use of algorithms.isomorphism.chains.MappedChain in project Smiles2Monomers by yoann-dufresne.
the class IsomorphismTests method notMatchingAromaticTest.
@Test
public void notMatchingAromaticTest() {
Polymer pep = new Polymer(0, "", "SC1CCCCC1", null);
List<MappedChain> mbs = Isomorphism.searchAChain(this.bloc, pep, MatchingType.STRONG);
Assert.assertFalse(mbs.size() > 0);
}
use of algorithms.isomorphism.chains.MappedChain in project Smiles2Monomers by yoann-dufresne.
the class IsomorphismTests method initMappingTest.
@Test
public void initMappingTest() {
List<MappedChain> mbs = Isomorphism.searchFromPreviousMapping(this.mb0, this.ext1, MatchingType.STRONG);
if (mbs.size() != 2)
fail("2 matches needed");
boolean isGood = true;
for (MappedChain mb : mbs) {
IMolecule mol = mb.getChemObject().getMolecule();
IAtom a1 = (mol.getAtom(mb.getAtomsMapping().get(0)));
IAtom a2 = (mol.getAtom(mb.getAtomsMapping().get(1)));
if (!((a1.getSymbol().equals("C") && a2.getSymbol().equals("S")) || (a1.getSymbol().equals("S") && a2.getSymbol().equals("C"))))
isGood = false;
}
Assert.assertTrue(isGood);
}
use of algorithms.isomorphism.chains.MappedChain in project Smiles2Monomers by yoann-dufresne.
the class IsomorphismTests method lightMatchingAromaticTest.
@Test
public void lightMatchingAromaticTest() {
Polymer pep = new Polymer(0, "", "SC1CCCCC1", null);
List<MappedChain> mbs = Isomorphism.searchAChain(this.bloc, pep, MatchingType.LIGHT);
Assert.assertTrue(mbs.size() > 0);
}
use of algorithms.isomorphism.chains.MappedChain in project Smiles2Monomers by yoann-dufresne.
the class IsomorphismTests method setUp.
@Before
public void setUp() throws Exception {
// Database
Monomer[] monos = new Monomer[1];
Polymer pepTest = new Polymer(0, "malformin A1", "O=C1NC2C(=O)NC(C(=O)NC(C(=O)NC(C(=O)NC1CSSC2)C(C)CC)CC(C)C)C(C)C", monos);
// Extensions
IAtom a = new Atom("C");
IBond b1 = new Bond(new Atom("S"), a, Order.SINGLE);
this.ext1 = new Extension(b1);
a = new Atom("C");
IAtom a2 = new Atom("C");
IBond b2 = new Bond(a, a2, Order.SINGLE);
this.ext2 = new Extension(b2);
// Mapped blocs
this.mb0 = new MappedChain(pepTest, null, new ArrayList<Integer>(), new ArrayList<Integer>(), new ArrayList<MatchingType>(), new HashMap<Integer, Integer>());
// For blocs Tests
this.bloc = new Chain("S,0,c,0,0,-1,-1;c,0,c,0,0,-1,1");
}
use of algorithms.isomorphism.chains.MappedChain in project Smiles2Monomers by yoann-dufresne.
the class IsomorphismTests method matchingAromaticTest.
@Test
public void matchingAromaticTest() {
Polymer pep = new Polymer(0, "", "Sc1ccccc1", null);
List<MappedChain> mbs = Isomorphism.searchAChain(this.bloc, pep, MatchingType.STRONG);
Assert.assertTrue(mbs.size() > 0);
}
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