Package org.jmol.modelset

Examples of org.jmol.modelset.Bond

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        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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      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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  public void highlightBond(int index, boolean isHover) {
    if (isHover && !isHoverEnabled())
      return;
    BitSet bs = null;
    if (index >= 0) {
      Bond b = modelSet.getBonds()[index];
      int i = b.getAtomIndex2();
      if (!isAtomAssignable(i))
        return;
      bs = BitSetUtil.setBit(i);
      bs.set(b.getAtomIndex1());
    }
    highlight(bs);
    refresh(3, "highlightBond");
  }
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    if (rotateBondIndex < 0)
      return;
    BitSet bsBranch = bsRotateBranch;
    Atom atom1, atom2;
    if (bsBranch == null) {
      Bond b = modelSet.getBonds()[rotateBondIndex];
      atom1 = b.getAtom1();
      atom2 = b.getAtom2();
      undoAction(atom1.index, AtomCollection.TAINT_COORD, true);
      Point3f pt = new Point3f(x, y, (atom1.screenZ + atom2.screenZ) / 2);
      transformManager.unTransformPoint(pt, pt);
      if (atom2.getCovalentBondCount() == 1
          || pt.distance(atom1) < pt.distance(atom2)
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          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);
      }
      str = TextFormat.formatString(str, "#", (n + 1));
      sout[n++] = str;
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      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:
            if (fv < fvMinMax)
              fvMinMax = fv;
            break;
          case Token.max:
            if (fv > fvMinMax)
              fvMinMax = 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 Token.xyz:
          switch (minmaxtype) {
          case Token.all:
            pt.set(bond.getAtom1());
            pt.add(bond.getAtom2());
            pt.scale(0.5f);
            vout.add(new Point3f(pt));
            break;
          default:
            pt.add(bond.getAtom1());
            pt.add(bond.getAtom2());
            n++;
          }
          break;
        case Token.color:
          Graphics3D.colorPointFromInt(viewer.getColorArgbOrGray(bond
              .getColix()), ptT);
          switch (minmaxtype) {
          case Token.all:
            vout.add(new Point3f(ptT));
            break;
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        boolean isEnergy = (pid == JmolConstants.PALETTE_ENERGY);
        BondIterator iter = (selectedBonds != null ? modelSet.getBondIterator(selectedBonds)
            : modelSet.getBondIterator(myMask, bs));
        while (iter.hasNext()) {
          bsColixSet.set(iter.nextIndex());
          Bond bond = iter.next();
          if (isEnergy) {
              bond.setColix(setColix(colix, pid, bond));
              bond.setPaletteID(pid);
          } else {
            bond.setColix(Graphics3D.getColix(JmolConstants.getArgbHbondType(bond.getOrder())));
          }
        }
        return;
      }
      if (colix == Graphics3D.USE_PALETTE && pid != JmolConstants.PALETTE_CPK)
        return; //palettes not implemented for bonds
      BondIterator iter = (selectedBonds != null ? modelSet.getBondIterator(selectedBonds)
          : modelSet.getBondIterator(myMask, bs));
      while (iter.hasNext()) {
        int iBond = iter.nextIndex();
        Bond bond = iter.next();
        bond.setColix(colix);
        bsColixSet.set(iBond, (colix != Graphics3D.INHERIT_ALL
            && colix != Graphics3D.USE_PALETTE));
      }
      return;
    }
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  }

  public void setModelClickability() {
    Bond[] bonds = modelSet.getBonds();
    for (int i = modelSet.getBondCount(); --i >= 0;) {
      Bond bond = bonds[i];
      if ((bond.getShapeVisibilityFlags() & myVisibilityFlag) == 0
          || modelSet.isAtomHidden(bond.getAtomIndex1())
          || modelSet.isAtomHidden(bond.getAtomIndex2()))
        continue;
      bond.getAtom1().setClickable(myVisibilityFlag);
      bond.getAtom2().setClickable(myVisibilityFlag);
    }
  }
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    }
    if (reportAll || bsOrderSet != null) {
      int i0 = (reportAll ? bondCount - 1 : bsOrderSet.nextSetBit(0));
      for (int i = i0; i >= 0; i = (reportAll ? i - 1 : bsOrderSet
          .nextSetBit(i + 1))) {
        Bond bond = bonds[i];
        if (reportAll || (bond.getOrder() & JmolEdge.BOND_NEW) == 0)
          setStateInfo(temp, i, "bondOrder "
              + JmolConstants.getBondOrderNameFromOrder(bond.getOrder()));
      }
    }
    if (bsColixSet != null)
      for (int i = bsColixSet.nextSetBit(0); i >= 0; i = bsColixSet
          .nextSetBit(i + 1)) {
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            + "\n" : "");
  }
 
  public boolean checkObjectHovered(int x, int y, BitSet bsVisible) {
    Point3fi pt = new Point3fi();
    Bond bond = findPickedBond(x, y, bsVisible, pt);
    if (bond == null)
      return false;
    viewer.highlightBond(bond.getIndex(), true);
    return true;
  }
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Related Classes of org.jmol.modelset.Bond

  • org.jmol.script.ScriptEvaluator
  • org.jmol.shape.Sticks
  • org.jmol.shapespecial.Dipoles
  • org.jmol.shapespecial.Polyhedra
  • org.jmol.viewer.StateManager$Connections
  • org.jmol.viewer.Viewer
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