@@ -133,56 +133,25 @@ public class PathFingerprinter implements Fingerprinter public BitSet getFingerprint(Molecule molecule) { - paths.clear(); - this.bloomFilter = new BloomFilter(1024); - this.writer = new PathWriter(bloomFilter); bloomFilter.clear(); - findAromatics(molecule); - - for (int i = 0; i < molecule.countAtoms(); i++) - { - Atom atom = molecule.getAtom(i); + Collection<List<Atom>> rings = ringFinder.findRings(molecule); + findAromatics(molecule, rings); - walker.walk(atom, writer); - } - - return bloomFilter.toBitSet(); - } - - private void findAromatics(Molecule molecule) - { - aromatics.clear(); - filter.filterAtoms(molecule, aromatics); - - for (Atom atom : aromatics) - { - aromatics.add(atom); - } + recordWalk(molecule); + + BitSet walkBits = bloomFilter.toBitSet(); + BitSet result = new BitSet(getFingerprintLength()); + + result.or(walkBits); + writeRingBits(result, rings); - writer.setAromatics(aromatics); + return result; } - -// public BitSet getFingerprint(Molecule molecule) -// { -// bloomFilter.clear(); -// Collection<List<Atom>> rings = ringFinder.findRings(molecule); -// findAromatics(molecule, rings); -// -// recordWalk(molecule); -// -// BitSet walkBits = bloomFilter.toBitSet(); -// BitSet result = new BitSet(getFingerprintLength()); -// -// result.or(walkBits); -//// writeRingBits(result, rings); -// -// return bloomFilter.toBitSet(); -// } + private void writeRingBits(BitSet bitset, Collection<List<Atom>> rings) { for (List<Atom> ring : rings) { -// System.out.println("ring: " + (ring.size() - 1)); if (ring.size() < ringBitCount) { int index = bloomFilter.getBitArraySize() + (ring.size() - 4); @@ -210,16 +179,5 @@ public class PathFingerprinter implements Fingerprinter aromatics.clear(); filter.filterAtoms(molecule.countAtoms(), rings, aromatics); writer.setAromatics(aromatics); - }// private void findAromatics(Molecule molecule) -// { -// aromatics.clear(); -// filter.filterAtoms(molecule, aromatics); -// -// for (Atom atom : aromatics) -// { -// aromatics.add(atom); -// } -// -// writer.setAromatics(aromatics); -// } + } } src/com/metamolecular/mx/fingerprint/PathFingerprinter.java @@ -30,7 +30,6 @@ import com.metamolecular.mx.io.Molecules; import com.metamolecular.mx.model.Atom; import com.metamolecular.mx.model.DefaultMolecule; import com.metamolecular.mx.model.Molecule; -import com.metamolecular.mx.model.MoleculeKit; import com.metamolecular.mx.ring.RingFilter; import java.util.BitSet; import junit.framework.TestCase; @@ -285,63 +284,12 @@ public class PathFingerprinterTest extends TestCase assertTrue(match(propane, acetone)); } -// public void testItDoesntMatchCyclooctaneToOctane() -// { -// BitSet cyclooctane = fingerprinter.getFingerprint(createCyclooctane()); -// BitSet octane = fingerprinter.getFingerprint(createOctane()); -// -// assertFalse(match(cyclooctane, octane)); -// } - -// public void testItWorks() -// { -// fingerprinter.setMaximumPathDepth(8); -// BitSet query = fingerprinter.getFingerprint(query()); -// -// Set<String> queryPaths = new HashSet(fingerprinter.paths()); -// -// System.out.println("query"); -// System.out.println(query); -// System.out.println("target"); -// BitSet target = fingerprinter.getFingerprint(target()); -// System.out.println(target); -// -// Set<String> targetPaths = new HashSet(fingerprinter.paths()); -// -// for (String path : queryPaths) -// { -// if (!targetPaths.contains(path)) -// { -// System.out.println("missing; " + path); -// } -// } -// -// for (int i = 0; i < query.size(); i++) -// { -// if (query.get(i) == true && !target.get(i) == true) -// { -// System.out.println("missing: " + i); -// } -// } -// } - - private Molecule target() + public void testItDoesntMatchCyclooctaneToOctane() { - String m = "[NO NAME]\n CHEMWRIT 2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n 10 11 0 0 0 0 0 0 0 0 0 V2000\n 1.0607 2.5607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0607 -1.0607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.5095 -0.6724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9266 -0.4635 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n -3.8083 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9266 1.9635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5000 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2 1 2 0 0 0 0\n 3 2 1 0 0 0 0\n 4 3 1 0 0 0 0\n 5 4 2 0 0 0 0\n 6 3 1 0 0 0 0\n 7 6 1 0 0 0 0\n 8 7 1 0 0 0 0\n 9 8 1 0 0 0 0\n 10 9 1 0 0 0 0\n 10 2 1 0 0 0 0\n 10 6 1 0 0 0 0\nM END"; -// String m = "[NO NAME]\n CHEMWRIT 2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n 12 13 0 0 0 0 0 0 0 0 0 V2000\n 1.0607 2.5607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0607 -1.0607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.5095 -0.6724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9266 -0.4635 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n -3.8083 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -4.9230 1.7537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -4.9230 -0.2537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9266 1.9635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5000 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2 1 2 0 0 0 0\n 3 2 1 0 0 0 0\n 4 3 1 0 0 0 0\n 5 4 2 0 0 0 0\n 6 3 1 0 0 0 0\n 7 6 1 0 0 0 0\n 8 7 1 0 0 0 0\n 9 8 1 0 0 0 0\n 10 8 1 0 0 0 0\n 11 8 1 0 0 0 0\n 12 11 1 0 0 0 0\n 12 2 1 0 0 0 0\n 12 6 1 0 0 0 0\nM END"; -// String m = "[NO NAME]\n CHEMWRIT 2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n 19 21 0 0 0 0 0 0 0 0 0 V2000\n 1.0607 2.5607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0607 -1.0607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.5095 -0.6724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.5702 -1.7331 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 4.9860 -1.2377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.2561 -2.0357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.4241 -3.5263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.3634 -4.5869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8728 -4.4190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.0748 -3.1489 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9266 -0.4635 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n -3.8083 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -4.9230 1.7537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -4.9230 -0.2537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9266 1.9635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5000 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2 1 2 0 0 0 0\n 3 2 1 0 0 0 0\n 4 3 1 0 0 0 0\n 5 4 2 0 0 0 0\n 6 5 1 0 0 0 0\n 7 6 1 0 0 0 0\n 8 7 1 0 0 0 0\n 9 8 1 0 0 0 0\n 10 9 1 0 0 0 0\n 11 10 1 0 0 0 0\n 12 11 1 0 0 0 0\n 12 6 1 0 0 0 0\n 13 3 1 0 0 0 0\n 14 13 1 0 0 0 0\n 15 14 1 0 0 0 0\n 16 15 1 0 0 0 0\n 17 15 1 0 0 0 0\n 18 15 1 0 0 0 0\n 19 18 1 0 0 0 0\n 19 2 1 0 0 0 0\n 19 13 1 0 0 0 0\nM END"; -// String m = "[NO NAME]\n CHEMWRIT 2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n 30 32 0 0 0 0 0 0 0 0 0 V2000\n 1.0607 2.5607 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0607 -1.0607 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.5095 -0.6724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.5702 -1.7331 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 4.9860 -1.2377 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.2561 -2.0357 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 6.4241 -3.5263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 5.3634 -4.5869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8728 -4.4190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.0748 -3.1489 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9266 -0.4635 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n -3.8083 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -4.9230 1.7537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -4.9230 -0.2537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.9266 1.9635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.3901 3.3901 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.3864 4.5048 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -4.8573 3.7020 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -5.3209 5.1286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -6.7881 5.4404 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -7.2516 6.8670 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -6.2479 7.9817 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -8.7188 7.1789 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -9.1824 8.6055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -10.2042 6.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -8.7712 5.6798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5000 1.5000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2 1 2 0 0 0 0\n 3 2 1 0 0 0 0\n 4 3 1 0 0 0 0\n 5 4 2 0 0 0 0\n 6 5 1 0 0 0 0\n 7 6 1 0 0 0 0\n 8 7 1 0 0 0 0\n 9 8 1 0 0 0 0\n 10 9 1 0 0 0 0\n 11 10 1 0 0 0 0\n 12 11 1 0 0 0 0\n 12 6 1 0 0 0 0\n 13 3 1 0 0 0 0\n 14 13 1 0 0 0 0\n 15 14 1 0 0 0 0\n 16 15 1 0 0 0 0\n 17 15 1 0 0 0 0\n 18 15 1 0 0 0 0\n 19 18 1 0 0 0 0\n 20 19 2 0 0 0 0\n 21 19 1 0 0 0 0\n 22 21 1 0 0 0 0\n 23 22 1 0 0 0 0\n 24 23 1 0 0 0 0\n 25 24 2 0 0 0 0\n 26 24 1 0 0 0 0\n 27 26 1 0 0 0 0\n 28 26 1 0 0 0 0\n 29 26 1 0 0 0 0\n 30 18 1 0 0 0 0\n 30 2 1 0 0 0 0\n 30 13 1 0 0 0 0\nM END"; + BitSet cyclooctane = fingerprinter.getFingerprint(createCyclooctane()); + BitSet octane = fingerprinter.getFingerprint(createOctane()); - return MoleculeKit.readMolfile(m); - } - - private Molecule query() - { - String m = "[NO NAME]\n CHEMWRIT 2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n 9 10 0 0 0 0 0 0 0 0 0 V2000\n 0.9900 4.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9900 3.5544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3900 3.5544 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3900 4.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 5.9443 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 3.3799 5.9443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5573 2.2229 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6900 1.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.8226 2.2229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\n 4 1 1 0 0 0 0\n 1 5 1 0 0 0 0\n 4 6 2 0 0 0 0\n 2 7 1 0 0 0 0\n 7 8 1 0 0 0 0\n 8 9 1 0 0 0 0\n 9 3 1 0 0 0 0\nM END"; -// String m = "[NO NAME]\n CHEMWRIT 2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n 11 12 0 0 0 0 0 0 0 0 0 V2000\n 0.9900 4.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9900 3.5544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3900 3.5544 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3900 4.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 5.9443 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 3.3799 5.9443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5573 2.2229 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6900 1.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.8226 2.2229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6900 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.9374 0.7644 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\n 4 1 1 0 0 0 0\n 1 5 1 0 0 0 0\n 4 6 2 0 0 0 0\n 2 7 1 0 0 0 0\n 7 8 1 0 0 0 0\n 8 9 1 0 0 0 0\n 9 3 1 0 0 0 0\n 8 10 1 0 0 0 0\n 8 11 1 0 0 0 0\nM END"; -// String m = "[NO NAME]\n CHEMWRIT 2D\nCreated with ChemWriter - http://metamolecular.com/chemwriter\n 11 12 0 0 0 0 0 0 0 0 0 V2000\n 0.9900 4.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.9900 3.5544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3900 3.5544 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3900 4.9544 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 5.9443 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 3.3799 5.9443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.5573 2.2229 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6900 1.4000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.8226 2.2229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.6900 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.9374 0.7644 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\n 4 1 1 0 0 0 0\n 1 5 1 0 0 0 0\n 4 6 2 0 0 0 0\n 2 7 1 0 0 0 0\n 7 8 1 0 0 0 0\n 8 9 1 0 0 0 0\n 9 3 1 0 0 0 0\n 8 10 1 0 0 0 0\n 8 11 1 0 0 0 0\nM END"; - - return MoleculeKit.readMolfile(m); + assertFalse(match(cyclooctane, octane)); } private boolean match(BitSet bitset, BitSet other) src/com/metamolecular/mx/test/PathFingerprinterTest.java @@ -124,6 +124,7 @@ public class PathWriterTest extends TestCase }); Atom atom1 = mockAtom("."); + when(bond.getMate(atom)).thenReturn(atom1); when(atom1.getBonds()).thenReturn(new Bond[] { bond @@ -140,7 +141,6 @@ public class PathWriterTest extends TestCase sequence.verify(paths).add(".%"); sequence.verify(paths).add(".%.%"); } - public void testItWritesSaturatedAtomForFirstAtomOfDoubleBond() { doNew(); @@ -153,6 +153,7 @@ public class PathWriterTest extends TestCase when(bond1.getType()).thenReturn(1); when(bond2.getType()).thenReturn(2); + when(bond2.getMate(atom2)).thenReturn(atom3); when(atom1.getBonds()).thenReturn(new Bond[] { bond1 @@ -161,6 +162,10 @@ public class PathWriterTest extends TestCase { bond1, bond2 }); + when(atom3.getBonds()).thenReturn(new Bond[] + { + bond2 + }); writer.walkStart(atom1); writer.atomFound(atom1); @@ -176,9 +181,11 @@ public class PathWriterTest extends TestCase sequence.verify(paths, times(1)).add("12"); sequence.verify(paths, times(1)).add("12%"); sequence.verify(paths, times(1)).add("12%3%"); + + verify(paths, times(4)).add(any(String.class)); } - public void testItClearsBondPathWhenBranchStarted() + public void testItWritesDoubleBondForRingClosure() { doNew(); @@ -187,32 +194,86 @@ public class PathWriterTest extends TestCase Atom atom3 = mockAtom("3"); Bond bond1 = mock(Bond.class); Bond bond2 = mock(Bond.class); + Bond bond3 = mock(Bond.class); - when(bond1.getType()).thenReturn(2); + when(bond1.getType()).thenReturn(1); + when(bond2.getType()).thenReturn(1); + when(bond3.getType()).thenReturn(2); + when(bond3.getMate(atom3)).thenReturn(atom1); when(atom1.getBonds()).thenReturn(new Bond[] { - bond1 + bond1, bond3 }); when(atom2.getBonds()).thenReturn(new Bond[] { bond1, bond2 }); + when(atom3.getBonds()).thenReturn(new Bond[] + { + bond2, bond3 + }); writer.walkStart(atom1); writer.atomFound(atom1); writer.bondFound(bond1); writer.atomFound(atom2); - writer.branchStart(atom1); writer.bondFound(bond2); writer.atomFound(atom3); - writer.branchEnd(atom1); + writer.bondFound(bond3); + writer.ringClosed(bond3); writer.walkEnd(atom1); InOrder sequence = inOrder(paths); sequence.verify(paths, times(1)).add("1%"); - sequence.verify(paths, times(1)).add("1%2%"); - sequence.verify(paths, times(1)).add("13"); + sequence.verify(paths, times(1)).add("1%2"); + sequence.verify(paths, times(1)).add("1%23%"); + sequence.verify(paths, times(1)).add("1%23%-3"); + + verify(paths, times(4)).add(any(String.class)); + } + public void testItClearsBondPathWhenBranchStarted() + { + doNew(); + + Atom atom1 = mockAtom("1"); + Atom atom2 = mockAtom("2"); + Atom atom3 = mockAtom("3"); + Bond bond1 = mock(Bond.class); + Bond bond2 = mock(Bond.class); + + when(bond1.getType()).thenReturn(1); + when(atom1.getBonds()).thenReturn(new Bond[] + { + bond1 + }); + when(atom2.getBonds()).thenReturn(new Bond[] + { + bond1, bond2 + }); + when(atom3.getBonds()).thenReturn(new Bond[] + { + bond2 + }); + + writer.walkStart(atom2); + writer.atomFound(atom2); + writer.bondFound(bond1); + writer.atomFound(atom1); + writer.branchStart(atom2); + writer.bondFound(bond2); + writer.atomFound(atom3); + writer.branchEnd(atom2); + writer.walkEnd(atom2); + + InOrder sequence = inOrder(paths); + + sequence.verify(paths, times(1)).add("2"); + sequence.verify(paths, times(1)).add("21"); + sequence.verify(paths, times(1)).add("2"); + sequence.verify(paths, times(1)).add("23"); + + verify(paths, times(4)).add(any(String.class)); } public void testItBacktracksWhenBranchStarted() @@ -371,7 +432,7 @@ public class PathWriterTest extends TestCase } } - public void testItRaisesWhenClosingToNonexistantAtom() + public void testItThrowsWhenClosingToNonexistantAtom() { doNew(); @@ -422,7 +483,6 @@ public class PathWriterTest extends TestCase assertEquals("Atom closes rings with size less than three " + shorty, e.getMessage()); } } - private void doNew() { writer = new PathWriter(paths); src/com/metamolecular/mx/test/PathWriterTest.java @@ -74,19 +74,12 @@ public class PathWriter implements Reporter public void atomFound(Atom atom) { -// System.out.println("atomFound: " + atom.getIndex()); if (atomPath.size() > 0 && (atomPath.size() != bondPath.size())) { throw new RuntimeException("Attempt to add Atom without first adding Bond"); } - atomPath.add(atom); -// for (Atom inpath : atomPath) -// { -// System.out.print(inpath.getIndex() + "-"); -// } -// -// System.out.println(); + atomPath.add(atom); pathDirty = true; } @@ -111,7 +104,7 @@ public class PathWriter implements Reporter throw new RuntimeException("Attempt to branch from nonexistant atom " + atom); } - chop(index); + chopPaths(index); } public void ringClosed(Bond bond) @@ -136,15 +129,13 @@ public class PathWriter implements Reporter { throw new RuntimeException("Atom closes rings with size less than three " + inPath); } - -// System.out.println("ringClosed: " + ringSize); - + pathDirty = true; writePaths(ringSize); } - private void chop(int index) + private void chopPaths(int index) { int atomChopCount = atomPath.size() - index - 1; @@ -172,54 +163,75 @@ public class PathWriter implements Reporter for (Atom atom : atomPath) { - write(atom, buffer); - - if (aromatics.contains(atom)) - { - buffer.append("%"); - } - else - { - for (Bond bond : atom.getBonds()) - { - if (bond.getType() == 2 && bondPath.contains(bond)) - { - buffer.append("%"); - - break; - } - - if (bond.getType() == 3 && bondPath.contains(bond)) - { - buffer.append("#"); + writeAtom(atom, buffer); - break; - } - } - } - -// System.out.println(buffer); output.add(buffer.toString()); } if (ringSize != 0) { -// System.out.println(buffer); output.add(buffer.toString() + "-" + ringSize); } - - else - { -// System.out.println("ring size 0: " +buffer); - } pathDirty = false; } - private void write(Atom atom, StringBuffer buffer) + private void writeAtom(Atom atom, StringBuffer buffer) + { + buffer.append(atom.getSymbol()); + writeAtomModifier(atom, buffer); + } + + private void writeAtomModifier(Atom atom, StringBuffer buffer) { - String type = atom.getSymbol(); + if (aromatics.contains(atom)) + { + buffer.append("%"); + } + else + { + for (Bond bond : atom.getBonds()) + { + if (bond.getType() == 1) + { + continue; + } + + int bondIndex = bondPath.indexOf(bond); + + if (bondIndex == -1) + { + continue; + } + + if (bond.getType() == 3) + { + buffer.append("#"); + break; + } - buffer.append(type); + if (bond.getType() == 2) + { + int atomIndex = atomPath.indexOf(atom); + + if (bondIndex == atomIndex) + { + if (!bond.getMate(atom).equals(atomPath.get(0))) + { + output.add(buffer.toString()); + } + + buffer.append("%"); + break; + } + + if (bondIndex == atomIndex - 1 || bondIndex == bondPath.size() - 1) + { + buffer.append("%"); + break; + } + } + } + } } } src/com/metamolecular/mx/walk/PathWriter.java f371b5f803406c593409aa1df7444d917c76c343 Rich Apodaca rapodaca@metamolecular.com http://github.com/metamolecular/mx/commit/2aa0e27ae9b1012eb3b6fca55d36dc33794c654c 2aa0e27ae9b1012eb3b6fca55d36dc33794c654c 2009-07-20T13:28:24-07:00 2009-07-20T13:28:24-07:00 pathwriter uses C and C% for leading alkene carbon 729c851198dc513eabbb91f6fd805eb6f1b5cd28 Rich Apodaca rapodaca@metamolecular.com