Package org.jmol.util

Examples of org.jmol.util.Quaternion

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      List sv = ((ScriptVariable) getToken(i)).getList();
      Point4f p4 = null;
      if (sv.size() == 0
          || (p4 = ScriptVariable.pt4Value((ScriptVariable)sv.get(0))) == null)
        error(ERROR_invalidArgument);
      return new Quaternion(p4);
    }
    return new Quaternion(getPoint4f(i));
  }
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        if (theTok == Token.point4f || !isPoint3f(i)) {
          propertyValue = getPoint4f(i);
          if (isFrame) {
            checkLast(iToken);
            if (!isSyntaxCheck)
              runScript((new Quaternion((Point4f) propertyValue)).draw(
                  (thisId == null ? "frame" : thisId), " " + swidth,
                  (center == null ? new Point3f() : center), intScale / 100f));
            return;
          }
          propertyName = "planedef";
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            + " haveFractionalCoord:" + someModelsHaveFractionalCoordinates);
        Logger.info(adapterModelCount + " model" + (modelCount == 1 ? "" : "s")
            + " in this collection. Use getProperty \"modelInfo\" or"
            + " getProperty \"auxiliaryInfo\" to inspect them.");
      }
      Quaternion q = (Quaternion) getModelSetAuxiliaryInfo("defaultOrientationQuaternion");
      if (q != null) {
        Logger.info("defaultOrientationQuaternion = " + q);
        Logger
            .info("Use \"set autoLoadOrientation TRUE\" before loading or \"restore orientation DEFAULT\" after loading to view this orientation.");
      }
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    // for PDB files, do not include NON-protein groups.
    int n = 0;
    List v = new ArrayList();
    for (int i = bsAtoms.nextSetBit(0); i >= 0 && n < nMax; i = bsAtoms.nextSetBit(i + 1)) {
      Group g = atoms[i].group;
      Quaternion q = g.getQuaternion(qtype);
      if (q == null) {
        if (g.seqcode == Integer.MIN_VALUE)
          q = g.getQuaternionFrame(atoms); // non-PDB just use first three atoms
        if (q == null)
          continue;
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      if (vNot.size() == 0)
        return;
      pt = Measure.getCenterAndPoints(vNot)[0];
      Vector3f v = new Vector3f(thisAtom);
      v.sub(pt);
      Quaternion q = new Quaternion(v, 180);
      rotateAtoms(null, q.getMatrix(), bsAtoms, thisAtom, true);
    }
  }
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        bsAtoms.clear(i);
    BitSet bsBonds = getCovalentBondsForAtoms(bsAtoms);
    if (bsAtoms.cardinality() == 0)
      return "";
    boolean isOK = true;
    Quaternion q = (doTransform ? viewer.getRotationQuaternion() : null);
    if (asSDF) {
      String header = mol.toString();
      mol = new StringBuffer();
      BitSet bsModels = getModelBitSet(bsAtoms, true);
      for (int i = bsModels.nextSetBit(0); i >= 0; i = bsModels
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    }

    v.normalize();
    if (haveAxis(iOrder, v))
      return false;
    Quaternion q = new Quaternion(v, (iOrder < firstProper ? 180 : 0) + 360 / (iOrder % firstProper));
    if (!checkOperation(q, center, iOrder))
      return false;
    addAxis(iOrder, v);
    // check for Sn:
    switch (iOrder) {
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    return nPlanes;
  }

  private int getPlane(Vector3f v3) {
    if (!haveAxis(0, v3)
        && checkOperation(new Quaternion(v3, 180), center,
            -1))
      axes[0][nAxes[0]++] = new Operation(v3);
    return nAxes[0];
  }
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    Operation(Vector3f v, int i) {
      index = ++nOps;
      type = (i < firstProper ? OPERATION_IMPROPER_AXIS : OPERATION_PROPER_AXIS);
      order = i % firstProper;
      normalOrAxis = new Quaternion(v, 180).getNormal();
      if (Logger.debugging)
        Logger.info("new operation -- " + (order == i ? "S" : "C") + order + " "
            + normalOrAxis);
    }
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    Operation(Vector3f v) {
      if (v == null)
        return;
      index = ++nOps;
      type = OPERATION_PLANE;
      normalOrAxis = new Quaternion(v, 180).getNormal();
      if (Logger.debugging)
        Logger.info("new operation -- plane " + normalOrAxis);
    }
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Related Classes of org.jmol.util.Quaternion

  • org.jmol.adapter.smarter.AtomSetCollectionReader
  • org.jmol.export.___Exporter
  • org.jmol.export._IdtfExporter
  • org.jmol.modelset.ModelCollection
  • org.jmol.modelset.ModelLoader
  • org.jmol.modelsetbio.BioPolymer
  • org.jmol.modelsetbio.Monomer
  • org.jmol.script.ScriptEvaluator
  • org.jmol.script.ScriptMathProcessor
  • org.jmol.symmetry.PointGroup
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