Examples of Bond

Examples of org.jmol.modelset.Bond

129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
        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;
    }
View Full Code Here

Examples of org.jmol.modelset.Bond

183
184
185
186
187
188
189
190
191
192
193
194
195
196
  }

  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);
    }
  }
View Full Code Here

Examples of org.jmol.modelset.Bond

212
213
214
215
216
217
218
219
220
221
222
223
224
225
    }
    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)) {
View Full Code Here

Examples of org.jmol.modelset.Bond

237
238
239
240
241
242
243
244
245
246
247
            + "\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;
  }
View Full Code Here

Examples of org.jmol.modelset.Bond

248
249
250
251
252
253
254
255
256
257
258
259
 

  public Point3fi checkObjectClicked(int x, int y, int modifiers,
                                    BitSet bsVisible) {
    Point3fi pt = new Point3fi();
    Bond bond = findPickedBond(x, y, bsVisible, pt);
    if (bond == null)
      return null;
    pt.index = bond.getIndex();
    viewer.setStatusAtomPicked(-3, "[\"bond\",\"" + bond.getIdentity() + "\"," + pt.x + "," + pt.y + "," + pt.z + "]");
    return pt;
  }
View Full Code Here

Examples of org.jmol.modelset.Bond

266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
    if (g3d.isAntialiased()) {
      x <<= 1;
      y <<= 1;
      dmin2 <<= 1;
    }
    Bond pickedBond = null;
    Point3f v = new Point3f();
    Bond[] bonds = modelSet.getBonds();
    for (int i = modelSet.getBondCount(); --i >= 0;) {
      Bond bond = bonds[i];
      if (bond.getShapeVisibilityFlags() == 0)
        continue;
      Atom atom1 = bond.getAtom1();
      Atom atom2 = bond.getAtom2();
      if (!atom1.isVisible(0) || !atom2.isVisible(0))
        continue;
      v.set(atom1);
      v.add(atom2);
      v.scale(0.5f);
View Full Code Here

Examples of org.jmol.modelset.Bond

382
383
384
385
386
387
388
389
390
391
392
393
394
395
    if (partialCharges == null)
      return;
    clear(true);
    Bond[] bonds = modelSet.getBonds();
    for (int i = bonds.length; --i >= 0;) {
      Bond bond = bonds[i];
      if (!bond.isCovalent())
        continue;
      float c1 = partialCharges[bond.getAtomIndex1()];
      float c2 = partialCharges[bond.getAtomIndex2()];
      if (c1 != c2)
        setDipole(bond.getAtom1(), bond.getAtom2(), c1, c2);
    }
  }
View Full Code Here

Examples of org.jmol.modelset.Bond

266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
    Bond[] bonds = atom.getBonds();
    if (bonds == null)
      return null;
    int bondCount = 0;
    for (int i = bonds.length; --i >= 0;) {
      Bond bond = bonds[i];
      Atom otherAtom = bond.getAtom1() == atom ? bond.getAtom2() : bond
          .getAtom1();
      if (bsVertices != null && !bsVertices.get(otherAtom.getIndex()))
        continue;
      if (radius > 0f && bond.getAtom1().distance(bond.getAtom2()) > radius)
        continue;
      otherAtoms[bondCount++] = otherAtom;
      if (bondCount == MAX_VERTICES)
        break;
    }
View Full Code Here

Examples of org.jquantlib.instruments.Bond

844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
              .withCouponRates(couponRates)
              .withPaymentAdjustment(BusinessDayConvention.ModifiedFollowing).Leg();
          // redemption
          cashflows.add(new SimpleCashFlow(faceAmount, cashflows.last().date()));

          final Bond bond = new Bond(settlementDays, new Brazil(Brazil.Market.SETTLEMENT),
                    faceAmount, cashflows.last().date(),
                    new Date(1,Month.January,2007), cashflows);

          final double cachedPrice = prices[bondIndex];

          final double price = faceAmount*bond.dirtyPrice(yield.rate(),
                                                       yield.dayCounter(),
                                                       yield.compounding(),
                                                       yield.frequency(),
                                                       today)/100;
          if (Math.abs(price-cachedPrice) > tolerance) {
View Full Code Here

Examples of org.jquantlib.instruments.Bond

855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
              .withCouponRates(couponRates)
              .withPaymentAdjustment(BusinessDayConvention.ModifiedFollowing).Leg();
          // redemption
          cashflows.add(new SimpleCashFlow(faceAmount, cashflows.last().date()));

          final Bond bond = new Bond(settlementDays, new Brazil(Brazil.Market.SETTLEMENT),
                    faceAmount, cashflows.last().date(),
                    new Date(1,Month.January,2007), cashflows);

          final double cachedPrice = prices[bondIndex];

          final double price = faceAmount*bond.dirtyPrice(yield.rate(),
                                                       yield.dayCounter(),
                                                       yield.compounding(),
                                                       yield.frequency(),
                                                       today)/100;
          if (Math.abs(price-cachedPrice) > tolerance) {
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.