Package org.jmol.renderbio

Class BioShapeRenderer

java.lang.Object
org.jmol.render.ShapeRenderer
org.jmol.renderbio.BioShapeRenderer
Direct Known Subclasses:
BackboneRenderer, StrandsRenderer
abstract class BioShapeRenderer extends ShapeRenderer
Author:
Alexander Rose, Bob Hanson

  • Field Details

    • invalidateMesh

      private boolean invalidateMesh

    • invalidateSheets

      private boolean invalidateSheets

    • isTraceAlpha

      private boolean isTraceAlpha

    • ribbonBorder

      private boolean ribbonBorder

    • haveControlPointScreens

      private boolean haveControlPointScreens

    • aspectRatio

      float aspectRatio

    • hermiteLevel

      int hermiteLevel

    • sheetSmoothing

      private float sheetSmoothing

    • cartoonsFancy

      protected boolean cartoonsFancy

    • monomerCount

      protected int monomerCount

    • monomers

      protected Monomer[] monomers

    • isNucleic

      protected boolean isNucleic

    • isPhosphorusOnly

      protected boolean isPhosphorusOnly

    • isCarbohydrate

      protected boolean isCarbohydrate

    • bsVisible

      protected javajs.util.BS bsVisible

    • ribbonTopScreens

      protected javajs.util.P3[] ribbonTopScreens

    • ribbonBottomScreens

      protected javajs.util.P3[] ribbonBottomScreens

    • controlPoints

      protected javajs.util.P3[] controlPoints

    • controlPointScreens

      protected javajs.util.P3[] controlPointScreens

    • leadAtomIndices

      protected int[] leadAtomIndices

    • wingVectors

      protected javajs.util.V3[] wingVectors

    • mads

      protected short[] mads

    • colixes

      protected short[] colixes

    • colixesBack

      protected short[] colixesBack

    • structureTypes

      protected STR[] structureTypes

    • isHighRes

      boolean isHighRes

    • wireframeOnly

      protected boolean wireframeOnly

    • needTranslucent

      private boolean needTranslucent

    • meshRenderer

      BioMeshRenderer meshRenderer

    • bioShape

      BioShape bioShape

    • pointT

      private final javajs.util.P3 pointT

    • iPrev

      int iPrev

    • iNext

      int iNext

    • iNext2

      int iNext2

    • iNext3

      int iNext3

    • diameterBeg

      int diameterBeg

    • diameterMid

      int diameterMid

    • diameterEnd

      int diameterEnd

    • madBeg

      short madBeg

    • madMid

      short madMid

    • madEnd

      short madEnd

    • colixBack

      short colixBack

    • reversed

      private javajs.util.BS reversed

    • isCyclic

      private boolean isCyclic

    • screenArrowTop

      private final javajs.util.P3 screenArrowTop

    • screenArrowTopPrev

      private final javajs.util.P3 screenArrowTopPrev

    • screenArrowBot

      private final javajs.util.P3 screenArrowBot

    • screenArrowBotPrev

      private final javajs.util.P3 screenArrowBotPrev

  • Constructor Details

    • BioShapeRenderer

      BioShapeRenderer()

  • Method Details

    • renderBioShape

      protected abstract void renderBioShape(BioShape bioShape)

    • render

      protected boolean render()
      Specified by:
      render in class ShapeRenderer

    • setGlobals

      private void setGlobals()

    • renderShapes

      private void renderShapes()

    • setBioColix

      protected boolean setBioColix(short colix)

    • freeTempArrays

      private void freeTempArrays()

    • initializePolymer

      private boolean initializePolymer(BioShape bioShape)

    • setStructureTypes

      private void setStructureTypes()

    • calcScreenControlPoints

      protected void calcScreenControlPoints()

    • calcScreens

      protected javajs.util.P3[] calcScreens(float offsetFraction, short[] mads)
      calculate screen points based on control points and wing positions (cartoon, strand, meshRibbon, and ribbon)
      Parameters:
      offsetFraction -
      mads -
      Returns:
      Point3i array THAT MUST BE LATER FREED

    • calc1Screen

      private void calc1Screen(javajs.util.P3 center, javajs.util.V3 vector, short mad, float offset_1000, javajs.util.P3 screen)

    • getLeadColix

      protected short getLeadColix(int i)

    • getLeadColixBack

      protected short getLeadColixBack(int i)

    • setNeighbors

      void setNeighbors(int i)

    • setColix

      protected boolean setColix(short colix)

    • setMads

      private boolean setMads(int i, boolean thisTypeOnly)
      set diameters for a bioshape
      Parameters:
      i -
      thisTypeOnly - true for Cartoon but not MeshRibbon
      Returns:
      true if a mesh is needed

    • renderHermiteCylinder

      protected void renderHermiteCylinder(javajs.util.P3[] screens, int i)

    • renderHermiteConic

      protected void renderHermiteConic(int i, boolean thisTypeOnly, int tension)

    • renderHermiteRibbon

      protected void renderHermiteRibbon(boolean doFill, int i, boolean thisTypeOnly)
      Parameters:
      doFill -
      i -
      thisTypeOnly - true for Cartoon but not MeshRibbon

    • renderHermiteArrowHead

      protected void renderHermiteArrowHead(int i)

    • drawSegmentAB

      protected void drawSegmentAB(Atom atomA, Atom atomB, short colixA, short colixB, float max)