Package org.openscience.cdk

Examples of org.openscience.cdk.AtomContainer.addAtom()

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        IAtomContainer ac = new AtomContainer();
        if (atoms.size() != 0) {
           ac = atoms.get(0).getBuilder().newInstance(IAtomContainer.class);
           for (IAtom atom : atoms) {
              ac.addAtom(atom);
           }
        }
       
        for (IBond bond : bonds) {
           ac.addBond(bond);
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     *
     * @throws Exception
     */
    @Test public void testGetInchiFromChlorineAtom() throws Exception {
        IAtomContainer ac = new AtomContainer();
        ac.addAtom(new Atom("Cl"));
        gen.setHydrogensNotAdded(true);
        Assert.assertEquals(gen.generateInchi(ac).getInChI(), "InChI=1S/Cl");
        gen.setHydrogensNotAdded(false);

    }
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     */
    @Test public void testGetInchiFromLithiumIon() throws Exception {
        IAtomContainer ac = new AtomContainer();
        IAtom a = new Atom("Li");
        a.setFormalCharge(+1);
        ac.addAtom(a);
        gen.setHydrogensNotAdded(true);
        Assert.assertEquals(gen.generateInchi(ac).getInChI(), "InChI=1S/Li/q+1");
        gen.setHydrogensNotAdded(false);

    }
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    */
    @Test public void testGetInchiFromChlorine37Atom() throws Exception {
        IAtomContainer ac = new AtomContainer();
        IAtom a = new Atom("Cl");
        a.setMassNumber(37);
        ac.addAtom(a);
        gen.setHydrogensNotAdded(true);
        Assert.assertEquals(gen.generateInchi(ac).getInChI(), "InChI=1S/Cl/i1+2");
        gen.setHydrogensNotAdded(false);
    }
   
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     */
    @Test public void testGetInchiFromHydrogenChlorideImplicitH() throws Exception {
        IAtomContainer ac = new AtomContainer();
        IAtom a = new Atom("Cl");
        a.setImplicitHydrogenCount(1);
        ac.addAtom(a);
        Assert.assertEquals(gen.generateInchi(ac).getInChI(), "InChI=1S/ClH/h1H");
    }
   
    /**
     * Tests radical state is correctly passed to InChI.
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        IAtomContainer ac = new AtomContainer();
        IAtom a1 = new Atom("C");
        IAtom a2 = new Atom("C");
        a1.setImplicitHydrogenCount(3);
        a2.setImplicitHydrogenCount(3);
        ac.addAtom(a1);
        ac.addAtom(a2);
        ac.addBond(new Bond(a1, a2, CDKConstants.BONDORDER_SINGLE));
        InChI inchi = gen.generateInchi(ac);
        Assert.assertEquals(inchi.getInChI(), "InChI=1S/C2H6/c1-2/h1-2H3");
        Assert.assertEquals("InChIKey=OTMSDBZUPAUEDD-UHFFFAOYSA-N", inchi.getKey());
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        IAtom a1 = new Atom("C");
        IAtom a2 = new Atom("C");
        a1.setImplicitHydrogenCount(3);
        a2.setImplicitHydrogenCount(3);
        ac.addAtom(a1);
        ac.addAtom(a2);
        ac.addBond(new Bond(a1, a2, CDKConstants.BONDORDER_SINGLE));
        InChI inchi = gen.generateInchi(ac);
        Assert.assertEquals(inchi.getInChI(), "InChI=1S/C2H6/c1-2/h1-2H3");
        Assert.assertEquals("InChIKey=OTMSDBZUPAUEDD-UHFFFAOYSA-N", inchi.getKey());
    }
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        IAtomContainer ac = new AtomContainer();
        IAtom a1 = new Atom("C");
        IAtom a2 = new Atom("C");
        a1.setImplicitHydrogenCount(2);
        a2.setImplicitHydrogenCount(2);
        ac.addAtom(a1);
        ac.addAtom(a2);
        ac.addBond(new Bond(a1, a2, CDKConstants.BONDORDER_DOUBLE));
        Assert.assertEquals(gen.generateInchi(ac).getInChI(), "InChI=1S/C2H4/c1-2/h1-2H2");
    }
   
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        IAtom a1 = new Atom("C");
        IAtom a2 = new Atom("C");
        a1.setImplicitHydrogenCount(2);
        a2.setImplicitHydrogenCount(2);
        ac.addAtom(a1);
        ac.addAtom(a2);
        ac.addBond(new Bond(a1, a2, CDKConstants.BONDORDER_DOUBLE));
        Assert.assertEquals(gen.generateInchi(ac).getInChI(), "InChI=1S/C2H4/c1-2/h1-2H2");
    }
   
    /**
 
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        IAtomContainer ac = new AtomContainer();
        IAtom a1 = new Atom("C");
        IAtom a2 = new Atom("C");
        a1.setImplicitHydrogenCount(1);
        a2.setImplicitHydrogenCount(1);
        ac.addAtom(a1);
        ac.addAtom(a2);
        ac.addBond(new Bond(a1, a2, CDKConstants.BONDORDER_TRIPLE));
        Assert.assertEquals(gen.generateInchi(ac).getInChI(), "InChI=1S/C2H2/c1-2/h1-2H");
    }
   
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