[Jmol-commits] SF.net SVN: jmol:[16801] trunk/Jmol/src/org/jmol/adapter

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

Revision: 16801
          http://jmol.svn.sourceforge.net/jmol/?rev=16801&view=rev
Author:   hansonr
Date:     2012-02-15 21:37:55 +0000 (Wed, 15 Feb 2012)
Log Message:
-----------
JCAMPDX reader: vibraionScale
 <ModelData id="1" type="XYZVIB" baseModel="acetophenone" vibrationScale=".1">
 
 scales down actual vibrations to better level.

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
    trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java

Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java	2012-02-15 21:22:55 UTC (rev 16800)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/JcampdxReader.java	2012-02-15 21:37:55 UTC (rev 16801)
@@ -31,6 +31,7 @@
 import java.util.List;
 
 import org.jmol.adapter.readers.molxyz.MolReader;
+import org.jmol.adapter.smarter.Atom;
 import org.jmol.adapter.smarter.AtomSetCollection;
 import org.jmol.adapter.smarter.AtomSetCollectionReader;
 import org.jmol.adapter.smarter.Bond;
@@ -203,6 +204,7 @@
     modelIdList += key;
     String baseModel = getAttribute(line, "baseModel");
     String modelType = getAttribute(line, "type").toLowerCase();
+    float vibScale = Parser.parseFloat(getAttribute(line, "vibrationScale"));
     if (modelType.equals("xyzvib"))
       modelType = "xyz";
     else if (modelType.length() == 0)
@@ -228,6 +230,12 @@
     if (baseModel.length() != 0)
       setBonding(a, baseModel); 
     }
+    if (!Float.isNaN(vibScale)) {
+      Logger.info("jdx applying vibrationScale of " + vibScale + " to " + a.getAtomCount() + " atoms");
+      Atom[] atoms = a.getAtoms();
+      for (int i = a.getAtomCount(); --i >= 0; )
+        atoms[i].scaleVector(vibScale);      
+    }
     Logger.info("jdx model=" + modelID + " type=" + a.getFileTypeName());
     return a;
   }

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java	2012-02-15 21:22:55 UTC (rev 16800)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Atom.java	2012-02-15 21:37:55 UTC (rev 16801)
@@ -288,4 +288,12 @@
     return isValidElementSymbolNoCaseSecondChar(chFirst, chSecond);
   }
 
+  public void scaleVector(float vibScale) {
+    if (Float.isNaN(vectorX))
+      return;
+    vectorX *= vibScale;
+    vectorY *= vibScale;
+    vectorZ *= vibScale;    
+  }
+
 }

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