@@ -36,16 +36,16 @@ public class DefaultAtomMatcher implements AtomMatcher private String symbol; private int maximumNeighbors; private int minimumNeighbors; - private int minimumValence; - private int maximumValence; + private int minimumUnsaturation; + private int maximumUnsaturation; public DefaultAtomMatcher() { symbol = null; maximumNeighbors = -1; minimumNeighbors = -1; - minimumValence = -1; - maximumValence = -1; + minimumUnsaturation = -1; + maximumUnsaturation = -1; } public DefaultAtomMatcher(Atom atom) @@ -54,7 +54,12 @@ public class DefaultAtomMatcher implements AtomMatcher this.symbol = atom.getSymbol(); this.minimumNeighbors = atom.countNeighbors(); - this.minimumValence = atom.countNeighbors() + atom.countVirtualHydrogens(); + this.minimumUnsaturation = getUnsaturation(atom); + + if (minimumUnsaturation == 0) + { + this.maximumUnsaturation = 0; + } } public boolean matches(Atom atom) @@ -74,12 +79,12 @@ public class DefaultAtomMatcher implements AtomMatcher return false; } - if (!matchMinimumValence(atom)) + if (!matchMinimumUnsaturation(atom)) { return false; } - if (!matchMaximumValence(atom)) + if (!matchMaximumUnsaturation(atom)) { return false; } @@ -87,22 +92,22 @@ public class DefaultAtomMatcher implements AtomMatcher return true; } - public void setMinimumValence(int minimum) + public void setMinimumUnsaturation(int minimum) { - if (minimum > maximumValence && maximumValence != -1) + if (minimum > maximumUnsaturation && maximumUnsaturation != -1) { throw new IllegalStateException("Minimum " + minimum + " exceeds maximum"); } - this.minimumValence = minimum; + this.minimumUnsaturation = minimum; } - public void setMaximumValence(int maximum) + public void setMaximumUnsaturation(int maximum) { - if (maximum < minimumValence) + if (maximum < minimumUnsaturation) { throw new IllegalStateException("Maximum " + maximum + " less than minimum"); } - this.maximumValence = maximum; + this.maximumUnsaturation = maximum; } public void setMaximumNeighbors(int maximum) @@ -129,6 +134,11 @@ public class DefaultAtomMatcher implements AtomMatcher { this.symbol = symbol; } + + private int getUnsaturation(Atom atom) + { + return atom.getValence() - atom.countNeighbors(); + } private boolean matchSymbol(Atom atom) { @@ -160,23 +170,23 @@ public class DefaultAtomMatcher implements AtomMatcher return atom.countNeighbors() >= minimumNeighbors; } - private boolean matchMinimumValence(Atom atom) + private boolean matchMinimumUnsaturation(Atom atom) { - if (minimumValence == -1) + if (minimumUnsaturation == -1) { return true; } - return atom.countNeighbors() + atom.countVirtualHydrogens() >= minimumValence; + return getUnsaturation(atom) >= this.minimumUnsaturation; } - private boolean matchMaximumValence(Atom atom) + private boolean matchMaximumUnsaturation(Atom atom) { - if (maximumValence == -1) + if (maximumUnsaturation == -1) { return true; } - return atom.countNeighbors() + atom.countVirtualHydrogens() <= maximumValence; + return getUnsaturation(atom) <= this.maximumUnsaturation; } } src/com/metamolecular/mx/query/DefaultAtomMatcher.java @@ -26,6 +26,7 @@ package com.metamolecular.mx.test; import com.metamolecular.mx.io.Molecules; +import com.metamolecular.mx.model.DefaultMolecule; import com.metamolecular.mx.model.Molecule; import com.metamolecular.mx.query.DefaultAtomMatcher; import junit.framework.TestCase; @@ -91,40 +92,40 @@ public class DefaultAtomMatcherTest extends TestCase assertFalse(matcher.matches(phenol.getAtom(6))); } - public void testItShouldMatchBasedOnMinimumValence() + public void testItShouldMatchBasedOnMinimumUnsaturation() { - matcher.setMinimumValence(3); + matcher.setMinimumUnsaturation(1); assertTrue(matcher.matches(phenol.getAtom(0))); } - public void testItShouldNotMatchBasedOnMinimumValence() + public void testItShouldNotMatchBasedOnMinimumUnsaturation() { - matcher.setMinimumValence(4); + matcher.setMinimumUnsaturation(4); assertFalse(matcher.matches(phenol.getAtom(0))); } - public void testItShouldMatchBasedOnMaximumValence() + public void testItShouldMatchBasedOnMaximumUnsaturation() { - matcher.setMaximumValence(3); + matcher.setMaximumUnsaturation(3); assertTrue(matcher.matches(phenol.getAtom(0))); } - public void testItShouldNotMatchBasedOnMaximumValence() + public void testItShouldNotMatchBasedOnMaximumUnsaturation() { - matcher.setMaximumValence(2); + matcher.setMaximumUnsaturation(0); assertFalse(matcher.matches(phenol.getAtom(0))); } - public void testItThrowsWhenMaximumValenceLessThanMinimumaValence() + public void testItThrowsWhenMaximumUnsaturationLessThanMinimumaUnsaturation() { - matcher.setMinimumValence(3); + matcher.setMinimumUnsaturation(3); try { - matcher.setMaximumValence(2); + matcher.setMaximumUnsaturation(2); fail(); } @@ -134,13 +135,13 @@ public class DefaultAtomMatcherTest extends TestCase } } - public void testItThrowsWhenMinimumValenceGreaterThanMaximumValence() + public void testItThrowsWhenMinimumUnsaturationGreaterThanMaximumUnsaturation() { - matcher.setMaximumValence(3); + matcher.setMaximumUnsaturation(3); try { - matcher.setMinimumValence(4); + matcher.setMinimumUnsaturation(4); fail(); } @@ -200,4 +201,99 @@ public class DefaultAtomMatcherTest extends TestCase assertFalse(matcher.matches(phenol.getAtom(2))); } + + public void testItDoesntMatchTolueneQuatToNeopentaneQuat() + { + Molecule toluene = Molecules.createToluene(); + Molecule neopentane = Molecules.createNeopentane(); + matcher = new DefaultAtomMatcher(toluene.getAtom(0)); + + assertFalse(matcher.matches(neopentane.getAtom(0))); + } + + public void testItMatchesEthyleneCarbonToAlleneQuatCarbon() + { + Molecule ethylene = createEthylene(); + Molecule allene = createAllene(); + matcher = new DefaultAtomMatcher(ethylene.getAtom(0)); + + assertTrue(matcher.matches(allene.getAtom(1))); + } + + public void testItDoesntMatchAlleneQuatCarbonToEthyleneCarbon() + { + Molecule ethylene = createEthylene(); + Molecule allene = createAllene(); + matcher = new DefaultAtomMatcher(allene.getAtom(1)); + + assertFalse(matcher.matches(ethylene.getAtom(0))); + } + + public void testItMatchesEthyleneCarbonToAcetyleneCarbon() + { + Molecule ethylene = createEthylene(); + Molecule acetylene = createAcetylene(); + matcher = new DefaultAtomMatcher(ethylene.getAtom(0)); + + assertTrue(matcher.matches(acetylene.getAtom(0))); + } + + public void testItDoesntMatchAcetyleneCarbonToEthyleneCarbon() + { + Molecule ethylene = createEthylene(); + Molecule acetylene = createAcetylene(); + matcher = new DefaultAtomMatcher(acetylene.getAtom(0)); + + assertFalse(matcher.matches(ethylene.getAtom(0))); + } + + public void testItDoesntMatchAcetoneOxygenToIsopropanolOxygen() + { + Molecule acetone = Molecules.createAcetone(); + Molecule ipa = createIsopropanol(); + matcher = new DefaultAtomMatcher(acetone.getAtom(3)); + + assertFalse(matcher.matches(ipa.getAtom(3))); + } + + public void testItDoesntMatchIsopropanolOxygenToAcetoneOxygen() + { + Molecule acetone = Molecules.createAcetone(); + Molecule ipa = createIsopropanol(); + matcher = new DefaultAtomMatcher(ipa.getAtom(3)); + + assertFalse(matcher.matches(acetone.getAtom(3))); + } + + private Molecule createEthylene() + { + Molecule result = new DefaultMolecule(); + result.connect(result.addAtom("C"), result.addAtom("C"), 2); + + return result; + } + + private Molecule createAcetylene() + { + Molecule result = createEthylene(); + result.getBond(0).setType(3); + + return result; + } + + private Molecule createAllene() + { + Molecule result = createEthylene(); + result.connect(result.getAtom(1), result.addAtom("C"), 2); + + return result; + } + + private Molecule createIsopropanol() + { + Molecule result = Molecules.createAcetone(); + result.getBond(2).setType(1); + + return result; + } } src/com/metamolecular/mx/test/DefaultAtomMatcherTest.java 00b9b4e8ee0627a8a4a965cebe510ecb50a5d6cd Richard Apodaca rapodaca@metamolecular.com http://github.com/rapodaca/mx/commit/0ab38bada2921c024a2abd159f8bf7be74796007 0ab38bada2921c024a2abd159f8bf7be74796007 2009-06-16T12:18:12-07:00 2009-06-16T12:13:01-07:00 changed matching concept from valence to unsaturation. Closes #6. e087addf71ec61f821eb11764fbca770f05bac73 Richard Apodaca rapodaca@metamolecular.com