyleLargeSet

void BondStyleLargeSet(unsigned int style)
void BondStyleLargeSet(const std::string &bondstyle)

Sets the default bond style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. This function accepts either a string or an enumerated representation as its parameter. The default is “lines”. For more information on this large molecule atom cutoff, see the MoleculeSizeCutoff function. See the BondStyleSetScoped function for more information about bond styles.

BondStyleNucleicGet

std::string BondStyleNucleicGet()

Returns the default bond style for nucleic acids. The default is to mirror the large molecule bond style. See the BondStyleLargeSet function for more information about large molecules and see the BondStyleSetScoped function for more information about bond styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

BondStyleNucleicSet

void BondStyleNucleicSet(unsigned int style)
void BondStyleNucleicSet(const std::string &bondstyle)

Sets the default bond style for nucleic acids. This function accepts either a string or an enumerated representation as its parameter. The default is to mirror the large molecule atom style. See the AtomStyleLargeSet function for more information about large molecules and see the AtomStyleSetScoped function for more information about atom styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

BondStyleProteinGet

std::string BondStyleProteinGet()

Returns the default bond style for proteins. The default is to mirror the large molecule bond style. See the BondStyleLargeSet function for more information about large molecules and see the BondStyleSetScoped function for more information about bond styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

BondStyleProteinSet

void BondStyleProteinSet(unsigned int style)
void BondStyleProteinSet(const std::string &bondstyle)

Sets the default bond style for proteins. The default is to mirror the large molecule bond style. See the BondStyleLargeSet function for more information about large molecules and see the BondStyleSetScoped function for more information about bond styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

BondStyleSet

void BondStyleSet(unsigned int style)
void BondStyleSet(const std::string &bondstyle)

Sets the default bond style. This function accepts either a string or an enumerated representation as its parameter. The default is “cylinders”. See the BondStyleSetScoped function for more information about bond styles.

BondStyleSetScoped

void BondStyleSetScoped(unsigned int style,
                        unsigned int scope = BestScope)
void BondStyleSetScoped(const std::string &bondstyle,
                        unsigned int scope = BestScope)

Sets the display style for the specified bonds. This function accepts either a string or an enumerated representation as its parameter. Available bonds styles include:

* "lines"     bonds are drawn as lines
* "cylinders" bonds are drawn as cylinders
* "none"      bonds are not drawn, but are still considered visible and thus selectable
* "hidden"    bonds are not drawn and are not considered visible and thus are not selectable

BondStyleToEnum

unsigned int BondStyleToEnum(const std::string &style)

This function returns the enumerated type associated the specified string bond style representation. See the BondStyleSetScoped function for more information about bond styles.

BondStyleToText

std::string BondStyleToText(unsigned int style)

This function returns the text string associated with the specified enumerated bond style representation. See the BondStyleSetScoped function for more information about bond styles.

BookmarkDelete

bool BookmarkDelete(const std::string &name)

Deletes the bookmark specified by name.

BookmarkExists

bool BookmarkExists(const std::string &name)

Returns whether or not the specified bookmark exists.

BookmarkLoad

bool BookmarkLoad(const std::string &name)

Loads the specified bookmark.

BookmarkMoveDown

bool BookmarkMoveDown(const std::string &name)

Moves the specified bookmark down in the order of the current set of bookmarks.

BookmarkMoveUp

bool BookmarkMoveUp(const std::string &name)

Moves the specified bookmark up in the order of the current set of bookmarks.

BookmarkOrganizeDialog

std::string BookmarkOrganizeDialog(bool exec=false)

Launches an interactive dialog which allows the user to delete, rename, and reorder the current set of bookmarks.

BookmarkRename

bool BookmarkRename(const std::string &oldName, const std::string &newName)

Changes the name of the bookmark specified by oldName to the name specified by newName.

BookmarkSave

bool BookmarkSave(const std::string &name)

Saves the current state of the application to a named bookmark specified by the parameter name.

Bookmarks

std::vector<std::string> Bookmarks()

Returns a list of the current set of bookmarks.

BookmarksClear

void BookmarksClear()

Clears the current list of bookmarks.

BookmarksLastLoaded

unsigned int BookmarksLastLoaded()

Returns the index (in the order of the current set of bookmarks) of the last bookmark that was loaded.

CATraceRadiusGet

float CATraceRadiusGet()

Returns the global property which specifies the width of CA Traces.

CATraceRadiusSet

float CATraceRadiusSet(float radius)

Sets the global property which specifies the width of CA Traces.

CATraceStyleGet

std::string CATraceStyleGet()
std::string CATraceStyleGet(const OEPropDB::OEKey &k)

Returns the global property which specifies the style in which CA Traces are drawn. Available styles include: “lines” and “cylinders”.

CATraceStyleSet

std::string CATraceStyleSet(const std::string &style)
std::string CATraceStyleSet(const OEPropDB::OEKey &k, const std::string &style)

Sets the global property which specifies the style in which CA Traces are drawn. Available styles include: “lines” and “cylinders”.

CATraceStyleSetScoped

std::string CATraceStyleSetScoped(const std::string &str,
                                  unsigned int scope = BestScope)

Sets the property which specifies the style in which CA Traces are drawn. Available styles include: “lines” and “cylinders”.

CenterSet

void CenterSet(const OEPropDB::OEKey &)
void CenterSet(const std::vector<OEPropDB::OEKey> &)

Sets the center of the scene to be at the center of the object(s) referenced by the specified key(s).

CenterSetScoped

void CenterSetScoped(unsigned int scope)

Scoped version of .

ColorGet

OESystem::OEColor ColorGet(const OEPropDB::OEKey &)

Returns the color of the object specified by the OEKey parameter key.

ColorSet

void ColorSet(const OEPropDB::OEKey &, const OESystem::OEColor &)

Sets the color of the object specified by the OEKey parameter key to be the specified color.

ColorSetScoped

void ColorSetScoped(const OESystem::OEColor &,
                    unsigned int scope = BestScope)

Sets the color for all of the objects in the specified scope to be the specified color.

ColorUniqueScoped

void ColorUniqueScoped(unsigned int scope = BestScope)

Assigns a “unique” color to each individual object found in the specified scope. For large numbers of objects in the scope, the colors used may eventually repeat.

ContourAutoCenterGet

bool ContourAutoCenterGet(unsigned int id=0)

Returns whether or not reentrant grids are automatically contoured at the center of the scene.

ContourAutoCenterSet

bool ContourAutoCenterSet(unsigned int id, bool center)

Sets whether or not reentrant grids are automatically contoured at the center of the scene. If this is set to true, translating the center of the scene will cause the grids to be recontoured as the scene moves.

ContourAutoContourGet

bool ContourAutoContourGet()

Returns whether or not reentrant grids are automatically recontoured when the center of the scene is changed.

ContourAutoContourRadiusScaleSet

bool ContourAutoContourRadiusScaleSet(float radius, float scale)

Sets the radius and scale parameters used in determining how to contour a reentrant grid around the center of the scene.

ContourAutoContourSet

void ContourAutoContourSet(bool autocontour)

Sets whether or not reentrant grids are automatically recontoured when the center of the scene is changed.

ContourCenter

std::vector<float> ContourCenter(unsigned int id=0)
std::vector<float> ContourCenter(unsigned int id, std::vector<float>)

Returns the scene center position associated with the specified contour.

ContourColorForIndexGet

OESystem::OEColor ContourColorForIndexGet(unsigned int id, unsigned int index)

Return the color of the grid contour specified by the grid id and contour index.

ContourColorForIndexGetScoped

OESystem::OEColor ContourColorForIndexGetScoped(unsigned int index,
                                                unsigned int scope = BestScope)

Returns the color of the grid contours in the specified scope at contour index index. This color is determined by looking at the first contour found in the specified scope.

ContourColorForIndexSet

OESystem::OEColor ContourColorForIndexSet(unsigned int id, unsigned int index,
                                          const OESystem::OEColor &color)

For grid id set the color of contour index to color.

ContourColorForIndexSetScoped

OESystem::OEColor ContourColorForIndexSetScoped(unsigned int index,
                                                const OESystem::OEColor &color,
                                                unsigned int scope = BestScope)

For all grids in scope set the color of contour index to color.

ContourColorSet

void ContourColorSet(const OEPropDB::OEKey &, const OESystem::OEColor &)

This function sets the color of the contour associated with the specified key.

ContourColorSetScoped

void ContourColorSetScoped(const OESystem::OEColor &,
                           unsigned int scope = BestScope)

This function sets the color of the contours in the specified scope.

ContourDrawAsSurfaceGet

bool ContourDrawAsSurfaceGet(unsigned int id=0)

Returns whether or not the contour should be drawn as a solid surface or as a mesh.

ContourDrawAsSurfaceSet

bool ContourDrawAsSurfaceSet(unsigned int id, bool draw)

Sets whether or not the contour should be drawn as a solid surface or as a mesh.

ContourDrawAsSurfaceSetScoped

void ContourDrawAsSurfaceSetScoped(bool draw,
                                   unsigned int scope = BestScope)

Returns the style of contour drawing for the surfaces in scope; essentially it returns the state of the first grid found in scope.

See .

ContourDrawStyleGet

std::string ContourDrawStyleGet(unsigned int id=0)

If “surface” the contours are drawn as a surface, otherwise the contour is drawn as a mesh.

ContourDrawStyleSet

void ContourDrawStyleSet(unsigned int id, const std::string &)

If set to “surface” the contours are drawn as a surface, otherwise the contour is drawn as a mesh.

ContourDrawStyleSetScoped

void ContourDrawStyleSetScoped(const std::string &style,
                               unsigned int scope = BestScope)

Set the drawstyle to all contours in scope.

ContourEntireGridGet

bool ContourEntireGridGet(unsigned int id=0)

Returns True if grid id is contoured over the whole grid. Returns False if only the portion near the center of the scene is contoured.

ContourEntireGridSet

bool ContourEntireGridSet(unsigned int id, bool entire)

If true contour the entire extent of grid id, otherwise only contour the portion near the center of the drawing scene.

ContourHideIndex

void ContourHideIndex(unsigned int index, bool hide)
void ContourHideIndex(unsigned int id, unsigned int index, bool hide)

This function controls the visibility of the contour specified by the grid id and contour index. If the hide parameter is set to true, the contour is hidden, otherwise the contour is shown.

ContourHideIndexGet

bool ContourHideIndexGet(unsigned int id, unsigned int index)

This function returns whether or not the contour specified by the grid id and contour index is hidden or not.

ContourHideIndexSet

void ContourHideIndexSet(unsigned int index, bool hide)
void ContourHideIndexSet(unsigned int id, unsigned int index, bool hide)

This function controls the visibility of the contour specified by the grid id and contour index. If the hide parameter is set to true, the contour is hidden, otherwise the contour is shown.

ContourLineWidthGet

float ContourLineWidthGet(unsigned int id=0)

Returns the line width for drawing mesh contours.

ContourLineWidthSet

float ContourLineWidthSet(unsigned int id, float rad)

Set the line width to width for drawing mesh contours.

ContourPickIsoSurfacesGet

bool ContourPickIsoSurfacesGet()

Returns whether or not contours are selectable by picking.

ContourPickIsoSurfacesSet

void ContourPickIsoSurfacesSet(bool pickable)

Sets whether or not contours are selectable by picking.

ContourTransparencySet

void ContourTransparencySet(const OEPropDB::OEKey &, unsigned int)

Sets the transparency of the contour associated with the specified key. The transparency is determined by the alpha parameter which corresponds to the color alpha value which can range from 0 (completely transparent) to 255 (completely opaque).

DefaultColorLabelGet

OESystem::OEColor DefaultColorLabelGet()

Returns the default color for a label.

DefaultColorLabelSet

OESystem::OEColor DefaultColorLabelSet(const OESystem::OEColor &)

Returns the default color for a label.

DefaultColorMarkedGet

OESystem::OEColor DefaultColorMarkedGet()

Returns the default color used when displaying marked objects.

DefaultColorMarkedSet

OESystem::OEColor DefaultColorMarkedSet(const OESystem::OEColor &)

Sets the default color used when displaying marked objects.

DefaultColorReferenceGet

OESystem::OEColor DefaultColorReferenceGet()

Returns the default reference molecule color.

DefaultColorReferenceSet

OESystem::OEColor DefaultColorReferenceSet(const OESystem::OEColor &)

Sets the default reference molecule color.

DefaultColorSelectedGet

OESystem::OEColor DefaultColorSelectedGet()

Returns the default selection color.

DefaultColorSelectedSet

OESystem::OEColor DefaultColorSelectedSet(const OESystem::OEColor &)

Sets the default selection color.

DefaultColorTitleGet

OESystem::OEColor DefaultColorTitleGet()

Returns the default title color.

DefaultColorTitleSet

OESystem::OEColor DefaultColorTitleSet(const OESystem::OEColor &)

Sets the default title color.

DefaultMonitorColorGet

OESystem::OEColor DefaultMonitorColorGet()

Returns the default monitor color.

DefaultMonitorColorSet

OESystem::OEColor DefaultMonitorColorSet(const OESystem::OEColor &)

Sets the default monitor color.

DistanceControlsVisibilityGet

bool DistanceControlsVisibilityGet()

Returns whether or not an atom’s or bond’s distance from the selected set will affect its visibility. The distance cutoff is specified by the AtomHaloSet function.

DistanceControlsVisibilitySet

void DistanceControlsVisibilitySet(bool state)

Sets whether or not an atom’s or bond’s distance from the selected set will affect its visibility. The distance cutoff is specified by the AtomHaloSet function.

DrawAtomsAndBondsGet

bool DrawAtomsAndBondsGet()

Returns whether or not the application has drawing of atoms and bonds enabled. Ordinarily, this function should not need to be called by the user.

DrawAtomsAndBondsSet

bool DrawAtomsAndBondsSet(bool draw)

Sets whether or not the application has drawing of atoms and bonds enabled. Ordinarily, this function should not need to be called by the user.

DrawAxesGet

bool DrawAxesGet()

Returns whether or not axes should be drawn in the application’s 3D display.

DrawAxesSet

bool DrawAxesSet(bool draw)

Sets whether or not axes should be drawn in the application’s 3D display.

DrawCATracesGet

bool DrawCATracesGet()
bool DrawCATracesGet(const OEPropDB::OEKey &k)

Returns whether or not the application has drawing of CA Traces enabled. Ordinarily, this function should not need to be called by the user.

DrawCATracesSet

bool DrawCATracesSet(bool draw)
bool DrawCATracesSet(const OEPropDB::OEKey &, bool draw)

Sets whether or not the application has drawing of CA Traces enabled. Ordinarily, this function should not need to be called by the user.

DrawCATracesSetScoped

bool DrawCATracesSetScoped(bool, unsigned int scope = BestScope)

Sets whether or not a CA Trace should be drawn the proteins in the specified scope.

DrawContoursGet

bool DrawContoursGet()

Returns true if the contours are being drawn. Returns false if no contours are being drawn.

DrawContoursSet

bool DrawContoursSet(bool draw)

If draw is true, then draw all contours for each visible grid. Otherwise no contours are drawn.

DrawLabelsGet

bool DrawLabelsGet()

Returns whether or not the application has drawing of labels enabled.

DrawLabelsSet

bool DrawLabelsSet(bool draw)

Sets whether or not the application has drawing of labels enabled.

DrawMatrixGet

bool DrawMatrixGet()

Returns whether or not the application has matrix (or tiled) displays enabled.

DrawMatrixSet

bool DrawMatrixSet(bool draw)

Sets whether or not the application has matrix (or tiled) displays enabled.

DrawRibbonsGet

bool DrawRibbonsGet()
bool DrawRibbonsGet(const OEPropDB::OEKey &k)

Returns whether or not the application has drawing of protein ribbons enabled. Ordinarily, this function should not need to be called by the user.

DrawRibbonsSet

bool DrawRibbonsSet(bool draw)
bool DrawRibbonsSet(const OEPropDB::OEKey &k, bool draw)

Sets whether or not the application has drawing of protein ribbons enabled. Ordinarily, this function should not need to be called by the user.

DrawRibbonsSetScoped

bool DrawRibbonsSetScoped(bool draw,
                          unsigned int scope = BestScope)

Sets whether or not a ribbon display should be shown for the proteins in the specified scope.

DrawSurfacesGet

bool DrawSurfacesGet()

Returns true if surfaces are being drawn, false if not.

DrawSurfacesSet

bool DrawSurfacesSet(bool draw)

If parameter draw if false, surface objects are not drawn. If draw is true surfaces are drawn.

DrawSymmetryGet

bool DrawSymmetryGet()

Returns whether or not the application has drawing of symmetry enabled.

DrawSymmetrySet

bool DrawSymmetrySet(bool draw)

Sets whether or not the application has drawing of symmetry enabled.

DrawTitlesGet

bool DrawTitlesGet()

Returns whether or not the application has drawing of titles enabled.

DrawTitlesSet

bool DrawTitlesSet(bool draw)

Sets whether or not the application has drawing of symmetry enabled.

DrawUnitCellGet

bool DrawUnitCellGet()

Returns whether or not the application has drawing of unit cells enabled.

DrawUnitCellSet

bool DrawUnitCellSet(bool draw)

Sets whether or not the application has drawing of symmetry enabled.

GridDefaultContourColorByIndexGet

OESystem::OEColor GridDefaultContourColorByIndexGet(unsigned int gridType,
                                                    unsigned int index)

Returns the default contour color for contour index for grids of type gridType.

GridDefaultContourColorByIndexSet

void GridDefaultContourColorByIndexSet(unsigned int gridType,
                                       unsigned int index,
                                       const OESystem::OEColor &color)

Set the default contour color for contour index for grids of type gridType.

GridDefaultDrawAsSurfaceGet

bool GridDefaultDrawAsSurfaceGet(unsigned int gridType)

Returns the default drawing style for contours of grid with type gridType.

If true, then the surface is drawn as a solid surface, otherwise the surface is drawn as a mesh.

GridDefaultDrawAsSurfaceSet

void GridDefaultDrawAsSurfaceSet(unsigned int gridType, bool asSurf)

Set the default drawing style asSurf for contours of grid with type gridType.

If asSurf is true, then the surface is drawn as a solid surface, otherwise the surface is drawn as a mesh.

GridShowCornersGet

bool GridShowCornersGet()

Returns true if grid corners are being shown false if not.

Grid corners are indicators of the extent of visible grids. They are useful for displaying uncontoured grids and showing whether grid space and molecules intersect.

GridShowCornersSet

void GridShowCornersSet(bool show)

Set show to true to show grid corners, false if not.

Grid corners are indicators of the extent of visible grids. They are useful for displaying uncontoured grids and showing whether grid space and molecules intersect.

GridShowLastMaskedGrid

unsigned int GridShowLastMaskedGrid(bool show=true)

Reserved for internal use.

HBondAddTarget

void HBondAddTarget(const OEPropDB::OEKey &key)

This function adds the molecule corresponding to the specified key to the list of targets to be considered when displaying hydrogen bonds. Calling this function on a molecule will cause hydrogens to be added to that molecule if they are not already present.

HBondAddTargetsScoped

void HBondAddTargetsScoped(unsigned int scope = BestScope)

This function adds of the molecules in the specified scope to the list of targets to be considered when displaying hydrogen bonds. Calling this function on a molecule will cause hydrogens to be added to that molecule if they are not already present.

HBondClearTargets

void HBondClearTargets()

This function clears the list of molecule targets to be considered when displaying hydrogen bonds.

HBondColorGet

OESystem::OEColor HBondColorGet()

Returns the current color being used when drawing hydrogen bonds.

HBondColorSet

void HBondColorSet(const OESystem::OEColor &)

Sets the color to be used when drawing hydrogen bonds.

HBondRemoveTarget

void HBondRemoveTarget(const OEPropDB::OEKey &key)

This function removes the molecule corresponding to the specified key from the list of molecule targets to be considered when displaying hydrogen bonds.

HBondRemoveTargetsScoped

void HBondRemoveTargetsScoped(unsigned int scope = BestScope)

This function removes all of the molecules in the specified scope from the list of molecule targets to be considered when displaying hydrogen bonds.

HBondShowExternalGet

bool HBondShowExternalGet()

Returns whether or not external hydrogen bonds (those between two separate molecules) should be displayed if present.

HBondShowExternalSet

void HBondShowExternalSet(bool show)

Sets whether or not external hydrogen bonds (those between two separate molecules) should be displayed if present.

HBondShowInternalGet

bool HBondShowInternalGet()

Returns whether or not internal hydrogen bonds should be displayed if present.

HBondShowInternalSet

void HBondShowInternalSet(bool show)

Sets whether or not internal hydrogen bonds should be displayed if present.

HaloColorDefaultGet

OESystem::OEColor HaloColorDefaultGet()

Returns the default color to be used when displaying halos.

HaloColorDefaultSet

void HaloColorDefaultSet(const OESystem::OEColor &c)

Sets the default color to be used when displaying halos.

HaloColorGet

OESystem::OEColor HaloColorGet(const OEPropDB::OEKey &)

Returns the color of the halo associated with the specified atom key.

HaloColorSet

void HaloColorSet(const OEPropDB::OEKey &k, const std::string &)
void HaloColorSet(const OEPropDB::OEKey &k, const OESystem::OEColor &c)

Sets the color of the halo associated with the specified atom key.

HaloColorSetScoped

void HaloColorSetScoped(const std::string &,
                        unsigned int scope = BestScope)
void HaloColorSetScoped(const OESystem::OEColor &,
                        unsigned int scope = BestScope)

Sets the color of the halos associated with the atoms in the specified scope.

HaloRadiusGet

float HaloRadiusGet(const OEPropDB::OEKey &)

Returns the radius of the halo associated with the specified atom key.

HaloRadiusSet

void HaloRadiusSet(const OEPropDB::OEKey &, float)
void HaloRadiusSet(const OEPropDB::OEKey &, const std::string &)

Sets the radius of the halo associated with the specified atom key.

HaloRadiusSetScoped

void HaloRadiusSetScoped(float, unsigned int scope = BestScope)
void HaloRadiusSetScoped(const std::string &,
                         unsigned int scope = BestScope)

Sets the radius of the halos associated with the atoms in the specified scope.

HaloScaleGet

float HaloScaleGet(const OEPropDB::OEKey &)

Returns the scaling factor for the size of the halo associated with the specified atom key.

HaloScaleSet

void HaloScaleSet(const OEPropDB::OEKey &, float)
void HaloScaleSet(const OEPropDB::OEKey &, const std::string &)

Sets the scaling factor for the size of the halo associated with the specified atom key.

HaloScaleSetScoped

void HaloScaleSetScoped(float, unsigned int scope = BestScope)
void HaloScaleSetScoped(const std::string &,
                        unsigned int scope = BestScope)

Sets the scaling factor for the size of the halo associated with the atoms in the specified scope.

HideNoneScoped

void HideNoneScoped(unsigned int scope = BestScope)

Makes visible any hidden atoms or bonds on all the molecules in the specified scope.

HideOthers

void HideOthers(const std::vector<OEPropDB::OEKey> &keys, bool value)

Hides everything except the objects specified by list of keys passed as a parameter to this function.

HideScoped

void HideScoped(bool value, unsigned int scope = BestScope)

Hides everything in the specified scope.

LabelClearColorScoped

void LabelClearColorScoped(unsigned int scope = BestScope)

This function restores the default label coloring to those labels within the specified scope.

LabelClearScoped

void LabelClearScoped(unsigned int scope = BestScope)

Clears the labels on all the atoms and bonds in the specified scope.

LabelColorScoped

void LabelColorScoped(const OESystem::OEColor &c,
                      unsigned int scope = BestScope)

This function sets the color of the labels in the specified scope to be the specified color c.

LabelDefaultColorGet

OESystem::OEColor LabelDefaultColorGet()

This function returns the default color for labels.

LabelDefaultColorSet

void LabelDefaultColorSet(const OESystem::OEColor &c)

This function sets the default color for labels.

LabelFixedSizeGet

bool LabelFixedSizeGet()

Returns whether or not labels are drawn using a fixed size on the screen or whether they scale with zooming of the scene.

LabelFixedSizeSet

void LabelFixedSizeSet(bool fixed)

Sets whether or not labels are drawn using a fixed size on the screen or whether they scale with zooming of the scene.

LabelGet

std::string LabelGet(const OEPropDB::OEKey &key, bool full=false,
                     bool coords=true)

Returns a description of the specified object. If the full parameter is True, it will also include information from the parent object (if one exists). The coords parameter specifies whether or not coordinates should be included in the description (primarily for atoms and vertices).

MoleculeAltLocationShow

bool MoleculeAltLocationShow(const OEPropDB::OEKey &, unsigned int, bool)
bool MoleculeAltLocationShow(const OEPropDB::OEKey &, unsigned int, unsigned int,
                             unsigned int)

Sets the visibility of the specified alternate locations for the specified molecule. This function is primarily intended for internal use only.

MoleculeAltLocationVisible

bool MoleculeAltLocationVisible(const OEPropDB::OEKey &, unsigned int)
bool MoleculeAltLocationVisible(const OEPropDB::OEKey &, unsigned int,
                                unsigned int)

Returns whether or the specified alternate locations on the specified molecule are visible. This function is primarily intended for internal use only.

MoleculeAtomBondStyleSetScoped

void MoleculeAtomBondStyleSetScoped(const std::string &atomStyle,
                                    const std::string &bondStyle,
                                    unsigned int scope = BestScope)

Set the combined style for atoms and bonds.

  • atomStyle is the style to set the atom , see AtomStyleSetScoped.
  • bondStyle is the style to set the bond, see BondStyleSetScoped.
  • scope is the default scope to use.

MoleculeColorByScoped

void MoleculeColorByScoped(const std::string &property,
                           const std::string &params="",
                           unsigned int scope = BestScope)

This color colors all the molecules in the specified scope according to the scheme specified by the property parameter. Valid properties include:

* "amino"
* "bfactor"
* "chain"
* "charge"
* "cpk"
* "cpknew"
* "formal charge"
* "group"
* "hbond"
* "hydrophobicity"
* "partial charge"
* "shapely"

If the specified property is hydrophobicity, the specific scale to be used can be specified in the params parameter. Valid scale options include:

* "charifson"
* "eisenberg"
* "kytedolittle"
* "whiteoctanol"

For more details on the specifics of these coloring scheme, please see the user manual.

MoleculeColorsResetScoped

void MoleculeColorsResetScoped(unsigned int scope = BestScope)

This function restores the default atom and bond coloring to those atoms and bonds in the specified scope. It is essentially equivalent to calling AtomClearColorScoped followed by BondClearColorScoped.

MoleculeDarkColorsGet

bool MoleculeDarkColorsGet()

Returns whether or not the application is using either the atom or residue color palette designed for dark colored backgrounds. Otherwise, the application is using the atom color palettes designed for light colored backgrounds. All of these palettes can be edited in the preferences. For more information, see the functions AtomDarkColorsGet and ResidueDarkColorsGet.

MoleculeDarkColorsSet

void MoleculeDarkColorsSet(bool dark)

Sets whether or not the application is using the atom and residue color palettes designed for dark colored backgrounds. Otherwise, the application is using the atom color palettes designed for light colored backgrounds. All of these palettes can be edited in the preferences. For more information, see the functions AtomDarkColorsSet and ResidueDarkColorsSet.

MoleculeShowfAntsyGet

bool MoleculeShowfAntsyGet()

Returns whether or not the application is using the high quality molecule representations as opposed to standard models.

MoleculeShowfAntsySet

bool MoleculeShowfAntsySet(bool show)

Sets whether or not the application is using the high quality molecule representations as opposed to standard models.

MoleculeStyleGet

std::string MoleculeStyleGet()

Returns the default molecule style. The default is “stick”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleGetScoped

unsigned int
  MoleculeStyleGetScoped(unsigned int scope = BestScope)

Returns the style of the molecules in the specified scope. If there are multiple styles present, the return type is “mixed”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleLargeGet

std::string MoleculeStyleLargeGet()

Returns the default molecule style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is “wireframe”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleLargeSet

void MoleculeStyleLargeSet(unsigned int style)
void MoleculeStyleLargeSet(const std::string &style)

Sets the default molecule style for large molecules, where large is determined by whether or not the number of atoms in the molecule exceeds the specified cutoff. For more information on this cutoff, see the MoleculeSizeCutoff function. The default is “wireframe”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleNucleicGet

std::string MoleculeStyleNucleicGet()

Returns the default molecule style for nucleic acids. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

MoleculeStyleNucleicSet

void MoleculeStyleNucleicSet(unsigned int style)
void MoleculeStyleNucleicSet(const std::string &style)

Sets the default molecule style for nucleic acids. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

MoleculeStyleProteinGet

std::string MoleculeStyleProteinGet()

Returns the default molecule style for proteins. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

MoleculeStyleProteinSet

void MoleculeStyleProteinSet(unsigned int style)
void MoleculeStyleProteinSet(const std::string &style)

Sets the default molecule style for proteins. The default is to mirror the large molecule style. See the MoleculeStyleLargeSet function for more information about large molecules and see the MoleculeStyleSetScoped function for more information about molecule styles.

Note: this function is a placeholder for a future implementation and therefore does not currently have any effect.

MoleculeStyleSet

void MoleculeStyleSet(unsigned int style)
void MoleculeStyleSet(const std::string &atomStyle)

Sets the default molecule style. This function accepts either a string or an enumerated representation as its parameter. The default is “stick”. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleSetScoped

void MoleculeStyleSetScoped(unsigned int style,
                            unsigned int scope = BestScope)
void MoleculeStyleSetScoped(const std::string &atomStyle,
                            unsigned int scope = BestScope)

Sets the display style for the specified molecules. This function accepts either a string or an enumerated representation as its parameter. Available molecule styles include:

* "ball and stick" molecules are drawn in ball and stick mode
* "cpk"            molecules are drawn in CPK mode
* "stars"          molecules are drawn in star mode
* "stick"          molecules are drawn in stick mode
* "wireframe"      molecules are drawn in wireframe mode
* "none"           molecules are not drawn, but are still considered visible and thus selectable
* "hidden"         molecules are not drawn and are not considered visible and thus are not selectable

MoleculeStyleToEnum

unsigned int MoleculeStyleToEnum(const std::string &style)

This function returns the enumerated type associated the specified string molecule style representation. See the MoleculeStyleSetScoped function for more information about molecule styles.

MoleculeStyleToText

std::string MoleculeStyleToText(unsigned int style)

This function returns the text string associated with the specified enumerated molecule style representation. See the MolStyleSetScoped function for more information about molecule styles.

MonitorAngleCreate

unsigned int MonitorAngleCreate(const OEPropDB::OEKey &key1,
                                const OEPropDB::OEKey &key2,
                                const OEPropDB::OEKey &key3)

Attempts to create an angle monitor between the atoms specified by the parameters key1, key2, and key3.

Returns the ID of the created monitor or 0 if one could not be created.

MonitorAngleDelete

void MonitorAngleDelete(const OEPropDB::OEKey &key1,
                        const OEPropDB::OEKey &key2,
                        const OEPropDB::OEKey &key3)

Deletes the monitor, if any, specified by atom keys: key1, key2, key3.

MonitorAngleExists

unsigned int MonitorAngleExists(const OEPropDB::OEKey &key1,
                                const OEPropDB::OEKey &key2,
                                const OEPropDB::OEKey &key3)

Returns the ID of the angle monitor defined by the specified atom keys or zero if no such monitor exists.

MonitorColorGet

OESystem::OEColor MonitorColorGet(const OEPropDB::OEKey &monitor)

Returns the color of the specified monitor.

MonitorColorSet

void MonitorColorSet(const OEPropDB::OEKey &monitor,
                     const OESystem::OEColor &clr)

Sets the color of the specified monitor.

MonitorDeleteScoped

void MonitorDeleteScoped(unsigned int scope = BestScope)

Deletes all the monitors in the specified scope.

MonitorDistanceCreate

unsigned int MonitorDistanceCreate(const OEPropDB::OEKey &key1,
                                   const OEPropDB::OEKey &key2)

Attempts to create a distance monitor between the two atoms specified by the parameters key1 and key2.

Returns the ID of the created monitor or 0 if one could not be created.

MonitorDistanceDelete

void MonitorDistanceDelete(const OEPropDB::OEKey &key1,
                           const OEPropDB::OEKey &key2)

Deletes the monitor specified by the two atom keys.

MonitorDistanceExists

unsigned int MonitorDistanceExists(const OEPropDB::OEKey &key1,
                                   const OEPropDB::OEKey &key2)

Returns the ID of the distance monitor determined by the two atom keys or zero if no such monitor exists.

MonitorSphereCreate

unsigned int MonitorSphereCreate(const OEPropDB::OEKey &key1,
                                 const std::string &name,
                                 const OESystem::OEColor &clr, float radius=0)
unsigned int MonitorSphereCreate(const OEPropDB::OEKey &parent,
                                 const std::string &name, float x, float y,
                                 float z, float radius,
                                 const OESystem::OEColor &color)

Create a sphere monitor on an atom specified by key1 or at the coordinates specified by x, y, and z. The monitor is only visible when the specified atom key or parent key (in the case of coordinate specification) is visible.

Returns the ID of the newly created monitor or 0 if one could not be created.

MonitorTorsionCreate

unsigned int MonitorTorsionCreate(const OEPropDB::OEKey &key1,
                                  const OEPropDB::OEKey &key2,
                                  const OEPropDB::OEKey &key3,
                                  const OEPropDB::OEKey &key4)

Attempts to create a torsion monitor between the atoms specified by key1, key2, key3, and key4.

Returns the ID of the created monitor or 0 if one could not be created.

MonitorTorsionDelete

void MonitorTorsionDelete(const OEPropDB::OEKey &key1,
                          const OEPropDB::OEKey &key2,
                          const OEPropDB::OEKey &key3,
                          const OEPropDB::OEKey &key4)

Deletes the torsion monitor, if any, specified by the atom keys: key1, key2, key3, key4.

MonitorTorsionExists

unsigned int MonitorTorsionExists(const OEPropDB::OEKey &key1,
                                  const OEPropDB::OEKey &key2,
                                  const OEPropDB::OEKey &key3,
                                  const OEPropDB::OEKey &key4)

Returns the ID of the torsion monitor determined by the specified four atom keys or zero if no such monitor exists.

MonitorsVisible

bool MonitorsVisible()

This function returns whether any monitors are currently visible.

MonitorsVisibleDelete

void MonitorsVisibleDelete()

Deletes all monitors that are currently being displayed.

PaneActivated

void PaneActivated(unsigned int pane)

In matrix (tiled) mode, sets the specified pane to be the active pane in the display. Ordinarily, this function should not need to be called by the user.

ProteinColorByBFactor

void ProteinColorByBFactor(const OEPropDB::OEKey &key, int bins=10)
void ProteinColorByBFactor(const OEPropDB::OEKey &key,
                           const std::vector<BFactorColor> &clrs)
void ProteinColorByBFactor(const OEPropDB::OEKey &key, float min, float max,
                           const OESystem::OEColor &clr)

Colors a protein referenced by key using bins values for blue and red. Bright blue is low temperature, Bright red is high temperature.

You can make a range of custom colors as follows. colors = [] colors.append(BFactorColor(10, 20, OEggColor(255, 0, 0))) colors.append(BFactorColor(20, 30, OEggColor(255, 255, 0))) colors.append(BFactorColor(20, 30, OEggColor(255, 255, 255)))

ProteinColorByBFactor(key, colors) Applies the bfactor coloring specified by colors to the protein specified by key.

ProteinColorByBFactorScoped

void ProteinColorByBFactorScoped(unsigned int scope, int bins=10)
void ProteinColorByBFactorScoped(unsigned int scope,
                                 const std::vector<BFactorColor> &clrs)
void ProteinColorByBFactorScoped(unsigned int scope, float min, float max,
                                 const OESystem::OEColor &clr)

Scoped versions of .

ResidueColorPaletteUpdate

void ResidueColorPaletteUpdate()

This function updates the default residue coloring palette based on whether or not the application is using a dark or light colored background scheme. This function is called internally and should not by called by the user.

ResidueDarkColorsGet

bool ResidueDarkColorsGet()

Returns whether or not the application is using the residue color palette designed for dark colored backgrounds. Otherwise, the application is using the residue color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.

ResidueDarkColorsSet

void ResidueDarkColorsSet(bool dark)

Sets whether or not the application is using the residue color palette designed for dark colored backgrounds. Otherwise, the application is using the residue color palette designed for light colored backgrounds. Both of these palettes can be edited in the preferences.

ResidueDefaultColorGet

OESystem::OEColor ResidueDefaultColorGet()
OESystem::OEColor ResidueDefaultColorGet(unsigned int res)

Returns the current default residue color. The default residue color is applied to every residue that does not have its own specific default color assigned. Calling this function with the res parameter returns the specific default color associated with the passed residue index.

ResidueDefaultColorSet

void ResidueDefaultColorSet(const OESystem::OEColor &c)
void ResidueDefaultColorSet(unsigned int res, const OESystem::OEColor &c)

Sets the current default residue color. The default residue color is applied to every residue that does not have its own specific default color assigned. Calling this function with the res parameter sets the specific default color associated with the passed residue index.

RibbonClearColorScoped

void RibbonClearColorScoped(unsigned int scope = BestScope)

This function restores the default ribbon coloring to those ribbons within the specified scope.

RibbonColorSetScoped

void RibbonColorSetScoped(const OESystem::OEColor &c,
                          unsigned int scope = BestScope)

This function sets the color of the ribbons in the specified scope to be the specified color c.

RibbonCrossResolutionGet

unsigned int RibbonCrossResolutionGet()

Returns the cross resolution used in calculating protein ribbons.

RibbonCrossResolutionSet

unsigned int RibbonCrossResolutionSet(unsigned int res)

Sets the cross resolution used in calculating protein ribbons.

RibbonGapGet

float RibbonGapGet()

Returns the gap value used in calculating protein ribbons.

RibbonGapSet

float RibbonGapSet(float gap)

Sets the gap value used in calculating protein ribbons.

RibbonHeightScaleGet

float RibbonHeightScaleGet()

Returns the height scale used in calculating protein ribbons.

RibbonHeightScaleSet

float RibbonHeightScaleSet(float scale)

Sets the height scale used in calculating protein ribbons.

RibbonRadiusGet

float RibbonRadiusGet()

Returns the radius used in calculating protein ribbons.

RibbonRadiusSet

float RibbonRadiusSet(float radius)

Sets the radius used in calculating protein ribbons.

RibbonResolutionGet

unsigned int RibbonResolutionGet()

Returns the resolution used in calculating protein ribbons.

RibbonResolutionSet

unsigned int RibbonResolutionSet(unsigned int res)

Sets the resolution used in calculating protein ribbons.

RibbonSplineTypeGet

std::string RibbonSplineTypeGet()

Returns the spline type used in calculating protein ribbons. Available types include: “CubicHermite” and “Beta”.

RibbonSplineTypeSet

std::string RibbonSplineTypeSet(const std::string &type)

Sets the spline type used in calculating protein ribbons. Available types include: “CubicHermite” and “Beta”.

RibbonStyleGet

std::string RibbonStyleGet()

Returns the style used in displaying protein ribbons. Available types include: “Round”, “Lines”, and “Cartoon”. The default is “Cartoon”.

RibbonStyleSet

std::string RibbonStyleSet(const std::string &style)
std::string RibbonStyleSet(const OEPropDB::OEKey &k, const std::string &style)

Sets the style used in displaying protein ribbons. Available types include: “Round”, “Lines”, and “Cartoon”. The default is “Cartoon”.

RibbonStyleSetScoped

std::string RibbonStyleSetScoped(const std::string &style,
                                 unsigned int scope = BestScope)

Sets the style used in displaying ribbons for the proteins in the specified scope. Available types include: “Round”, “Lines”, and “Cartoon”. The default is “Cartoon”.

RibbonWidthScaleGet

float RibbonWidthScaleGet()

Returns the width scale used in calculating protein ribbons.

RibbonWidthScaleSet

float RibbonWidthScaleSet(float scale)

Sets the width scale used in calculating protein ribbons.

SceneDrawActiveBorderGet

bool SceneDrawActiveBorderGet()

Returns whether or not a border is drawn (in matrix mode) around the cell containing the focused object.

SceneDrawActiveBorderSet

void SceneDrawActiveBorderSet(bool draw)

Sets whether or not a border is drawn (in matrix mode) around the cell containing the focused object.

SceneMatrixModeGet

std::string SceneMatrixModeGet()

Returns the display style for the individual cells when the application is in matrix mode. Available styles are: “OnePerView”, “LockedOnAll”, and “LockedPerView”.

SceneMatrixModeSet

std::string SceneMatrixModeSet(std::string mode)

Sets the display style for the individual cells when the application is in matrix mode. Available styles are: “OnePerView”, “LockedOnAll”, and “LockedPerView”.

SelectionColorBlendFactorGet

float SelectionColorBlendFactorGet()

Returns the alpha buffer coloring blending factor for selection colors. The default value is 1.0 which corresponds to zero blending with the selection color being the one displayed. A value of 0.0 also corresponds to zero blending but with the underlying color being the one displayed. A value of 0.5 corresponds to even blending of the underlying color and the selected color.

SelectionColorBlendFactorSet

float SelectionColorBlendFactorSet(float alpha)

Sets the alpha buffer coloring blending factor for selection colors. The default value is 1.0 which corresponds to zero blending with the selection color being the one displayed. A value of 0.0 also corresponds to zero blending but with the underlying color being the one displayed. A value of 0.5 corresponds to even blending of the underlying color and the selected color.

ShowESGridScoped

void ShowESGridScoped(bool show=true,
                      unsigned int scope = BestScope)

If show is true, attach and show electrostatic grids to all molecules in scope.

If show if false, hide all attached electrostatic grids to molecules in scope.

ShowSurface

void ShowSurface(const OEPropDB::OEKey &, const std::string &, bool show)

Sets whether or not a property surface of the specified type is displayed for the molecule associated with the specified key. Valid types are “molecular” and “accessible”.

ShowSurfaceScoped

void ShowSurfaceScoped(const std::string &type, bool show,
                       unsigned int scope = BestScope)

Scoped version of .

SurfaceAlterTransparency

void SurfaceAlterTransparency(unsigned int id, unsigned int alpha)

Sets the transparency of the surface associated with the specified id. The transparency is specified by the alpha parameter which determines the alpha component of the surface color. The alpha values ranges from 0 (completely transparent) to 255 (completely opaque).

SurfaceColorBy

std::string SurfaceColorBy(const std::string &mode="")
void SurfaceColorBy(const OEPropDB::OEKey &key, const std::string &mode,
                    const std::string &params="")

This function colors the surface referenced by the specified key using the specified style. Valid styles include:

  • atom - colors the surface based on the color of the nearest atom to the

    vertex being colored

  • concavity - colors the surface by concavity, red is high concavity.

  • curvature - colors the surface by curvature, green is positive curvature.

  • distance - colors the surface by its distance to the currently selected atoms.

    Each color band represents two angstroms.

  • electrostatics - colors the surface using a red-to-blue scheme based on the

    electrostatic potential observed at the surface.

  • hydrogen bonds - colors the surface by the underlying atom hydrogen-bond

    donor/acceptor properties. Donors are red and acceptors are blue.

  • hydrophobicity - colors the surface using a hydrophobic color scale. There

    are four different hydrophobic scales available: charifson, eisenberg, kytedolittle, and whiteoctanol. The desired scale can be set in the application preferences.

  • potential - colors the surface based using a red-to-blue scheme (low to high)

    over the values in the surface’s potential array. This is not the same as coloring by electrostatics.

SurfaceColorByScoped

void SurfaceColorByScoped(const std::string &colorby,
                          const std::string &params="",
                          unsigned int scope = BestScope)

Scoped version of .

SurfaceColorGet

OESystem::OEColor SurfaceColorGet(unsigned int id)

Returns the color of the specified surface.

SurfaceColorGetScoped

OESystem::OEColor
  SurfaceColorGetScoped(unsigned int scope = BestScope)

Returns the color of the first surface found in the specified scope.

SurfaceColorSet

OESystem::OEColor SurfaceColorSet(unsigned int id,
                                  const OESystem::OEColor &color)

Set the color of the surface id to color.

SurfaceColorSetScoped

void SurfaceColorSetScoped(const OESystem::OEColor &color,
                           unsigned int scope = BestScope)

Set the color of the surfaces in scope to color.

SurfaceGrowTriangle

void SurfaceGrowTriangle(unsigned int oerid, const OEPropDB::OEKey &trikey,
                         bool addtriangle=false)

Grow the surface selection when a triangle is double clicked. Ordinarily this function does not need to be called.

SurfaceLineWidthGet

float SurfaceLineWidthGet(unsigned int id=0)

Returns the line width used when drawing the surface specified by id in mesh mode.

SurfaceLineWidthSet

float SurfaceLineWidthSet(unsigned int id, float width)

Sets the line width used when drawing the surface specified by id in mesh mode.

SurfaceStyleGet

std::string SurfaceStyleGet(unsigned int id)

Returns the default style of surfaces. The style is one of:

  • mesh - the surfaces are drawn as meshes.
  • points - the surfaces are drawn as points.
  • solid - the surfaces are drawn as solid objects.

SurfaceStyleGetScoped

std::string SurfaceStyleGetScoped(unsigned int scope = BestScope)

Return the style for the surfaces in scope. The value returned is from the first surface found in scope and is not indicative of all surfaces.

See for a list of surface styles.

SurfaceStyleSet

std::string SurfaceStyleSet(unsigned int id, const std::string &style)

Set the surface id to on of the following styles:

  • mesh - the surface is drawn as a mesh.
  • points - the surface is drawn as points.
  • solid - the surface is drawn as a solid object.

SurfaceStyleSetScoped

void SurfaceStyleSetScoped(const std::string &style,
                           unsigned int scope = BestScope)

Scoped version of .

SurfaceTransparencySet

void SurfaceTransparencySet(unsigned int id, unsigned int alpha)

Set the transparency to all surfaces in scope to transparency.

SurfaceTransparencySetScoped

void SurfaceTransparencySetScoped(unsigned int transparency,
                                  unsigned int scope = BestScope)

Set the transparency to all surfaces in scope to transparency.

SurfaceVertexFloodScoped

int SurfaceVertexFloodScoped(unsigned int scope = BestScope)

Get the surface vertex flood of all surfaces in scope. This is essentially the flood of the focused surface or the surface of the focused or first visible molecule.

SymmetryColorModeGet

unsigned int SymmetryColorModeGet()

SymmetryColorModeSet

unsigned int SymmetryColorModeSet(unsigned int mode)

TitleDefaultColorGet

OESystem::OEColor TitleDefaultColorGet()

Returns the default color for titles.

TitleDefaultColorSet

void TitleDefaultColorSet(const OESystem::OEColor &c)

Sets the default color for titles.

TitlesDrawAboveGet

bool TitlesDrawAboveGet()

Returns whether or not titles are drawn at the top of the scene or the bottom of the scene.

TitlesDrawAboveSet

void TitlesDrawAboveSet(bool top)

Sets whether or not titles are drawn at the top of the scene or the bottom of the scene.

TransparencySet

void TransparencySet(const OEPropDB::OEKey &, unsigned int alpha)

This function sets the transparency of the object associated with the specified key. The transparency is determined by the specified parameter alpha which corresponds to the desired alpha value of the object’s color. Alpha can range from 0 (completely transparent) to 255 (completely opaque).

TransparencySetScoped

void TransparencySetScoped(unsigned int alpha,
                           unsigned int scope = BestScope)

This function sets the transparency of all the objects in the specified scope. The transparency is determined by the specified parameter alpha which corresponds to the desired alpha value of the object’s color. Alpha can range from 0 (completely transparent) to 255 (completely opaque).

ViewerAmbientLightGet

OESystem::OEColor ViewerAmbientLightGet()

Returns the OpenGL ambient light property.

ViewerAmbientLightSet

OESystem::OEColor ViewerAmbientLightSet(const OESystem::OEColor &color)

Sets the OpenGL ambient light property.

ViewerAmbientMaterialGet

OESystem::OEColor ViewerAmbientMaterialGet()

Returns the OpenGL ambient material property.

ViewerAmbientMaterialSet

OESystem::OEColor ViewerAmbientMaterialSet(const OESystem::OEColor &color)

Sets the OpenGL ambient material property.

ViewerAnimate

void ViewerAnimate(const std::vector<float> &centers,
                   const std::vector<float> &look,
                   const std::vector<float> &up,
                   unsigned int              msec,
                   unsigned int              fps)

Reserved for future use.

ViewerAnimateTo

void ViewerAnimateTo( const std::string &bookmark,
                      unsigned int       msec,
                      unsigned int       fps)
void ViewerAnimateTo( const OEPropDB::OEKey &centerKey,
                      const OEPropDB::OEKey &refKey,
                      unsigned int           msec,
                      unsigned int           fps,
                      float                  zoom = 0.0 )
void ViewerAnimateTo( const std::vector<float> &center,
                      const std::vector<float> &look,
                      const std::vector<float> &up,
                      unsigned int              msec,
                      unsigned int              fps,
                      float                     zoom = 0.0 )

Animates the scene from the current position to the specified position. All implementations of this function take an msec and fps parameters. The msec parameter specifies how long it should take the animation to be performed. Please note that this time is only a suggestion, as many factors including CPU speed, GPU speed, and available memory will influence the actual performance of the animation. The fps parameters specifies how many frames per second should be used in the animation.

The first implementation takes a bookmark name as its only other parameter. The second implementation takes two OEKey parameters corresponding to the desired final center and viewing point positions for the scene. The third implementation takes three arrays corresponding to the center coordinates, a vector defining the viewing angle, and a vector defining the up direction for the scene.

ViewerAntialiasGet

bool ViewerAntialiasGet()

Returns whether or not antialiasing is turned on for line drawing.

ViewerAntialiasSet

bool ViewerAntialiasSet(bool state)

Sets whether or not antialiasing is turned on for line drawing.

ViewerAutoCenterGet

bool ViewerAutoCenterGet()

Returns whether or not the scene will automatically be recentered when a change in the scene occurs (e.g. a new object is made active, objects are hidden or shown).

ViewerAutoCenterPanesGet

bool ViewerAutoCenterPanesGet()

Returns whether or not the scene in each pane in multi-pane display mode is automatically centered or whether all panes observe the same center.

ViewerAutoCenterPanesSet

void ViewerAutoCenterPanesSet(bool center)

Sets whether or not the scene in each pane in multi-pane display mode is automatically centered or whether all panes observe the same center.

ViewerAutoCenterSet

bool ViewerAutoCenterSet(bool ac)

Sets whether or not the scene will automatically be recentered when a change in the scene occurs (e.g. a new object is made active, objects are hidden or shown).

ViewerAutoFitGet

bool ViewerAutoFitGet()

Returns whether or not the contents of the scene will automatically be fit to the screen when a scene change occurs.

ViewerAutoFitSet

bool ViewerAutoFitSet(bool af)

Sets whether or not the contents of the scene will automatically be fit to the screen when a scene change occurs.

ViewerBackgroundColorGet

OESystem::OEColor ViewerBackgroundColorGet()

Returns the background color of the 3D display.

ViewerBackgroundColorSet

OESystem::OEColor ViewerBackgroundColorSet(const OESystem::OEColor &color)

Sets the background color of the 3D display.

ViewerBookmarkLoad

bool ViewerBookmarkLoad(std::string bm)

Loads the specified bookmark.

ViewerBookmarksGetAnimated

bool ViewerBookmarksGetAnimated()

Returns whether or not the transition between bookmarks is animated.

ViewerBookmarksGetAnimationTime

unsigned int ViewerBookmarksGetAnimationTime()

Returns the default desired time for how long the transition between bookmarks should take if animated.

ViewerBookmarksSetAnimated

void ViewerBookmarksSetAnimated(bool animated)

Sets whether or not the transition between bookmarks is animated.

ViewerBookmarksSetAnimationTime

void ViewerBookmarksSetAnimationTime(unsigned int msecs)

Sets the default desired time for how long the transition between bookmarks should take if animated.

ViewerCenterAndRadiusGet

std::vector<float> ViewerCenterAndRadiusGet()

Returns the current center and radius of the scene in the 3D display in a four-membered list. The first three values in the list are the x,y,z coordinates of the center. The fourth value is the radius.

ViewerCenterAndRadiusSet

std::vector<float> ViewerCenterAndRadiusSet(float x, float y, float z,
                                            float radius, bool redraw=true)

Sets the current center and radius of the scene in the 3D display. The redraw parameter determines whether or not the scene should be redrawn immediately.

ViewerCenterGet

std::vector<float> ViewerCenterGet()

Returns the current center of the scene as a list of three values corresponding to the x,y,z coordinates. If for some reason the 3D display is invalid, the list returned will be empty.

ViewerCenterSet

std::vector<float> ViewerCenterSet(unsigned int, bool redraw=true)
std::vector<float> ViewerCenterSet(float x, float y, float z, bool redraw=true)

Sets the current center of the scene. The function that takes three floating point parameters explicitly sets the center of the scene to the coordinates specified by the x, y, and z parameters. The redraw parameter specifies whether or not the scene should be immediately redrawn.

The function that takes a single unsigned integer parameter (id) attempts to center the scene based on the geometry of the object corresponding to the id parameter. If for some reason, a center could not be calculated, this function will return an empty list, otherwise it will return the new center.

ViewerCenterSetScoped

std::vector<float>
  ViewerCenterSetScoped(unsigned int scope = BestScope,
                        bool redraw=true)

Sets the current center of the scene based on the geometry of the objects found within the specified scope. The redraw parameter specifies whether or not the scene should be immediately redrawn. If for some reason, a center could not be calculated, this function will return an empty list, otherwise it will return the new center.

ViewerDepthCueFollowsSlab

bool ViewerDepthCueFollowsSlab()
bool ViewerDepthCueFollowsSlab(bool enable)

Sets whether or not the depthcue parameters should be adjusted as the slabbing parameters change to maintain the best possible lighting for the scene.

ViewerDepthcueEndGet

float ViewerDepthcueEndGet()

Returns the spatial end point used in depthcue calculations. Ordinarily, this function should not need to be called by the user.

ViewerDepthcueEndSet

float ViewerDepthcueEndSet(float end, bool redraw=true)

Sets the spatial end point used in depthcue calculations. Ordinarily, this function should not need to be called by the user.

ViewerDepthcueGet

bool ViewerDepthcueGet()

Returns whether or not depthcueing is currently enabled in the 3D display.

ViewerDepthcueSet

bool ViewerDepthcueSet(bool state)

Sets whether or not depthcueing is currently enabled in the 3D display.

ViewerDepthcueStartGet

float ViewerDepthcueStartGet()

Returns the spatial start point used in depthcue calculations. Ordinarily, this function should not need to be called by the user.

ViewerDepthcueStartSet

float ViewerDepthcueStartSet(float start, bool redraw=true)

Sets the spatial start point used in depthcue calculations. Ordinarily, this function should not need to be called by the user.

ViewerDiffuseLightGet

OESystem::OEColor ViewerDiffuseLightGet()

Returns the OpenGL diffuse light property.

ViewerDiffuseLightSet

OESystem::OEColor ViewerDiffuseLightSet(const OESystem::OEColor &color)

Sets the OpenGL diffuse light property.

ViewerDiffuseMaterialGet

OESystem::OEColor ViewerDiffuseMaterialGet()

Returns the OpenGL diffuse material property.

ViewerDiffuseMaterialSet

OESystem::OEColor ViewerDiffuseMaterialSet(const OESystem::OEColor &color)

Set the OpenGL diffuse material property.

ViewerDrawDepictionsGet

bool ViewerDrawDepictionsGet()

Returns whether or not a 2D depiction is drawn in the 3D display for the active molecule.

ViewerDrawDepictionsSet

bool ViewerDrawDepictionsSet(bool show)

Sets whether or not a 2D depiction is drawn in the 3D display for the active molecule.

ViewerFit

void ViewerFit(float buffer=0.0f)
void ViewerFit(const std::vector<OEPropDB::OEKey> &keys, float buffer=0.0f)

This function ensures that the entire contents of the scene fit within the 3D display window. The buffer parameter allows specification of an additional buffer applied to the radius of the scene.

The function that takes a list of keys as a parameter will perform the same function as above, but will only ensure that those objects corresponding to the specified keys will be guaranteed to fit within the 3D display window.

ViewerFontSizeGet

unsigned int ViewerFontSizeGet()

Return the size of the font used for text drawn in the 3D display.

ViewerFontSizeSet

void ViewerFontSizeSet(unsigned int sz)

Sets the size of the font used for text drawn in the 3D display.

ViewerForwardGet

std::vector<float> ViewerForwardGet()

Returns the forward facing vector for the OpenGL camera.

ViewerLODGet

int ViewerLODGet()

Returns the level of display (rendering quality) being used in 3D display window.

ViewerLODSet

int ViewerLODSet(unsigned int lod, bool redraw=true)

Sets the level of display (rendering quality) being used in the 3D display.

ViewerLightPositionGet

std::vector<float> ViewerLightPositionGet()

Returns the position of the OpenGL light source.

ViewerLightPositionSet

std::vector<float> ViewerLightPositionSet(const std::vector<float> &pos)

Sets the position of the OpenGL light source.

ViewerLookAt

void ViewerLookAt(const OEPropDB::OEKey &centerKey,
                  const OEPropDB::OEKey &refKey, bool redraw=true)
void ViewerLookAt(const std::vector<float> &center,
                  const std::vector<float> &look,
                  const std::vector<float> &up, bool redraw=true)

Sets up the display such that the object corresponding to centerKey is at the center of the display with the camera looking down the axis between centerKey and the object corresponding to refKey.

ViewerMirrorSlabsGet

bool ViewerMirrorSlabsGet()

Returns whether or not the position of the front and back clipping planes mirror each other.

ViewerMirrorSlabsSet

bool ViewerMirrorSlabsSet(bool mirror)

Sets whether or not the position of the front and back clipping planes mirror each other.

ViewerNiceFontsGet

bool ViewerNiceFontsGet()

Returns whether or not text is rendered in the 3D display using high-quality fonts versus simple fonts. Some graphics cards cannot properly handle the high-quality fonts and it is recommended in those situations not to use “nice” fonts.

ViewerNiceFontsSet

bool ViewerNiceFontsSet(bool nice)

Sets whether or not text is rendered in the 3D display using high-quality fonts versus simple fonts. Some graphics cards cannot properly handle the high-quality fonts and it is recommended in those situations not to use “nice” fonts.

ViewerOrientationGet

std::vector<float> ViewerOrientationGet()

Returns the OpenGL camera orientation matrix.

ViewerOrientationSet

std::vector<float> ViewerOrientationSet(std::vector<float> orientationMatrix)

Sets the OpenGL camera orientation matrix.

ViewerProjectorModeGet

bool ViewerProjectorModeGet()

Returns whether or not the display is being drawn in “Projector Mode”. “Projector Mode” is a display mode which is designed to improve visibility when the application is projected using an LCD projector by using a lighter background and a different atom coloring scheme.

ViewerProjectorModeSet

void ViewerProjectorModeSet(bool state)

Sets whether or not the display is being drawn in “Projector Mode”. “Projector Mode” is a display mode which is designed to improve visibility when the application is projected using an LCD projector by using a lighter background and a different atom coloring scheme.

ViewerRadiusGet

float ViewerRadiusGet()

Returns the current radius of the scene in the 3D display window.

ViewerRadiusSet

float ViewerRadiusSet(float radius, bool redraw=true)

Sets the current radius of the scene in the 3D display window. The redraw parameter specifies whether or not to immediately redraw the scene.

ViewerRecenter

void ViewerRecenter()

This function recenters the scene based on the geometry of the contents of the scene.

ViewerReprobeStereo

bool ViewerReprobeStereo()

This function rechecks to see whether hardware stereo is supported on the current machine. Ordinarily, this function should not need to be called by the user.

ViewerRotate

void ViewerRotate(const std::string &axis, float angle, bool redraw=true)

This function rotates the display around the specified axis (valid parameters: ‘x’,’y’,’z’ for screen or trackball axis, ‘X’, ‘Y’, ‘Z’ for world axis) by angle degrees. The center of rotation is the world center. The redraw parameter specifies whether or not to immediately redraw the scene.

ViewerScaleGet

float ViewerScaleGet()

Returns the scale of the scene in the 3D display window.

ViewerScaleSet

float ViewerScaleSet(float radius, bool redraw=true)

Sets the scale of the scene in the 3D display window.

ViewerShininessMaterialGet

float ViewerShininessMaterialGet()

Returns the OpenGL material shininess property.

ViewerShininessMaterialSet

float ViewerShininessMaterialSet(float shine)

Sets the OpenGL material shininess property.

ViewerShowActiveBorderGet

bool ViewerShowActiveBorderGet()

Returns whether or not a blue border is drawn around the active pane in multi-pane display mode.

ViewerShowActiveBorderSet

void ViewerShowActiveBorderSet(bool show)

Sets whether or not a blue border is drawn around the active pane in multi-pane display mode.

ViewerShowGridGet

bool ViewerShowGridGet()

Returns whether or not borders are drawn around individual panes in multi-pane display mode.

ViewerShowGridSet

void ViewerShowGridSet(bool show)

Sets whether or not borders are drawn around individual panes in multi-pane display mode.

ViewerShowTrackballGuideSet

void ViewerShowTrackballGuideSet(bool show)

Sets whether or not a trackball guide will be displayed on the 3D display window to help guide what is considered inside and outside with respect to mouse actions. Please see ViewerMouseOutsideAwareGet/Set functions for more details.

ViewerSlabEnableGet

bool ViewerSlabEnableGet()

Returns whether or not slabbing (clipping) of the 3D display is enabled.

ViewerSlabEnableSet

bool ViewerSlabEnableSet(bool enable)

Sets whether or not slabbing (clipping) of the 3D display is enabled. The redraw parameter specifies whether or not the scene should be immediately redrawn.

ViewerSlabFarGet

float ViewerSlabFarGet()

Returns the spatial position of the far clipping plane. Ordinarily, this function should not need to be called by the user.

ViewerSlabFarSet

float ViewerSlabFarSet(float radius, bool redraw=true)

Sets the spatial position of the far clipping plane. The redraw parameter specifies whether or not the scene should be immediately redrawn. Ordinarily, this function should not need to be called by the user.

ViewerSlabNearGet

float ViewerSlabNearGet()

Returns the spatial position of the near clipping plane. Ordinarily, this function should not need to be called by the user.

ViewerSlabNearSet

float ViewerSlabNearSet(float radius, bool redraw=true)

Sets the spatial position of the near clipping plane. The redraw parameter specifies whether or not the scene should be immediately redrawn. Ordinarily, this function should not need to be called by the user.

ViewerSlabWidthGet

float ViewerSlabWidthGet()

Returns the distance between the near and far clipping planes. Ordinarily, this function should not need to be called by the user.

ViewerSlabWidthSet

float ViewerSlabWidthSet(float width, bool redraw=true)

Sets the distance between the near and far clipping planes. The redraw parameter specifies whether or not the scene should be immediately redrawn. Ordinarily, this function should not need to be called by the user.

ViewerSpecularMaterialGet

OESystem::OEColor ViewerSpecularMaterialGet()

Returns the OpenGL specular material property.

ViewerSpecularMaterialSet

OESystem::OEColor ViewerSpecularMaterialSet(const OESystem::OEColor &color)

Sets the OpenGL specular material property.

ViewerStereoAngleGet

float ViewerStereoAngleGet()

Returns the angle used when calculating stereographic display offsets.

ViewerStereoAngleSet

float ViewerStereoAngleSet(float angle)

Sets the angle used when calculating stereographic display offsets.

ViewerStereoCrossEyedGet

bool ViewerStereoCrossEyedGet()

Returns whether or not the stereographic display is in cross-eyed mode.

ViewerStereoCrossEyedSet

bool ViewerStereoCrossEyedSet(bool cross)

Sets whether or not the stereographic display is in cross-eyed mode.

ViewerStereoEnableGet

bool ViewerStereoEnableGet()

Returns whether or not stereographic display is enabled.

ViewerStereoEnableSet

bool ViewerStereoEnableSet(bool enabled)

Sets whether or not stereographic display is enabled.

ViewerStereoHardwareGet

bool ViewerStereoHardwareGet()

Returns whether or not stereo hardware is being used for the stereographic display.

ViewerStereoHardwareSet

bool ViewerStereoHardwareSet(bool hardware)

Sets whether or not stereo hardware is being used for the stereographic display.

ViewerStereoSeparationGet

float ViewerStereoSeparationGet()

Returns the eye separation used in stereographic display mode.

ViewerStereoSeparationSet

float ViewerStereoSeparationSet(float separation)

Sets the eye separation used in stereographic display mode.

ViewerStereoStyleGet

unsigned char ViewerStereoStyleGet()

Sets the stereographic display mode (hardware, splitscreen, or none).

ViewerStereoStyleSet

unsigned char ViewerStereoStyleSet(unsigned char style)

Sets the stereographic display mode (hardware, stencil, splitscreen, or none).

ViewerStyleControlVisibleGet

bool ViewerStyleControlVisibleGet(const std::string &style)

Returns whether or not the specified style control widget is currently visible above the 3D display. Available style widgets include: “color”, “selection”, “style”, “contours”, and “graphics”.

ViewerStyleControlVisibleSet

void ViewerStyleControlVisibleSet(const std::string &style, bool vis)

Sets whether or not the specified style control widget is currently visible above the 3D display. Available style widgets include: “color”, “selection”, “style”, “contours”, and “graphics”.

ViewerSupportsHWStereo

bool ViewerSupportsHWStereo()

Returns whether or not the machine the application is being run on supports the use hardware stereo.

ViewerTextFontGet

std::string ViewerTextFontGet()

Returns the font currently being used when rendering text in the 3D display. This font only applies when using “nice” fonts.

ViewerTextFontSet

void ViewerTextFontSet(const std::string &)

Sets the font currently being used when rendering text in the 3D display. This font only applies when using “nice” fonts.

ViewerTextScaleGet

float ViewerTextScaleGet()

Returns the current global scale for text drawn in the 3D display window.

ViewerTextScaleSet

float ViewerTextScaleSet(float scale, bool redraw=true)

Sets the current global scale for text drawn in the 3D display window.

ViewerToggleRenderFeatures

void ViewerToggleRenderFeatures(unsigned int features, bool on)

Toggles the use of certain advanced visualization features.

ViewerTranslateX

void ViewerTranslateX(float val)

Translates the display along the X axis by the specified amount (in Angstroms).

ViewerTranslateY

void ViewerTranslateY(float val)

Translates the display along the Y axis by the specified amount (in Angstroms).

ViewerTranslateZ

void ViewerTranslateZ(float val)

Translates the display along the Z axis by the specified amount (in Angstroms).

ViewerUpGet

std::vector<float> ViewerUpGet()

Returns the OpenGL camera up vector.

ViewerUseDisplayListGet

bool ViewerUseDisplayListGet()

Returns whether or not the 3D renderer uses a display list to encapsulate the master scene. The default is false. Ordinarily, this function does not need to be called by the user.

ViewerUseDisplayListSet

bool ViewerUseDisplayListSet(bool use)

Sets whether or not the 3D renderer uses a display list to encapsulate the master scene. The default is false. Ordinarily, this function does not need to be called by the user. Setting this property to true may have cause significant negative performance on certain machines.

ViewerUseSystemFontsGet

bool ViewerUseSystemFontsGet()

Returns whether or not the 3D renderer uses system fonts when displaying text.

ViewerUseSystemFontsSet

bool ViewerUseSystemFontsSet(bool state)

Sets whether or not the 3D renderer uses system fonts when display text.

ViewerSetShowObjectToolbar

void ViewerSetShowObjectToolbar(bool state)

Sets whether or not the style & color buttons are shown in the bottom toolbar for the active object

ViewerGetShowObjectToolbar

bool ViewerGetShowObjectToolbar()

Sets whether or not the style & color buttons are shown in the bottom toolbar for the active object

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