Examples of bonds()

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

444
445
446
447
448
449
450
451
452
453
454
                }
                ShapeSelection container = new RectangleSelection();
                for (IAtom atom : wholeModel.atoms()) {
                    container.atoms.add(atom);
                }
                for (IBond bond : wholeModel.bonds()) {
                    container.bonds.add(bond);
                }
                renderModel.setSelection(container);
            }
            else {
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

467
468
469
470
471
472
473
474
475
476
477
                }
                ShapeSelection container = new RectangleSelection();
                for (IAtom atom : wholeModel.atoms()) {
                    container.atoms.add(atom);
                }
                for (IBond bond : wholeModel.bonds()) {
                    container.bonds.add(bond);
                }
                renderModel.setSelection(container);
            }
            else {
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

490
491
492
493
494
495
496
497
498
499
500
                }
                ShapeSelection container = new RectangleSelection();
                for (IAtom atom : wholeModel.atoms()) {
                    container.atoms.add(atom);
                }
                for (IBond bond : wholeModel.bonds()) {
                    container.bonds.add(bond);
                }
                renderModel.setSelection(container);
            }
            else {
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

1895
1896
1897
1898
1899
1900
1901
1902
1903
1904
1905
        .getAllAtomContainers(chemModel);
    Iterator<IAtomContainer> iterator = containersList.iterator();
    Map<IBond, IBond.Order[]> changedBonds = new HashMap<IBond, IBond.Order[]>();
    while (iterator.hasNext()) {
      IAtomContainer ac = (IAtomContainer) iterator.next();
      for (IBond bond : ac.bonds()) {
        IBond.Order[] orders = new IBond.Order[2];
        orders[1] = bond.getOrder();
        changedBonds.put(bond, orders);
      }
      satChecker.saturate(ac);
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

1901
1902
1903
1904
1905
1906
1907
1908
1909
1910
1911
        IBond.Order[] orders = new IBond.Order[2];
        orders[1] = bond.getOrder();
        changedBonds.put(bond, orders);
      }
      satChecker.saturate(ac);
      for (IBond bond : ac.bonds()) {
        IBond.Order[] orders = changedBonds.get(bond);
        orders[0] = bond.getOrder();
        changedBonds.put(bond, orders);
      }
    }
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

1925
1926
1927
1928
1929
1930
1931
1932
1933
1934
1935
        .getAllAtomContainers(chemModel);
    Iterator<IAtomContainer> iterator = containersList.iterator();
    Map<IBond, IBond.Order[]> changedBonds = new HashMap<IBond, IBond.Order[]>();
    while (iterator.hasNext()) {
      IAtomContainer ac = iterator.next();
      for (IBond bond : ac.bonds()) {
        IBond.Order[] orders = new IBond.Order[2];
        orders[1] = bond.getOrder();
        orders[0] = Order.SINGLE;
        changedBonds.put(bond, orders);
        bond.setOrder(Order.SINGLE);
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

2050
2051
2052
2053
2054
2055
2056
2057
2058
2059
2060
        coords[1] = oldCoord;
        atomCoordsMap.put(atom, coords);
      }
    }
    // Stereo bonds must be flipped as well to keep the structure
    for (IBond bond : toflip.bonds()) {
      if (bond.getStereo() == IBond.Stereo.UP)
        bond.setStereo(IBond.Stereo.DOWN);
      else if (bond.getStereo() == IBond.Stereo.DOWN)
        bond.setStereo(IBond.Stereo.UP);
      else if (bond.getStereo() == IBond.Stereo.UP_INVERTED)
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

2078
2079
2080
2081
2082
2083
2084
2085
2086
2087
2088
            .getAtomCount() != 0) {
      toflip = renderModel.getSelection().getConnectedAtomContainer();
    } else
      return;

    for (IBond bond : toflip.bonds()) {
      if (bond.getStereo() == IBond.Stereo.UP)
        bond.setStereo(IBond.Stereo.DOWN);
      else if (bond.getStereo() == IBond.Stereo.DOWN)
        bond.setStereo(IBond.Stereo.UP);
      else if (bond.getStereo() == IBond.Stereo.UP_INVERTED)
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

2220
2221
2222
2223
2224
2225
2226
2227
2228
2229
2230
          ac.addBond(bond);
        }
      }
      ChemModelManipulator.removeAtomAndConnectedElectronContainers(
                                       chemModel, atom);
      for (IBond bond : ac.bonds()) {
        if (bond.getAtom(0) == atom)
          updateAtom(bond.getAtom(1));
        else
          updateAtom(bond.getAtom(0));
      }
View Full Code Here

Examples of org.openscience.cdk.interfaces.IAtomContainer.bonds()

455
456
457
458
459
460
461
462
463
464
465
      IBond connBond = connbonds.next();
      ac.addBond(connBond);
    }
    ChemModelManipulator.removeAtomAndConnectedElectronContainers(
        chemModel, atom);
    for (IBond bond : ac.bonds()) {
      if (bond.getAtom(0) == atom)
        updateAtom(bond.getAtom(1));
      else
        updateAtom(bond.getAtom(0));
    }
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.