Examples of org.jmol.modelset.ModelSet

org.jmol.modelset.ModelSet


  short getColixAtomPalette(Atom atom, byte pid) {
    int argb = 0;
    int index;
    short id;
    ModelSet modelSet;
    int modelIndex;
    float lo, hi;
    switch (pid) {
    case JmolConstants.PALETTE_PROPERTY:
      return (colorData == null || atom.index >= colorData.length
          ? Graphics3D.GRAY : getColixForPropertyValue(colorData[atom.index]));
    case JmolConstants.PALETTE_NONE:
    case JmolConstants.PALETTE_CPK:
      // Note that CPK colors can be changed based upon user preference
      // therefore, a changeable colix is allocated in this case
      id = atom.getAtomicAndIsotopeNumber();
      if (id < Elements.elementNumberMax)
        return g3d.getChangeableColix(id, argbsCpk[id]);
      id = (short) Elements.altElementIndexFromNumber(id);
      return g3d.getChangeableColix((short) (Elements.elementNumberMax + id),
          altArgbsCpk[id]);
    case JmolConstants.PALETTE_PARTIAL_CHARGE:
      // This code assumes that the range of partial charges is [-1, 1].
      index = ColorEncoder.quantize(atom.getPartialCharge(), -1, 1,
          JmolConstants.PARTIAL_CHARGE_RANGE_SIZE);
      return g3d.getChangeableColix(
          (short) (JmolConstants.PARTIAL_CHARGE_COLIX_RED + index),
          JmolConstants.argbsRwbScale[index]);
    case JmolConstants.PALETTE_FORMAL_CHARGE:
      index = atom.getFormalCharge() - JmolConstants.FORMAL_CHARGE_MIN;
      return g3d.getChangeableColix(
          (short) (JmolConstants.FORMAL_CHARGE_COLIX_RED + index),
          JmolConstants.argbsFormalCharge[index]);
    case JmolConstants.PALETTE_TEMP:
    case JmolConstants.PALETTE_FIXEDTEMP:
      if (pid == JmolConstants.PALETTE_TEMP) {
        modelSet = viewer.getModelSet();
        lo = modelSet.getBfactor100Lo();
        hi = modelSet.getBfactor100Hi();
      } else {
        lo = 0;
        hi = 100 * 100; // scaled by 100
      }
      return propertyColorEncoder.getColorIndexFromPalette(
          atom.getBfactor100(), lo, hi, ColorEncoder.BWR, false);
    case JmolConstants.PALETTE_STRAIGHTNESS:
      return propertyColorEncoder.getColorIndexFromPalette(atom
          .getGroupParameter(Token.straightness), -1, 1, ColorEncoder.BWR,
          false);
    case JmolConstants.PALETTE_SURFACE:
      hi = viewer.getSurfaceDistanceMax();
      return propertyColorEncoder.getColorIndexFromPalette(atom
          .getSurfaceDistance100(), 0, hi, ColorEncoder.BWR, false);
    case JmolConstants.PALETTE_AMINO:
      return propertyColorEncoder.getColorIndexFromPalette(atom.getGroupID(),
          0, 0, ColorEncoder.AMINO, false);
    case JmolConstants.PALETTE_SHAPELY:
      return propertyColorEncoder.getColorIndexFromPalette(atom.getGroupID(),
          0, 0, ColorEncoder.SHAPELY, false);
    case JmolConstants.PALETTE_GROUP:
      // viewer.calcSelectedGroupsCount() must be called first ...
      // before we call getSelectedGroupCountWithinChain()
      // or getSelectedGropuIndexWithinChain
      // however, do not call it here because it will get recalculated
      // for each atom
      // therefore, we call it in Eval.colorObject();
      return propertyColorEncoder.getColorIndexFromPalette(atom
          .getSelectedGroupIndexWithinChain(), 0, atom
          .getSelectedGroupCountWithinChain() - 1, ColorEncoder.BGYOR, false);
    case JmolConstants.PALETTE_POLYMER:
      Model m = viewer.getModelSet().getModels()[atom.modelIndex];
      return propertyColorEncoder.getColorIndexFromPalette(atom
          .getPolymerIndexInModel(), 0, m.getBioPolymerCount() - 1,
          ColorEncoder.BGYOR, false);
    case JmolConstants.PALETTE_MONOMER:
      // viewer.calcSelectedMonomersCount() must be called first ...
      return propertyColorEncoder.getColorIndexFromPalette(atom
          .getSelectedMonomerIndexWithinPolymer(), 0, atom
          .getSelectedMonomerCountWithinPolymer() - 1, ColorEncoder.BGYOR,
          false);
    case JmolConstants.PALETTE_MOLECULE:
      modelSet = viewer.getModelSet();
      return propertyColorEncoder.getColorIndexFromPalette(modelSet
          .getMoleculeIndex(atom.getIndex()), 0, modelSet
          .getMoleculeCountInModel(atom.getModelIndex()) - 1,
          ColorEncoder.ROYGB, false);
    case JmolConstants.PALETTE_ALTLOC:
      modelSet = viewer.getModelSet();
      //very inefficient!
      modelIndex = atom.getModelIndex();
      return propertyColorEncoder
          .getColorIndexFromPalette(modelSet.getAltLocIndexInModel(modelIndex,
              atom.getAlternateLocationID()), 0, modelSet
              .getAltLocCountInModel(modelIndex), ColorEncoder.ROYGB, false);
    case JmolConstants.PALETTE_INSERTION:
      modelSet = viewer.getModelSet();
      //very inefficient!
      modelIndex = atom.getModelIndex();
      return propertyColorEncoder.getColorIndexFromPalette(modelSet
          .getInsertionCodeIndexInModel(modelIndex, atom.getInsertionCode()),
          0, modelSet.getInsertionCountInModel(modelIndex), ColorEncoder.ROYGB,
          false);
    case JmolConstants.PALETTE_JMOL:
      id = atom.getAtomicAndIsotopeNumber();
      argb = getJmolOrRasmolArgb(id, Token.jmol);
      break;

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    String saveName;
    int bondCount;
    Connection[] connections;


    Connections() {
      ModelSet modelSet = viewer.getModelSet();
      if (modelSet == null)
        return;
      bondCount = modelSet.getBondCount();
      connections = new Connection[bondCount + 1];
      Bond[] bonds = modelSet.getBonds();
      for (int i = bondCount; --i >= 0;) {
        Bond b = bonds[i];
        connections[i] = new Connection(b.getAtomIndex1(), b.getAtomIndex2(), b
            .getMad(), b.getColix(), b.getOrder(), b.getEnergy(), b.getShapeVisibilityFlags());
      }

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            .getMad(), b.getColix(), b.getOrder(), b.getEnergy(), b.getShapeVisibilityFlags());
      }
    }


    void restore() {
      ModelSet modelSet = viewer.getModelSet();
      if (modelSet == null)
        return;
      modelSet.deleteAllBonds();
      for (int i = bondCount; --i >= 0;) {
        Connection c = connections[i];
        int atomCount = modelSet.getAtomCount();
        if (c.atomIndex1 >= atomCount || c.atomIndex2 >= atomCount)
          continue;
        Bond b = modelSet.bondAtoms(modelSet.atoms[c.atomIndex1],
            modelSet.atoms[c.atomIndex2], c.order, c.mad, null, c.energy, true);
        b.setColix(c.colix);
        b.setShapeVisibilityFlags(c.shapeVisibilityFlags);
      }
      for (int i = bondCount; --i >= 0;)
        modelSet.getBondAt(i).setIndex(i);
      viewer.setShapeProperty(JmolConstants.SHAPE_STICKS, "reportAll", null);
    }

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    setCurrentModelIndex(modelIndex, true);  
  }
  
  void setCurrentModelIndex(int modelIndex, boolean clearBackgroundModel) {
    int formerModelIndex = currentModelIndex;
    ModelSet modelSet = viewer.getModelSet();
    int modelCount = (modelSet == null ? 0 : modelSet.getModelCount());
    if (modelCount == 1)
      currentModelIndex = modelIndex = 0;
    else if (modelIndex < 0 || modelIndex >= modelCount)
      modelIndex = -1;
    String ids = null;

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          : currentModelIndex);
  }
  
  int backgroundModelIndex = -1;
  void setBackgroundModelIndex(int modelIndex) {
    ModelSet modelSet = viewer.getModelSet();
    if (modelSet == null || modelIndex < 0 || modelIndex >= modelSet.getModelCount())
      modelIndex = -1;
    backgroundModelIndex = modelIndex;
    if (modelIndex >= 0)
      viewer.setTrajectory(modelIndex);
    viewer.setTainted(true);

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  void hide(BitSet bs, boolean isQuiet) {
    bsHidden.clear();
    if (bs != null)
      bsHidden.or(bs);
    ModelSet modelSet = viewer.getModelSet();
    if (modelSet != null)
      modelSet.setBsHidden(bsHidden);
    if (!isQuiet)
      viewer.reportSelection(GT._("{0} atoms hidden", ""
          + bsHidden.cardinality()));
  }

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    } else {
      bsHidden.or(bsAll);
      bsHidden.andNot(bs);
    }
    BitSetUtil.andNot(bsHidden, bsDeleted);
    ModelSet modelSet = viewer.getModelSet();
    if (modelSet != null)
      modelSet.setBsHidden(bsHidden);
    if (!isQuiet)
      viewer.reportSelection(GT._("{0} atoms hidden", ""
          + bsHidden.cardinality()));
  }

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    if (bs == null || isSyntaxCheck || isAtoms && pt < 0) {
      if (label == null)
        label = "";
      return isExplicitlyAll ? new String[] { label } : (Object) label;
    }
    ModelSet modelSet = viewer.getModelSet();
    int n = 0;
    int[] indices = (isAtoms || !useAtomMap ? null : ((BondSet) tokenValue)
        .getAssociatedAtoms());
    if (indices == null && label != null && label.indexOf("%D") > 0)
      indices = viewer.getAtomIndices(bs);
    boolean asIdentity = (label == null || label.length() == 0);
    Hashtable htValues = (isAtoms || asIdentity ? null : LabelToken
        .getBondLabelValues());
    LabelToken[] tokens = (asIdentity ? null : isAtoms ? LabelToken.compile(
        viewer, label, '\0', null) : LabelToken.compile(viewer, label, '\1',
        htValues));
    int nmax = (haveIndex ? 1 : BitSetUtil.cardinalityOf(bs));
    String[] sout = new String[nmax];
    for (int j = (haveIndex ? index : bs.nextSetBit(0)); j >= 0; j = bs
        .nextSetBit(j + 1)) {
      String str;
      if (isAtoms) {
        if (asIdentity)
          str = modelSet.atoms[j].getInfo();
        else
          str = LabelToken.formatLabel(viewer, modelSet.atoms[j], null, tokens,
              '\0', indices);
      } else {
        Bond bond = modelSet.getBondAt(j);
        if (asIdentity)
          str = bond.getIdentity();
        else
          str = LabelToken.formatLabel(viewer, bond, tokens, htValues, indices);
      }

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    case Token.max:
      ivMinMax = Integer.MIN_VALUE;
      fvMinMax = -Float.MAX_VALUE;
      break;
    }
    ModelSet modelSet = viewer.getModelSet();
    int mode = (isPt ? 3 : isString ? 2 : isInt ? 1 : 0);
    if (isAtoms) {
      boolean haveBitSet = (bs != null);
      int iModel = -1;
      int i0, i1;
      if (haveIndex) {
        i0 = index;
        i1 = index + 1;
      } else if (haveBitSet) {
        i0 = bs.nextSetBit(0);
        i1 = Math.min(atomCount, bs.length());
      } else {
        i0 = 0;
        i1 = atomCount;
      }
      if (isSyntaxCheck)
        i1 = 0;
      for (int i = i0; i >= 0 && i < i1; i = (haveBitSet ? bs.nextSetBit(i + 1)
          : i + 1)) {
        n++;
        Atom atom = modelSet.atoms[i];
        switch (mode) {
        case 0: // float
          float fv = Float.MAX_VALUE;
          switch (tok) {
          case Token.function:
            bsAtom.set(i);
            fv = ScriptVariable.fValue(runFunction(null, userFunction, params,
                tokenAtom, true));
            bsAtom.clear(i);
            break;
          case Token.property:
            fv = (data == null ? 0 : data[i]);
            break;
          case Token.distance:
            if (planeRef != null)
              fv = Measure.distanceToPlane(planeRef, atom);
            else
              fv = atom.distance(ptRef);
            break;
          default:
            fv = Atom.atomPropertyFloat(viewer, atom, tok);
          }
          if (fv == Float.MAX_VALUE || Float.isNaN(fv)
              && minmaxtype != Token.all) {
            n--; // don't count this one
            continue;
          }
          switch (minmaxtype) {
          case Token.min:
            if (fv < fvMinMax)
              fvMinMax = fv;
            break;
          case Token.max:
            if (fv > fvMinMax)
              fvMinMax = fv;
            break;
          case Token.allfloat:
            fout[i] = fv;
            break;
          case Token.all:
            vout.add(new Float(fv));
            break;
          case Token.sum2:
          case Token.stddev:
            sum2 += ((double) fv) * fv;
            // fall through
          case Token.sum:
          default:
            sum += fv;
          }
          break;
        case 1: // isInt
          int iv = 0;
          switch (tok) {
          case Token.symop:
            // a little weird:
            // First we determine how many operations we have in this model.
            // Then we get the symmetry bitset, which shows the assignments
            // of symmetry for this atom.
            if (atom.getModelIndex() != iModel)
              iModel = atom.getModelIndex();
            BitSet bsSym = atom.getAtomSymmetry();
            int p = 0;
            switch (minmaxtype) {
            case Token.min:
              ivvMinMax = Integer.MAX_VALUE;
              break;
            case Token.max:
              ivvMinMax = Integer.MIN_VALUE;
              break;
            }
            for (int k = bsSym.nextSetBit(0); k >= 0; k = bsSym
                .nextSetBit(k + 1)) {
              iv += k + 1;
              switch (minmaxtype) {
              case Token.min:
                ivvMinMax = Math.min(ivvMinMax, k + 1);
                break;
              case Token.max:
                ivvMinMax = Math.max(ivvMinMax, k + 1);
                break;
              }
              p++;
            }
            switch (minmaxtype) {
            case Token.min:
            case Token.max:
              iv = ivvMinMax;
            }
            n += p - 1;
            break;
          case Token.configuration:
          case Token.cell:
            error(ERROR_unrecognizedAtomProperty, Token.nameOf(tok));
          default:
            iv = Atom.atomPropertyInt(atom, tok);
          }
          switch (minmaxtype) {
          case Token.min:
            if (iv < ivMinMax)
              ivMinMax = iv;
            break;
          case Token.max:
            if (iv > ivMinMax)
              ivMinMax = iv;
            break;
          case Token.allfloat:
            fout[i] = iv;
            break;
          case Token.all:
            vout.add(new Integer(iv));
            break;
          case Token.sum2:
          case Token.stddev:
            sum2 += ((double) iv) * iv;
            // fall through
          case Token.sum:
          default:
            sum += iv;
          }
          break;
        case 2: // isString
          String s = Atom.atomPropertyString(atom, tok); 
          switch (minmaxtype) {
          case Token.allfloat:
            fout[i] = Parser.parseFloat(s);
            break;
          default:
            vout.add(s);
          }
          break;
        case 3: // isPt
          Tuple3f t = Atom.atomPropertyTuple(atom, tok);
          if (t == null)
            error(ERROR_unrecognizedAtomProperty, Token.nameOf(tok));
          switch (minmaxtype) {
          case Token.allfloat:
            fout[i] = (float) Math.sqrt(t.x * t.x + t.y * t.y + t.z * t.z);
            break;
          case Token.all:
            vout.add(new Point3f(t));
            break;
          default:
            pt.add(t);
          }
          break;
        }
        if (haveIndex)
          break;
      }
    } else { // bonds
      boolean isAll = (bs == null);
      int i0 = (isAll ? 0 : bs.nextSetBit(0));
      int i1 = viewer.getBondCount();
      for (int i = i0; i >= 0 && i < i1; i = (isAll ? i + 1 : bs
          .nextSetBit(i + 1))) {
        n++;
        Bond bond = modelSet.getBondAt(i);
        switch (tok) {
        case Token.length:
          float fv = bond.getAtom1().distance(bond.getAtom2());
          switch (minmaxtype) {
          case Token.min:

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  private BitSet compareFloat(int tokWhat, float[] data, int tokOperator,
                              float comparisonFloat) {
    BitSet bs = new BitSet();
    int atomCount = viewer.getAtomCount();
    ModelSet modelSet = viewer.getModelSet();
    Atom[] atoms = modelSet.atoms;
    float propertyFloat = 0;
    viewer.autoCalculate(tokWhat);
    for (int i = atomCount; --i >= 0;) {
      boolean match = false;

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Related Classes of org.jmol.modelset.ModelSet

org.jmol.api.SymmetryInterface

org.jmol.atomdata.RadiusData

org.jmol.script.ScriptEvaluator

org.jmol.viewer.AnimationManager

org.jmol.viewer.ColorManager

org.jmol.viewer.SelectionManager

org.jmol.viewer.StateManager$Connections

java.util.Hashtable

java.util.List

javax.vecmath.Point3f

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