Examples of bonds()


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

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

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

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

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

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

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

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

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

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

      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));
    }
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