Examples of ProteinStructure

Examples of org.jmol.modelsetbio.ProteinStructure

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  }

  protected void render1() {
    boolean lastWasSheet = false;
    boolean lastWasHelix = false;
    ProteinStructure previousStructure = null;
    ProteinStructure thisStructure;

    // Key structures that must render properly
    // include 1crn and 7hvp

    // this loop goes monomerCount --> 0, because
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Examples of org.jmol.modelsetbio.ProteinStructure

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                                  int aspectRatio) {
    setNeighbors(i);
    if (controlPoints[i].distance(controlPoints[iNext]) == 0)
      return false;
    if (isHelix(i)) {
      ProteinStructure p = ((AlphaMonomer) monomers[i]).getProteinStructure();
      p.calcAxis();
      /*
       *
      dumpPoint(p.center, Graphics3D.YELLOW);
      dumpPoint(p.axisA, Graphics3D.YELLOW);
      dumpPoint(p.axisB, Graphics3D.YELLOW);
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Examples of org.jmol.modelsetbio.ProteinStructure

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  }

  protected void calcRopeMidPoints(boolean isNewStyle) {
    int midPointCount = monomerCount + 1;
    cordMidPoints = viewer.allocTempPoints(midPointCount);
    ProteinStructure proteinstructurePrev = null;
    Point3f point;
    for (int i = 0; i < monomerCount; ++i) {
      point = cordMidPoints[i];
      Monomer residue = monomers[i];
      if (isNewStyle && renderArrowHeads) {
          point.set(controlPoints[i]);
      } else if (isHelix(i) ||  !isNewStyle && isSheet(i)) {
        ProteinStructure proteinstructure = residue.getProteinStructure();
        point.set(i - 1 != proteinstructure.getMonomerIndex() ?
            proteinstructure.getAxisStartPoint() :
            proteinstructure.getAxisEndPoint());
        proteinstructurePrev = proteinstructure;
      } else {
        if (proteinstructurePrev != null)
          point.set(proteinstructurePrev.getAxisEndPoint());
        else {
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Examples of org.jmol.modelsetbio.ProteinStructure

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    }
    renderPending();
  }

  protected void renderSpecialSegment(Monomer monomer, short thisColix, short thisMad) {
    ProteinStructure proteinstructure = monomer.getProteinStructure();
    if (tPending) {
      if (proteinstructure == proteinstructurePending && thisMad == mad
          && thisColix == colix
          && proteinstructure.getIndex(monomer) == endIndexPending + 1) {
        ++endIndexPending;
        return;
      }
      renderPending();
    }
    proteinstructurePending = proteinstructure;
    startIndexPending = endIndexPending = proteinstructure.getIndex(monomer);
    colix = thisColix;
    mad = thisMad;
    tPending = true;
  }
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