Renamed the ligancy classes to use the term tetrahedral since they im…

…plicitly encode for tetrahedral chirality Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
cdk · May 24, 2010 · d80628e · d80628e
1 parent e36a2a1
commit d80628e
Show file tree

Hide file tree

Showing 2 changed files with 148 additions and 0 deletions.
diff --git a/src/main/org/openscience/cdk/interfaces/ITetrahedralChirality.java b/src/main/org/openscience/cdk/interfaces/ITetrahedralChirality.java
@@ -0,0 +1,65 @@
+/* Copyright (C) 2010  Egon Willighagen <egonw@users.sf.net>
+ *
+ * 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.interfaces;
+
+/**
+ * Stereochemistry specification for quadrivalent atoms. The data model defines the central, chiral {@link IAtom},
+ * and its four ligand {@link IAtom}s, directly bonded to the chiral atom via an {@link IBond}. The ordering of the
+ * four ligands is important, and defines together with the {@link Stereo} to spatial geometry around the chiral atom.
+ * The first ligand points towards to observer, and the three other ligands point away from the observer; the
+ * {@link Stereo} then defines the order of the second, third, and fourth ligand to be clockwise or anti-clockwise.
+ *
+ * @cdk.module interfaces
+ */
+public interface ITetrahedralChirality extends IStereoElement {
+
+    /**
+     * Enumeration that defines the two possible chiralities for this stereochemistry type.
+     */
+    public enum Stereo {
+        CLOCKWISE,
+        ANTI_CLOCKWISE
+    }
+
+    /**
+     * Returns an array of ligand atoms around the chiral atom.
+     *
+     * @return an array of four {@link IAtom}s.
+     */
+    public IAtom[] getLigands();
+
+    /**
+     * Atom that is the chirality center.
+     *
+     * @return the chiral {@link IAtom}.
+     */
+    public IAtom getChiralAtom();
+
+    /**
+     * Defines the stereochemistry around the chiral atom. The value depends on the order of ligand atoms.
+     *
+     * @return the {@link Stereo} for this stereo element.
+     */
+    public Stereo getStereo();
+
+}
diff --git a/src/main/org/openscience/cdk/stereo/TetrahedralChirality.java b/src/main/org/openscience/cdk/stereo/TetrahedralChirality.java
@@ -0,0 +1,83 @@
+/* Copyright (C) 2010  Egon Willighagen <egonw@users.sf.net>
+ *
+ * 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.stereo;
+
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.ITetrahedralChirality;
+
+/**
+ * Stereochemistry specification for quadrivalent atoms. See {@link org.openscience.cdk.interfaces.ITetrahedralChirality} for
+ * further details.
+ *
+ * @cdk.module data
+ *
+ * @see org.openscience.cdk.interfaces.ITetrahedralChirality
+ */
+public class TetrahedralChirality implements ITetrahedralChirality {
+
+    private IAtom chiralAtom;
+    private IAtom[] ligandAtoms;
+    private Stereo stereo;
+
+    public TetrahedralChirality(IAtom chiralAtom, IAtom[] ligandAtoms, Stereo chirality) {
+        this.chiralAtom = chiralAtom;
+        this.ligandAtoms = ligandAtoms;
+        this.stereo = chirality;
+    }
+
+    /**
+     * Returns an array of ligand atoms around the chiral atom.
+     *
+     * @return an array of four {@link IAtom}s.
+     */
+    public IAtom[] getLigands() {
+        IAtom[] arrayCopy = new IAtom[4];
+        System.arraycopy(ligandAtoms, 0, arrayCopy, 0, 4);
+        return arrayCopy;
+    }
+
+    /**
+     * Atom that is the chirality center.
+     *
+     * @return the chiral {@link IAtom}.
+     */
+    public IAtom getChiralAtom() {
+        return chiralAtom;
+    }
+
+    /**
+     * Defines the stereochemistry around the chiral atom. The value depends on the order of ligand atoms.
+     *
+     * @return the {@link Stereo} for this stereo element.
+     */
+    public Stereo getStereo() {
+        return stereo;
+    }
+
+    public IChemObjectBuilder getBuilder() {
+        return DefaultChemObjectBuilder.getInstance();
+    }
+
+}