Package org.openscience.cdk

Examples of org.openscience.cdk.Bond

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        if(verbose) System.out.println("Uncharged?");
        if(mol.getAtom(i).getFormalCharge() != 0) continue;
        List l = mol.getConnectedBondsList(mol.getAtom(i));
        if(verbose) System.out.println("One bond?");
        if(l.size() != 1) continue;
        Bond b = (Bond)l.get(0);
        if(verbose) System.out.println("Not a stereo bond?");
        if(b.getStereo() != CDKConstants.STEREO_BOND_NONE) continue;
        IAtom otherAtom = b.getConnectedAtom(mol.getAtom(i));
        // Special cases
        /*if(getInstance().valencies.containsKey(otherAtom.getAtomicNumber())) {
          int valency = getInstance().valencies.get(otherAtom.getAtomicNumber());
          if(valency == 1) {
            if(otherAtom.getFormalCharge() != 0) valency = 0;
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      if(a.getFormalCharge() == 1 || a.getFormalCharge() == -1) c += 1;
      int hr = 4 - c;
      for(int j=0;j<hr;j++) {
        IAtom ha = new Atom("H");
        isotopeFactory.configure(ha);
        IBond b = new Bond(a, ha);
        mol.addAtom(ha);
        mol.addBond(b);
      }
    }
  }
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        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 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 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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        acE.addAtom(a1E);
        acE.addAtom(a2E);
        acE.addAtom(a3E);
        acE.addAtom(a4E);

        acE.addBond(new Bond(a1E, a2E, CDKConstants.BONDORDER_DOUBLE));
        acE.addBond(new Bond(a1E, a3E, CDKConstants.BONDORDER_SINGLE));
        acE.addBond(new Bond(a2E, a4E, CDKConstants.BONDORDER_SINGLE));
       
        Assert.assertEquals(gen.generateInchi(acE).getInChI(), "InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1+");
       
        // (Z)-1,2-dichloroethene
        IAtomContainer acZ = new AtomContainer();
        IAtom a1Z = new Atom("C", new Point2d(2.866, -0.440));
        IAtom a2Z = new Atom("C", new Point2d(3.732, 0.060));
        IAtom a3Z = new Atom("Cl", new Point2d(2.000, 0.060));
        IAtom a4Z = new Atom("Cl", new Point2d(3.732, 1.060));
        a1Z.setImplicitHydrogenCount(1);
        a2Z.setImplicitHydrogenCount(1);
        acZ.addAtom(a1Z);
        acZ.addAtom(a2Z);
        acZ.addAtom(a3Z);
        acZ.addAtom(a4Z);

        acZ.addBond(new Bond(a1Z, a2Z, CDKConstants.BONDORDER_DOUBLE));
        acZ.addBond(new Bond(a1Z, a3Z, CDKConstants.BONDORDER_SINGLE));
        acZ.addBond(new Bond(a2Z, a4Z, CDKConstants.BONDORDER_SINGLE));
       
        Assert.assertEquals(gen.generateInchi(acZ).getInChI(), "InChI=1S/C2H2Cl2/c3-1-2-4/h1-2H/b2-1-");

    }
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        acL.addAtom(a3L);
        acL.addAtom(a4L);
        acL.addAtom(a5L);
        acL.addAtom(a6L);
       
        acL.addBond(new Bond(a1L, a2L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a1L, a3L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a1L, a4L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a2L, a5L, CDKConstants.BONDORDER_SINGLE));
        acL.addBond(new Bond(a2L, a6L, CDKConstants.BONDORDER_DOUBLE));
       
        Assert.assertEquals(gen.generateInchi(acL).getInChI(), "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1");
       
       
        // D-Alanine
        IAtomContainer acD = new AtomContainer();
        IAtom a1D = new Atom("C", new Point3d(0.358, 0.819, 20.655));
        IAtom a2D = new Atom("C", new Point3d(1.598, -0.032, 20.905));
        IAtom a3D = new Atom("N", new Point3d(0.275, 2.014, 21.574));
        IAtom a4D = new Atom("C", new Point3d(-0.952, 0.043, 20.838));
        IAtom a5D = new Atom("O", new Point3d(2.678, 0.479, 21.093));
        IAtom a6D = new Atom("O", new Point3d(1.596, -1.239, 20.958));
        a1D.setImplicitHydrogenCount(1);
        a3D.setImplicitHydrogenCount(2);
        a4D.setImplicitHydrogenCount(3);
        a5D.setImplicitHydrogenCount(1);
        acD.addAtom(a1D);
        acD.addAtom(a2D);
        acD.addAtom(a3D);
        acD.addAtom(a4D);
        acD.addAtom(a5D);
        acD.addAtom(a6D);
       
        acD.addBond(new Bond(a1D, a2D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a1D, a3D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a1D, a4D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a2D, a5D, CDKConstants.BONDORDER_SINGLE));
        acD.addBond(new Bond(a2D, a6D, CDKConstants.BONDORDER_DOUBLE));
       
                                                             //"InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1");
        Assert.assertEquals(gen.generateInchi(acL).getInChI(), "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1");

    }
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Related Classes of org.openscience.cdk.Bond

  • org.openscience.jchempaint.inchi.StdInChIGeneratorTest
  • uk.ac.cam.ch.wwmm.ptclib.cdk.HydrogenRemover
  • uk.ac.cam.ch.wwmm.ptclib.cdk.StructureConverter
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