[Jmol-commits] SF.net SVN: jmol:[17917] trunk/Jmol/src/org/jmol/adapter/readers/pymol

[<ha...@us...>]

Revision: 17917
          http://jmol.svn.sourceforge.net/jmol/?rev=17917&view=rev
Author:   hansonr
Date:     2013-02-06 18:00:35 +0000 (Wed, 06 Feb 2013)
Log Message:
-----------
PyMOL reading - custom colors

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
    trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java

Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java	2013-02-06 17:05:09 UTC (rev 17916)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOL.java	2013-02-06 18:00:35 UTC (rev 17917)
@@ -1,5 +1,8 @@
 package org.jmol.adapter.readers.pymol;
 
+import java.util.Hashtable;
+import java.util.Map;
+
 /**
  * PyMOL settings and constants. 
  * 
@@ -6136,7 +6139,20 @@
   };
 
   static int getRGB(int color) {
-    return (color < colors.length && color >= 0 ? colors[color] : 0);
+    if (color < colors.length)
+      return (colors[color]);
+    if (moreColors != null) {
+      Integer c = moreColors.get(Integer.valueOf(color));
+      if (c != null)
+        return c.intValue();
+    }
+    return 0;
   }
   
+  private final static Map<Integer, Integer> moreColors = new Hashtable<Integer, Integer>();
+  
+  static void addColor(Integer id, int value) {
+    moreColors.put(id, Integer.valueOf(value));
+  }
+  
 }

Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java	2013-02-06 17:05:09 UTC (rev 17916)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java	2013-02-06 18:00:35 UTC (rev 17917)
@@ -44,6 +44,7 @@
 import org.jmol.util.BitSet;
 import org.jmol.util.BitSetUtil;
 import org.jmol.util.Colix;
+import org.jmol.util.ColorUtil;
 import org.jmol.util.Escape;
 import org.jmol.util.Logger;
 import org.jmol.util.Point3f;
@@ -112,15 +113,17 @@
   		"set navigationMode off;" +
       "set zoomLarge false;" +
       "set measurementUnits ANGSTROMS;" +
-      "set ssBondsBackbone FALSE;')";
+      "set ssBondsBackbone FALSE;" +
+      "')";
 
   private void process(Map<String, Object> map) {
 
     // immediate execution prior to file loading
-
     if (!isStateScript)
       viewer.evaluateExpression(preScript);
 
+    addColors(getMapList(map, "colors"));
+
     for (int i = 0; i < 17; i++)
       reps[i] = BitSet.newN(1000);
     settings = getMapList(map, "settings");
@@ -128,14 +131,14 @@
       try {
         width = getInt(getMapList(map, "main"), 0);
         height = getInt(getMapList(map, "main"), 1);
+        if (width > 0 && height > 0) {
+          atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
+              "perferredWidthHeight", new int[] { width, height });
+          viewer.resizeInnerPanel(width, height);
+        }
       } catch (Exception e) {
         // ignore
       }
-    if (width > 0 && height > 0) {
-      atomSetCollection.setAtomSetCollectionAuxiliaryInfo(
-          "perferredWidthHeight", new int[] { width, height });
-      viewer.resizeInnerPanel(width, height);
-    }
     valence = getBooleanSetting(PyMOL.valence);
     cartoonTranslucency = getFloatSetting(PyMOL.cartoon_transparency);
     List<Object> names = getMapList(map, "names");
@@ -150,6 +153,17 @@
     setRendering(getMapList(map, "view"));
   }
 
+  private void addColors(List<Object> colors) {
+    if (colors == null || colors.size() == 0)
+      return;
+    Point3f pt = new Point3f();
+    for (int i = colors.size(); --i >= 0;) {
+      List<Object> c = getList(colors, i);
+      PyMOL.addColor((Integer) c.get(1), ColorUtil.colorPtToInt(getPoint(getList(c, 2), 0,
+          pt)));
+    }
+  }
+
   /**
    * This is what a normal reader would not have.
    * Only executed if NOT in a state script
@@ -450,8 +464,7 @@
     BoxInfo.addPointXYZ(x, y, z, xyzMin, xyzMax, 0);
     //System.out.println(chainID +  " " + fileAtomIndex + " " + serNo + " " + x  + " " + y + " " + z);
     processAtom2(atom, serNo, x, y, z, charge);
-    int color = getInt(a, 21);
-    color = PyMOL.getRGB(color);
+    int color = PyMOL.getRGB(getInt(a, 21));
     colixList.add(Integer.valueOf(Colix.getColixO(Integer.valueOf(color))));    
   }
 

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