Examples with ComponentGroup ambit2.core.groups.ComponentGroup used on opensource projects

Example 1 with ComponentGroup

use of ambit2.core.groups.ComponentGroup in project ambit-mirror by ideaconsult.

the class MDLV2000ReaderExtendedTest method testMixture.

@Test
public void testMixture() throws Exception {
    IChemObject mol = readSGroup("mixture_unordered.mol");
    Assert.assertNotNull(mol);
    Assert.assertTrue(mol instanceof SuppleAtomContainer);
    SuppleAtomContainer sca = (SuppleAtomContainer) mol;
    sca.setFiltered(false);
    Assert.assertEquals(11, sca.getBondCount());
    Assert.assertEquals(15 + 4, sca.getAtomCount());
    List<ISGroup> superatom = getGroup(sca);
    Assert.assertNotNull(superatom);
    Assert.assertEquals(4, superatom.size());
    for (int i = 0; i < superatom.size(); i++) {
        if (superatom.get(i) instanceof ComponentGroup) {
            Assert.assertNotNull(superatom.get(i));
            Assert.assertNull(((ComponentGroup) superatom.get(i)).getOrder());
        } else if (superatom.get(i) instanceof ContainerGroup) {
            Assert.assertEquals(3, ((ContainerGroup) superatom.get(i)).getComponents().size());
        }
    }
    sca.setFiltered(true);
    verify((IAtomContainer) mol, superatom, false, 15, 11, true);
    verify((IAtomContainer) mol, superatom, true, 15, 11, true);
}

Example 2 with ComponentGroup

use of ambit2.core.groups.ComponentGroup in project ambit-mirror by ideaconsult.

the class MDLV2000ReaderExtendedTest method testFormulation.

@Test
public void testFormulation() throws Exception {
    IChemObject mol = readSGroup("mixture_ordered.mol");
    Assert.assertNotNull(mol);
    Assert.assertTrue(mol instanceof SuppleAtomContainer);
    SuppleAtomContainer sca = (SuppleAtomContainer) mol;
    sca.setFiltered(false);
    Assert.assertEquals(29, sca.getBondCount());
    Assert.assertEquals(31 + 3, sca.getAtomCount());
    List<ISGroup> superatom = getGroup(sca);
    Assert.assertNotNull(superatom);
    Assert.assertEquals(3, superatom.size());
    for (int i = 0; i < superatom.size(); i++) {
        if (superatom.get(i) instanceof ComponentGroup) {
            Assert.assertNotNull(superatom.get(i));
            Assert.assertNotNull(((ComponentGroup) superatom.get(i)).getOrder());
            System.out.println(((ComponentGroup) superatom.get(i)).getSubscript());
        } else if (superatom.get(i) instanceof ContainerGroup) {
            Assert.assertEquals(2, ((ContainerGroup) superatom.get(i)).getComponents().size());
            Assert.assertEquals(ContainerGroup.SGROUP_MIXTURE.FORMULATION, ((ContainerGroup) superatom.get(i)).getType());
            Assert.assertEquals("f", ((ContainerGroup) superatom.get(i)).getSubscript());
        }
    }
    sca.setFiltered(true);
    verify((IAtomContainer) mol, superatom, false, 31, 29, false);
    verify((IAtomContainer) mol, superatom, true, 31, 29, false);
}

Example 3 with ComponentGroup

use of ambit2.core.groups.ComponentGroup in project ambit-mirror by ideaconsult.

the class MDLV2000ReaderExtendedTest method testCopolymer.

@Test
public void testCopolymer() throws Exception {
    IChemObject mol = readSGroup("copolymer.mol");
    Assert.assertNotNull(mol);
    Assert.assertTrue(mol instanceof SuppleAtomContainer);
    SuppleAtomContainer sca = (SuppleAtomContainer) mol;
    sca.setFiltered(false);
    Assert.assertEquals(20, sca.getBondCount());
    Assert.assertEquals(20 + 2, sca.getAtomCount());
    List<ISGroup> superatom = getGroup(sca);
    Assert.assertNotNull(superatom);
    Assert.assertEquals(2, superatom.size());
    for (int i = 0; i < superatom.size(); i++) {
        if (superatom.get(i) instanceof ComponentGroup) {
            Assert.assertNotNull(superatom.get(i));
            Assert.assertNull(((ComponentGroup) superatom.get(i)).getOrder());
        } else if (superatom.get(i) instanceof ContainerGroup) {
            Assert.assertEquals(1, ((ContainerGroup) superatom.get(i)).getComponents().size());
        }
    }
    sca.setFiltered(true);
    verify((IAtomContainer) mol, superatom, false, 20, 20, true);
    verify((IAtomContainer) mol, superatom, true, 20, 20, true);
}