Package org.jmol.modelset

Examples of org.jmol.modelset.Bond$BondSet

442
443
444
445
446
447
448
449
450
451
        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());
      }
    }
View Full Code Here
458
459
460
461
462
463
464
465
466
467
468
469
470
471
      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);
    }
View Full Code Here
7677
7678
7679
7680
7681
7682
7683
7684
7685
7686
7687
7688
7689
7690
7691
  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");
  }
View Full Code Here
7723
7724
7725
7726
7727
7728
7729
7730
7731
7732
7733
7734
7735
    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)
View Full Code Here
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
          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;
View Full Code Here
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
      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;
View Full Code Here
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
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
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
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
TOP

Related Classes of org.jmol.modelset.Bond$BondSet

  • 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
    • Copyright © 2018 www.massapicom. 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.