Package edu.mssm.crover.domain2d.rbdg.xml

Class Summary
Colors Groups color-related options
ColorScheme Selects the color-scheme.
ColorSchemeDescriptor Class ColorSchemeDescriptor.
ColorsDescriptor Class ColorsDescriptor.
ControlPoints Use only when subunit type is FreeLoop, Nterm or Cterm.
ControlPointsDescriptor Class ControlPointsDescriptor.
Cpoint A control point.
CpointDescriptor Class CpointDescriptor.
Define Define a new color.
DefineDescriptor Class DefineDescriptor.
Diagram Groups the main sections that determine how the diagram will appear.
DiagramDescriptor Class DiagramDescriptor.
DiagramLayout Describes the graphical arrangement of secondary structure units on the 2D page.
DiagramLayoutDescriptor Class DiagramLayoutDescriptor.
Direction Direction is a vector(x,y) which indicates the orientation of a subunit (helix or loop) within the plane.
DirectionDescriptor Class DirectionDescriptor.
DisulfideBridge Describes a disulfide bridge.
DisulfideBridgeDescriptor Class DisulfideBridgeDescriptor.
Elipses Groups elipses related options
ElipsesDescriptor Class ElipsesDescriptor.
Exclude Excludes elipses from a range of residues.
ExcludeDescriptor Class ExcludeDescriptor.
ExcludeResidueRangeType Class ExcludeResidueRangeType.
ExcludeResidueRangeTypeDescriptor Class ExcludeResidueRangeTypeDescriptor.
Image Select options for an image output of the diagram.
ImageDescriptor Class ImageDescriptor.
ImageMap Output an image map document.
ImageMapDescriptor Class ImageMapDescriptor.
Include Allows elipses to be included in a range of residues.
IncludeDescriptor Class IncludeDescriptor.
IncludeResidueRangeType Class IncludeResidueRangeType.
IncludeResidueRangeTypeDescriptor Class IncludeResidueRangeTypeDescriptor.
Line_drawing Describes a specified line between two residues.
Line_drawingDescriptor Class Line_drawingDescriptor.
Links Describes hyperlinks attached to various components of the diagram.
LinksDescriptor Class LinksDescriptor.
Options Groups options that can affect how the diagram is rendered.
OptionsDescriptor Class OptionsDescriptor.
Output Groups options related to the diagram output.
OutputDescriptor Class OutputDescriptor.
Page Generates an XML document that describes one diagram.
PageDescriptor Class PageDescriptor.
Protein Describes the protein to be rendered.
ProteinDescriptor Class ProteinDescriptor.
RbdeDiagram Input file for construction of one diagram.
RbdeDiagramDescriptor Class RbdeDiagramDescriptor.
Residue Links a residue to a URL.
ResidueBackground Fill color for the background of a residue
ResidueBackgroundDescriptor Class ResidueBackgroundDescriptor.
ResidueColor Color one residue on the sequence.
ResidueColorDescriptor Class ResidueColorDescriptor.
ResidueDescriptor Class ResidueDescriptor.
ResidueShape Determines how individual residues will be rendered.
ResidueShapeDescriptor Class ResidueShapeDescriptor.
SecondaryStructure Defines the secondary structure for this protein.
SecondaryStructureDescriptor Class SecondaryStructureDescriptor.
Segment Defines the limits of of segment of secondary structure.
SegmentDescriptor Class SegmentDescriptor.
Spacer The separation between the first residue of the subunit and the last, on the page.
SpacerDescriptor Class SpacerDescriptor.
Subunit Each subunit is located on the page according to the location and spacer of the subunit that preceeds it.
SubunitDescriptor Class SubunitDescriptor.
SubunitRef Links a subunit to a URL.
SubunitRefDescriptor Class SubunitRefDescriptor.
TmBundle Use the bundle to layout integral membrane proteins.
TmBundleDescriptor Class TmBundleDescriptor.

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