New classes for Rasmol color scheme

egonw · Dec 22, 2009 · 66ca51f · 66ca51f
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diff --git a/src/main/org/openscience/cdk/renderer/color/RasmolColors.java b/src/main/org/openscience/cdk/renderer/color/RasmolColors.java
@@ -0,0 +1,107 @@
+/* 
+ * Copyright (C) 2009  Mark Rijnbeek <mark_rynbeek@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.
+ *
+ * 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.renderer.color;
+
+/**
+ * Atom coloring following RasMol/Chime Color scheme     
+ * http://www.umass.edu/microbio/rasmol/rascolor.htm 
+ *
+ * @cdk.module render
+ * @cdk.githash
+ * 
+*/
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.openscience.cdk.interfaces.IAtom;
+
+public class RasmolColors implements IAtomColorer, java.io.Serializable {
+
+    private static final long serialVersionUID = 2588969984094169759L;
+
+    private final static Color DEFAULT        = new Color(255,20,147);
+
+    private static Map<String,Color> colorMap;
+
+    /*
+     * Color map with RasMol/Chime Color RGB Values.
+     * Excepted H and C (too light).
+     */
+    static {
+       colorMap = new HashMap<String,Color>(); 
+
+       colorMap.put("C" , new Color(144,144,144 ));
+       colorMap.put("H" , new Color(144,144,144 ));
+       colorMap.put("O" , new Color(240,0,0     ));
+       colorMap.put("N" , new Color(143,143,255 ));
+       colorMap.put("S" , new Color(255,200,50  ));
+       colorMap.put("Cl", new Color(0,255,0     ));
+       colorMap.put("B" , new Color(0,255,0     ));
+       colorMap.put("P" , new Color(255,165,0   ));
+       colorMap.put("Fe", new Color(255,165,0   ));
+       colorMap.put("Ba", new Color(255,165,0   ));
+       colorMap.put("Na", new Color(0,0,255     ));
+       colorMap.put("Mg", new Color(34,139,34   ));
+       colorMap.put("Zn", new Color(165,42,42   ));
+       colorMap.put("Cu", new Color(165,42,42   ));
+       colorMap.put("Ni", new Color(165,42,42   ));
+       colorMap.put("Br", new Color(165,42,42   ));
+       colorMap.put("Ca", new Color(128,128,144 ));
+       colorMap.put("Mn", new Color(128,128,144 ));
+       colorMap.put("Al", new Color(128,128,144 ));
+       colorMap.put("Ti", new Color(128,128,144 ));
+       colorMap.put("Cr", new Color(128,128,144 ));
+       colorMap.put("Ag", new Color(128,128,144 ));
+       colorMap.put("F" , new Color(218,165,32  ));
+       colorMap.put("Si", new Color(218,165,32  ));
+       colorMap.put("Au", new Color(218,165,32  ));
+       colorMap.put("I" , new Color(160,32,240  ));
+       colorMap.put("Li", new Color(178,34,34   ));
+       colorMap.put("He", new Color(255,192,203 ));
+
+    }
+
+    /**
+     * Returns the Rasmol color for the given atom's element.
+     * @param a IAtom to get a color for
+     */
+    public Color getAtomColor(IAtom a) {
+        return getAtomColor(a, DEFAULT);
+    }
+
+    /**
+     * Returns the Rasmol color for the given atom's element, or
+     * defaults to the given color if no color is defined.
+     *
+     * @param atom         IAtom to get a color for
+     * @param defaultColor Color returned if this scheme does not define
+     *                     a color for the passed IAtom
+     */
+    public Color getAtomColor(IAtom atom, Color defaultColor) {
+        Color color = defaultColor;
+        String symbol = atom.getSymbol();
+        if(colorMap.containsKey(symbol)) {
+            color = colorMap.get(symbol);
+        }
+        return color;
+    }
+}
diff --git a/src/test/org/openscience/cdk/renderer/color/RasmolColorsTest.java b/src/test/org/openscience/cdk/renderer/color/RasmolColorsTest.java
@@ -0,0 +1,49 @@
+/* 
+ * Copyright (C) 2009  Mark Rijnbeek <mark_rynbeek@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.
+ *
+ * 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.renderer.color;
+
+import java.awt.Color;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import org.openscience.cdk.Atom;
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.interfaces.IAtom;
+
+/**
+ * @cdk.module test-render
+ */
+public class RasmolColorsTest extends CDKTestCase {
+
+	@Test public void testGetAtomColor() {
+		RasmolColors colors = new RasmolColors();
+
+		Assert.assertNotNull(colors);
+		IAtom sulfur = new Atom("S"); 
+		Assert.assertEquals(new Color(255,200,50), colors.getAtomColor(sulfur));
+
+		IAtom helium = new Atom("He"); 
+		Assert.assertEquals(new Color(255,192,203 ), colors.getAtomColor(helium));
+	}
+
+}
+