Package org.jmol.modelset

Examples of org.jmol.modelset.Group

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  static BioPolymer allocateBioPolymer(Group[] groups, int firstGroupIndex,
                                       boolean checkConnections) {
    Monomer previous = null;
    int count = 0;
    for (int i = firstGroupIndex; i < groups.length; ++i) {
      Group group = groups[i];
      Monomer current;
      if (!(group instanceof Monomer)
          || (current = (Monomer) group).bioPolymer != null || previous != null
          && previous.getClass() != current.getClass()
          || checkConnections && !current.isConnectedAfter(previous))
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      return false;
    boolean haveCrossLink = false;
    boolean checkPrevious = (vReturn == null && group == null);
    for (int j = 0; j < bonds.length; j++) {
      Atom a = bonds[j].getOtherAtom(atom);
      Group g = a.getGroup();
      if (group != null && g != group)
        continue;
      int iPolymer = g.getBioPolymerIndexInModel();
      int igroup = g.getMonomerIndex();
      if (checkPrevious) {
        if (iPolymer == ibp && igroup == monomerIndex - 1)
          return true;
      } else if (iPolymer >= 0
          && igroup >= 0
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  }
 
  public void clearBioPolymers(Group[] groups, int groupCount,
                               BitSet alreadyDefined) {
    for (int i = 0; i < groupCount; ++i) {
      Group group = groups[i];
      if (group instanceof Monomer) {
        Monomer monomer = (Monomer) group;
        if (monomer.getBioPolymer() != null
            && (alreadyDefined == null || !alreadyDefined.get(monomer.getModelIndex())))
          monomer.setBioPolymer(null, -1);
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      int zSlab = atom.screenZ - atom.screenDiameter / 2 - 3;
      if (zSlab < 1)
        zSlab = 1;
      int zBox = zSlab;     
      if (labelsGroup) {
        Group group = atom.getGroup();
        int ig = group.getGroupIndex();
        if (ig != iGroup) {
          minZ = getMinZ(atoms, group);
          iGroup = ig;
        }
        zBox = minZ;
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      Atom p1 = getAtomFromOffsetIndex(O1P);
      Atom p2 = getAtomFromOffsetIndex(O2P);
      Bond[] bonds = ptNorP.getBonds();
      if (bonds == null)
        return null;
      Group g = ptNorP.getGroup();
      for (int i = 0; i < bonds.length; i++) {
        Atom atom = bonds[i].getOtherAtom(ptNorP);
        if (p1 != null && atom.index == p1.index)
          continue;
        if (p2 != null && atom.index == p2.index)
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    boolean haveCrossLinks = false;
    for (int i = 0; i < bonds.length; i++) {
      //System.out.println(bonds[i].getOtherAtom(N).getInfo());
      if (bonds[i].isHydrogen()) {
        Atom N2 = bonds[i].getOtherAtom(N);
        Group g = N2.getGroup();
        if (!(g instanceof NucleicMonomer))
          continue;
        NucleicMonomer m = (NucleicMonomer) g;
        if ((isPurine ? m.getN3() : m.getN1()) == N2) {
          if (vReturn == null)
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Related Classes of org.jmol.modelset.Group

  • org.jmol.modelsetbio.BioPolymer
  • org.jmol.modelsetbio.Monomer
  • org.jmol.modelsetbio.NucleicMonomer
  • org.jmol.modelsetbio.Resolver
  • org.jmol.shape.LabelsRenderer
  • javax.vecmath.Vector3f
  • javax.vecmath.Point3f
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