Initial commit of signature package

.classpath

@@ -1,6 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <classpath>
-	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
 	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
 	<classpathentry kind="src" path="src/main"/>
 	<classpathentry kind="src" path="src/test"/>
@@ -18,7 +17,8 @@
 	<classpathentry exported="true" kind="lib" path="develjar/com-sun-tools-doclets-Taglet.jar" sourcepath="org.openscience.cdksrc.zip"/>
 	<classpathentry exported="true" kind="lib" path="develjar/junit-4.5.jar"/>
 	<classpathentry kind="lib" path="jar/cmlxom-2.5-b1.jar"/>
-	<classpathentry kind="lib" path="develjar/doccheck.jar"/>
 	<classpathentry kind="lib" path="develjar/ojdcheck.jar"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="lib" path="jar/signatures-1.0-SNAPSHOT.jar"/>
 	<classpathentry kind="output" path="bin"/>
 </classpath>

src/main/org/openscience/cdk/signature/AtomSignature.java

@@ -0,0 +1,120 @@
+/* Copyright (C) 2009-2010 maclean {gilleain.torrance@gmail.com}
+*
+* Contact: cdk-devel@lists.sourceforge.net
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Lesser General Public License
+* as published by the Free Software Foundation; either version 2.1
+* of the License, or (at your option) any later version.
+* All we ask is that proper credit is given for our work, which includes
+* - but is not limited to - adding the above copyright notice to the beginning
+* of your source code files, and to any copyright notice that you may distribute
+* with programs based on this work.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU Lesser General Public License for more details.
+*
+* You should have received a copy of the GNU Lesser General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+*/
+package org.openscience.cdk.signature;
+
+import java.util.List;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+
+import signature.AbstractVertexSignature;
+
+/**
+ * The signature for a molecule rooted at a particular atom.
+ * 
+ * @cdk.module signature
+ * @author maclean
+ *
+ */
+@TestClass("org.openscience.cdk.signature.AtomSignatureTest")
+public class AtomSignature extends AbstractVertexSignature {
+
+    /**
+     * The atom container to make signatures from
+     */
+    private IAtomContainer molecule;
+
+    /**
+     * Create an atom signature starting at <code>atomIndex</code>.
+     * 
+     * @param atomIndex the index of the atom that roots this signature
+     * @param molecule the molecule to create the signature from
+     */
+    public AtomSignature(int atomIndex, IAtomContainer molecule) {
+        super();
+        this.molecule = molecule;
+        super.createMaximumHeight(atomIndex, molecule.getAtomCount());
+    }
+
+    /**
+     * Create an atom signature starting at <code>atomIndex</code> and with a
+     * maximum height of <code>h</code>.
+     * 
+     * @param atomIndex the index of the atom that roots this signature
+     * @param height the maximum height of the signature 
+     * @param molecule the molecule to create the signature from
+     */
+    public AtomSignature(int atomIndex, int height, IAtomContainer molecule) {
+        super();
+        this.molecule = molecule;
+        super.create(atomIndex, molecule.getAtomCount(), height);
+    }
+
+    /* (non-Javadoc)
+     * @see signature.AbstractVertexSignature#getConnected(int)
+     */
+    @Override
+    public int[] getConnected(int vertexIndex) {
+        IAtom atom  = this.molecule.getAtom(vertexIndex);
+        List<IAtom> connected = this.molecule.getConnectedAtomsList(atom);
+        int[] connectedIndices = new int[connected.size()];
+        int i = 0;
+        for (IAtom otherAtom : connected) {
+            connectedIndices[i++] = this.molecule.getAtomNumber(otherAtom);
+        }
+        return connectedIndices;
+    }
+
+    /* (non-Javadoc)
+     * @see signature.AbstractVertexSignature#getEdgeLabel(int, int)
+     */
+    @Override
+    public String getEdgeLabel(int vertexIndex, int otherVertexIndex) {
+        IAtom atomA = this.molecule.getAtom(vertexIndex);
+        IAtom atomB = this.molecule.getAtom(otherVertexIndex);
+        IBond bond = this.molecule.getBond(atomA, atomB);
+        if (bond != null) {
+            switch (bond.getOrder()) {
+//                case SINGLE: return "-";
+                case SINGLE: return "";
+                case DOUBLE: return "=";
+                case TRIPLE: return "#";
+                case QUADRUPLE: return "$";
+                default: return "";
+            }
+        } else {
+            return "";
+        }
+    }
+
+    /* (non-Javadoc)
+     * @see signature.AbstractVertexSignature#getVertexSymbol(int)
+     */
+    @Override
+    public String getVertexSymbol(int vertexIndex) {
+        return this.molecule.getAtom(vertexIndex).getSymbol();
+    }
+
+}

src/main/org/openscience/cdk/signature/MoleculeFromSignatureBuilder.java

@@ -0,0 +1,110 @@
+/* Copyright (C) 2009-2010 maclean {gilleain.torrance@gmail.com}
+*
+* Contact: cdk-devel@lists.sourceforge.net
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Lesser General Public License
+* as published by the Free Software Foundation; either version 2.1
+* of the License, or (at your option) any later version.
+* All we ask is that proper credit is given for our work, which includes
+* - but is not limited to - adding the above copyright notice to the beginning
+* of your source code files, and to any copyright notice that you may distribute
+* with programs based on this work.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU Lesser General Public License for more details.
+*
+* You should have received a copy of the GNU Lesser General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+*/
+package org.openscience.cdk.signature;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+
+import signature.AbstractGraphBuilder;
+
+/**
+ * Builds a molecule from a signature.
+ * 
+ * @cdk.module signature
+ * @author maclean
+ * 
+ */
+@TestClass("org.openscience.cdk.signature.MoleculeFromSignatureBuilderTest")
+public class MoleculeFromSignatureBuilder extends AbstractGraphBuilder {
+
+    /**
+     * The chem object builder
+     */
+    private IChemObjectBuilder builder;
+
+    /**
+     * The container that is being constructed
+     */
+    private IAtomContainer container;
+
+    /**
+     * This default constructor uses a {@link NoNotificationChemObjectBuilder}
+     */
+    public MoleculeFromSignatureBuilder() {
+        this.builder = NoNotificationChemObjectBuilder.getInstance();
+    }
+
+    /**
+     * Uses the chem object builder for making molecules.
+     * 
+     * @param builder a builder for CDK molecules.
+     */
+    public MoleculeFromSignatureBuilder(IChemObjectBuilder builder) {
+        this.builder = builder;
+    }
+
+    /* (non-Javadoc)
+     * @see signature.AbstractGraphBuilder#makeEdge(int, int, java.lang.String, java.lang.String, java.lang.String)
+     */
+    @Override
+    public void makeEdge(int vertexIndex1, int vertexIndex2,
+            String vertexSymbol1, String vertexSymbol2, String edgeLabel) {
+        if (edgeLabel.equals("")) {
+            container.addBond(vertexIndex1, vertexIndex2, IBond.Order.SINGLE);
+        } else if (edgeLabel.equals("=")) {
+            container.addBond(vertexIndex1, vertexIndex2, IBond.Order.DOUBLE);
+        } else if (edgeLabel.equals("#")) {
+            container.addBond(vertexIndex1, vertexIndex2, IBond.Order.TRIPLE);
+        }
+    }
+
+    /* (non-Javadoc)
+     * @see signature.AbstractGraphBuilder#makeGraph()
+     */
+    @Override
+    public void makeGraph() {
+        this.container = this.builder.newInstance(IAtomContainer.class);
+    }
+
+    /* (non-Javadoc)
+     * @see signature.AbstractGraphBuilder#makeVertex(java.lang.String)
+     */
+    @Override
+    public void makeVertex(String label) {
+        this.container.addAtom(this.builder.newInstance(IAtom.class, label));
+    }
+
+    /**
+     * Gets the atom container.
+     * 
+     * @return the constructed atom container
+     */
+    public IAtomContainer getAtomContainer() {
+        return this.container;
+    }
+
+}

src/main/org/openscience/cdk/signature/MoleculeSignature.java

@@ -0,0 +1,145 @@
+/* Copyright (C) 2009-2010 maclean {gilleain.torrance@gmail.com}
+*
+* Contact: cdk-devel@lists.sourceforge.net
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Lesser General Public License
+* as published by the Free Software Foundation; either version 2.1
+* of the License, or (at your option) any later version.
+* All we ask is that proper credit is given for our work, which includes
+* - but is not limited to - adding the above copyright notice to the beginning
+* of your source code files, and to any copyright notice that you may distribute
+* with programs based on this work.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+* GNU Lesser General Public License for more details.
+*
+* You should have received a copy of the GNU Lesser General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+*/
+package org.openscience.cdk.signature;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.openscience.cdk.annotations.TestClass;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IMolecule;
+
+import signature.AbstractGraphSignature;
+import signature.AbstractVertexSignature;
+import signature.ColoredTree;
+import signature.SymmetryClass;
+
+/**
+ * A signature for an entire molecule.
+ * 
+ * @cdk.module signature
+ * @author maclean
+ *
+ */
+@TestClass("org.openscience.cdk.signature.MoleculeSignatureTest")
+public class MoleculeSignature extends AbstractGraphSignature {
+
+    private IAtomContainer molecule;
+
+    /**
+     * Creates a signature that represents this molecule.
+     * 
+     * @param molecule the molecule to convert to a signature
+     */
+    public MoleculeSignature(IAtomContainer molecule) {
+        super();
+        this.molecule = molecule;
+    }
+
+    /**
+     * Creates a signature with a maximum height of <code>height</code>
+     * for molecule <code>molecule</code>.
+     *  
+     * @param molecule the molecule to convert to a signature
+     * @param height the maximum height of the signature
+     */
+    public MoleculeSignature(IMolecule molecule, int height) {
+        super(height);
+        this.molecule = molecule;
+    }
+
+    @Override
+    public int getVertexCount() {
+        return this.molecule.getAtomCount();
+    }
+
+    @Override
+    public String signatureStringForVertex(int vertexIndex) {
+        AtomSignature atomSignature;
+        int height = super.getHeight();
+        if (height == -1) {
+            atomSignature = new AtomSignature(vertexIndex, this.molecule);
+        } else {
+            atomSignature = 
+                new AtomSignature(vertexIndex, height, this.molecule);
+        }
+        return atomSignature.toCanonicalString();
+    }
+
+    @Override
+    public String signatureStringForVertex(int vertexIndex, int height) {
+        AtomSignature atomSignature = 
+            new AtomSignature(vertexIndex, height, this.molecule);
+        return atomSignature.toCanonicalString();
+    }
+
+    @Override
+    public AbstractVertexSignature signatureForVertex(int vertexIndex) {
+        return new AtomSignature(vertexIndex, this.molecule);
+    }
+
+    /**
+     * Calculates the orbits of the atoms of the molecule. 
+     * 
+     * @return a list of orbits
+     */
+    public List<Orbit> calculateOrbits() {
+        List<Orbit> orbits = new ArrayList<Orbit>();
+        List<SymmetryClass> symmetryClasses = super.getSymmetryClasses();
+        for (SymmetryClass symmetryClass : symmetryClasses) {
+            Orbit orbit = new Orbit(symmetryClass.getSignatureString(), -1);
+            for (int atomIndex : symmetryClass) {
+                orbit.addAtom(atomIndex);
+            }
+            orbits.add(orbit);
+        }
+        return orbits;
+    }
+
+    /**
+     * Builder for molecules (rather, for atom containers) from signature 
+     * strings.
+     * 
+     * @param signatureString the signature string to use
+     * @return an atom container
+     */
+    public static IAtomContainer fromSignatureString(String signatureString) {
+        ColoredTree tree = AtomSignature.parse(signatureString);
+        MoleculeFromSignatureBuilder builder =
+            new MoleculeFromSignatureBuilder();
+        builder.makeFromColoredTree(tree);
+        return builder.getAtomContainer();
+    }
+
+    public String toCanonicalSignatureString(int height) {
+        String canonicalSignature = null;
+        for (int i = 0; i < getVertexCount(); i++) {
+            String signatureForI = signatureStringForVertex(i, height);
+            if (canonicalSignature == null || 
+                    canonicalSignature.compareTo(signatureForI) < 0) {
+                canonicalSignature = signatureForI;
+            }
+        }
+        return canonicalSignature;
+    }
+}