Package org.jmol.modelsetbio

Examples of org.jmol.modelsetbio.Monomer

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    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 {
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  protected void render1() {
    tPending = false;
    for (int i = bsVisible.nextSetBit(0); i >= 0; i = bsVisible
        .nextSetBit(i + 1)) {
      Monomer monomer = monomers[i];
      if (isHelix(i) || isSheet(i)) {
        renderSpecialSegment(monomer, getLeadColix(i), mads[i]);
      } else {
        renderPending();
        renderHermiteConic(i, true);
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    atoms = modelSet.atoms;
    initialize();
  }

  public int getSize(Group group) {
    Monomer m = (Monomer) group;
    int groupIndex = m.getGroupIndex();
    int leadAtomIndex = m.getLeadAtom().getIndex();
    for (int i = bioShapes.length; --i >= 0;) {
      BioShape bioShape = bioShapes[i];
      for (int j = 0; j < bioShape.monomerCount; j++) {
        if (bioShape.monomers[j].getGroupIndex() == groupIndex
          && bioShape.monomers[j].getLeadAtom().getIndex() == leadAtomIndex)
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Related Classes of org.jmol.modelsetbio.Monomer

  • org.jmol.modelset.Atom
  • org.jmol.modelset.Group
  • org.jmol.shapebio.BioShapeCollection
  • org.jmol.shapebio.RocketsRenderer
  • org.jmol.util.Quaternion
  • java.util.Hashtable
  • java.util.Map
  • javax.vecmath.Point3f
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