org.openscience.cdk.Bond.<init>()方法的使用及代码示例

x33g5p2x  于2022-01-16 转载在 其他  
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本文整理了Java中org.openscience.cdk.Bond.<init>()方法的一些代码示例，展示了Bond.<init>()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。Bond.<init>()方法的具体详情如下：
包路径：org.openscience.cdk.Bond
类名称：Bond
方法名：<init>

Bond.<init>介绍

[英]Constructs an empty bond.
[中]构造一个空的键。

代码示例

代码示例来源：origin: cdk/cdk

/**
 * {@inheritDoc}
 */
@Override
public IBond newBond() {
  return new Bond();
}

代码示例来源：origin: org.openscience.cdk/cdk-data

/**
 * {@inheritDoc}
 */
@Override
public IBond newBond() {
  return new Bond();
}

代码示例来源：origin: cdk/cdk

public DebugRing(int ringSize, String elementSymbol) {
  this(ringSize);
  super.atomCount = ringSize;
  super.bondCount = ringSize;
  atoms[0] = new DebugAtom(elementSymbol);
  for (int i = 1; i < ringSize; i++) {
    atoms[i] = new DebugAtom(elementSymbol);
    super.bonds[i - 1] = new Bond(atoms[i - 1], atoms[i], IBond.Order.SINGLE);
  }
  super.bonds[ringSize - 1] = new Bond(atoms[ringSize - 1], atoms[0], IBond.Order.SINGLE);
}

代码示例来源：origin: cdk/cdk

@Override
  public IChemObject newTestObject() {
    return new Bond();
  }
});

代码示例来源：origin: cdk/cdk

@Test
public void testGetMinimumBondOrder_HigherOrders() {
  List<IBond> bonds = new ArrayList<IBond>();
  IBond bond = new Bond();
  bond.setOrder(IBond.Order.QUINTUPLE);
  bonds.add(bond);
  bond = new Bond();
  bond.setOrder(IBond.Order.SEXTUPLE);
  bonds.add(bond);
  Assert.assertEquals(IBond.Order.QUINTUPLE, BondManipulator.getMinimumBondOrder(bonds.iterator()));
}

代码示例来源：origin: cdk/cdk

@BeforeClass
public static void setUp() {
  setTestObjectBuilder(new ITestObjectBuilder() {
    @Override
    public IChemObject newTestObject() {
      return new Bond();
    }
  });
}

代码示例来源：origin: cdk/cdk

@Test
public void testGetMaximumBondOrder_IBond_IBond() {
  IBond bond1 = new Bond();
  bond1.setOrder(IBond.Order.SINGLE);
  IBond bond2 = new Bond();
  bond2.setOrder(IBond.Order.QUADRUPLE);
  Assert.assertEquals(IBond.Order.QUADRUPLE, BondManipulator.getMaximumBondOrder(bond1, bond2));
}

代码示例来源：origin: cdk/cdk

@Test
@Override
public void testCompare_Object() {
  IChemObject object = newChemObject();
  IAtom c = object.getBuilder().newInstance(IAtom.class, "C");
  IAtom o = object.getBuilder().newInstance(IAtom.class, "O");
  IBond b = new Bond(c, o, IBond.Order.DOUBLE); // C=O bond
  IBond b2 = new Bond(c, o, IBond.Order.DOUBLE); // same C=O bond
  Assert.assertTrue(b.compare(b2));
}

代码示例来源：origin: cdk/cdk

static IBond bond(IAtomContainer m, int v, int w, IBond.Order ord, boolean arom) {
    IBond b = new Bond(m.getAtom(v), m.getAtom(w));
    b.setOrder(ord);
    b.setFlag(CDKConstants.ISAROMATIC, arom);
    return b;
  }
}

代码示例来源：origin: cdk/cdk

private int alignmentTestHelper(IAtom zero, IAtom... pos) {
    IAtomContainer mol = new AtomContainer();
    mol.addAtom(zero);
    for (IAtom atom : pos) {
      mol.addAtom(atom);
      mol.addBond(new Bond(zero, atom));
    }
    return GeometryUtil.getBestAlignmentForLabelXY(mol, zero);
  }
}

代码示例来源：origin: cdk/cdk

@Test(expected = CDKException.class)
public void testUnsupportedBondOrder() throws Exception {
  IAtomContainer molecule = new AtomContainer();
  molecule.addAtom(new Atom("C"));
  molecule.addAtom(new Atom("C"));
  molecule.addBond(new Bond(molecule.getAtom(0), molecule.getAtom(1), Order.QUADRUPLE));
  MDLV2000Writer mdlWriter = new MDLV2000Writer(new StringWriter());
  mdlWriter.write(molecule);
  mdlWriter.close();
}

代码示例来源：origin: cdk/cdk

@Test
public void testGetAtomArray_IBond() {
  IAtom atom1 = new Atom(Elements.CARBON);
  IAtom atom2 = new Atom(Elements.CARBON);
  IBond bond = new Bond(atom1, atom2, Order.TRIPLE);
  IAtom[] atoms = BondManipulator.getAtomArray(bond);
  Assert.assertEquals(2, atoms.length);
  Assert.assertEquals(atom1, atoms[0]);
  Assert.assertEquals(atom2, atoms[1]);
}

代码示例来源：origin: cdk/cdk

@Test
public void iupacMethylPreferred() {
  IAtom a1 = new Atom("C");
  IAtom a2 = new Atom("C");
  IBond bond = new Bond(a1, a2);
  a1.setPoint2d(new Point2d(0, 0));
  a2.setPoint2d(new Point2d(0, 0));
  assertTrue(SymbolVisibility.iupacRecommendations().visible(a1, Arrays.asList(bond), new RendererModel()));
}

代码示例来源：origin: cdk/cdk

@Test
public void ethaneNonTerminal() {
  IAtom a1 = new Atom("C");
  IAtom a2 = new Atom("C");
  a1.setPoint2d(new Point2d(0, 0));
  a2.setPoint2d(new Point2d(0.5, -0.5));
  IBond bond1 = new Bond(a1, a2);
  a1.setImplicitHydrogenCount(3);
  a2.setImplicitHydrogenCount(3);
  assertTrue(SymbolVisibility.iupacRecommendationsWithoutTerminalCarbon()
                .visible(a1, Collections.singletonList(bond1), new RendererModel()));
}

代码示例来源：origin: cdk/cdk

@Test
public void testGetLength2D_IBond() {
  Atom o = new Atom("O", new Point2d(0.0, 0.0));
  Atom c = new Atom("C", new Point2d(1.0, 0.0));
  Bond bond = new Bond(c, o);
  Assert.assertEquals(1.0, GeometryUtil.getLength2D(bond), 0.001);
}

代码示例来源：origin: cdk/cdk

@Test
public void testHighlightedBond() {
  RendererModel model = new RendererModel();
  // test default
  Assert.assertNull(model.getHighlightedBond());
  IBond content = new Bond();
  model.setHighlightedBond(content);
  Assert.assertEquals(content, model.getHighlightedBond());
  model.setHighlightedBond(null);
  Assert.assertNull(model.getHighlightedBond());
}

代码示例来源：origin: cdk/cdk

@Test(expected = IllegalArgumentException.class)
public void unplacedNonHydrogen() {
  HydrogenPlacer hydrogenPlacer = new HydrogenPlacer();
  // c2 is unplaced
  IAtom c1 = new Atom("C", new Point2d(0, 0));
  IAtom c2 = new Atom("C");
  IAtomContainer m = new AtomContainer();
  m.addAtom(c1);
  m.addAtom(c2);
  m.addBond(new Bond(c1, c2));
  hydrogenPlacer.placeHydrogens2D(m, 1.5);
}

代码示例来源：origin: cdk/cdk

@Test
public void testGetTotalCharge() throws IOException, ClassNotFoundException, CDKException {
  IAtomContainer container = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
  IAtom atom1 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class, "C");
  atom1.setCharge(1.0);
  IAtom atom2 = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class, "N");
  container.addAtom(atom1);
  container.addAtom(atom2);
  container.addBond(new Bond(atom1, atom2, Order.SINGLE));
  double totalCharge = AtomContainerManipulator.getTotalCharge(container);
  Assert.assertEquals(1.0, totalCharge, 0.01);
}

代码示例来源：origin: cdk/cdk

@Test
public void testBond_IAtom_IAtom() {
  IChemObject object = newChemObject();
  IAtom c = object.getBuilder().newInstance(IAtom.class, "C");
  IAtom o = object.getBuilder().newInstance(IAtom.class, "O");
  IBond bond = new Bond(c, o);
  Assert.assertEquals(2, bond.getAtomCount());
  Assert.assertEquals(c, bond.getBegin());
  Assert.assertEquals(o, bond.getEnd());
  Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder());
  Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo());
}

代码示例来源：origin: cdk/cdk

@Test
public void testBond_IAtom_IAtom_IBond_Order() {
  IChemObject object = newChemObject();
  IAtom c = object.getBuilder().newInstance(IAtom.class, "C");
  IAtom o = object.getBuilder().newInstance(IAtom.class, "O");
  IBond bond = new Bond(c, o, IBond.Order.DOUBLE);
  Assert.assertEquals(2, bond.getAtomCount());
  Assert.assertEquals(c, bond.getBegin());
  Assert.assertEquals(o, bond.getEnd());
  Assert.assertTrue(bond.getOrder() == IBond.Order.DOUBLE);
  Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo());
}

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