[Jmol-commits] SF.net SVN: jmol:[12966] trunk/Jmol/src/org/jmol/adapter

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

Revision: 12966
          http://jmol.svn.sourceforge.net/jmol/?rev=12966&view=rev
Author:   hansonr
Date:     2010-04-28 21:11:13 +0000 (Wed, 28 Apr 2010)

Log Message:
-----------
version=12.0.RC9_dev # bug fix: CSF reader upgrade

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/adapter/readers/quantum/CsfReader.java
    trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java

Modified: trunk/Jmol/src/org/jmol/adapter/readers/quantum/CsfReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/quantum/CsfReader.java	2010-04-28 21:00:16 UTC (rev 12965)
+++ trunk/Jmol/src/org/jmol/adapter/readers/quantum/CsfReader.java	2010-04-28 21:11:13 UTC (rev 12966)
@@ -95,8 +95,6 @@
   }
  
   public void finalizeReader() throws Exception {
-    for (int i = 0; i < nAtoms; i++)
-      atomSetCollection.getAtom(i).sequenceNumber = Integer.MIN_VALUE;
     super.finalizeReader();
   }
   /*
@@ -243,6 +241,7 @@
         if (connectors.containsKey(thisBondID)) {
           int[] connect = (int[])connectors.get(thisBondID);
           connect[1] = thisAtomID;
+          System.out.println("*" + thisBondID +  " " + thisAtomID);
           if (htBonds != null) {
             Bond bond = (Bond) htBonds.get(thisBondID);
             setBond(bond, connect);
@@ -250,6 +249,7 @@
         } else {
           int[] connect = new int[2];
           connect[0] = thisAtomID;
+          System.out.println("" + thisBondID +  " " + thisAtomID);
           connectors.put(thisBondID, connect);
         }
       }
@@ -300,11 +300,11 @@
           Logger.warn("field == null in " + line);
         switch (fieldTypes[i]) {
         case ID:
-          atom.sequenceNumber = Parser.parseInt(field);
+          atom.atomSerial = Parser.parseInt(field);
           break;
         case sym:
           atom.elementSymbol = field;
-          atom.atomName = field + atom.sequenceNumber;
+          atom.atomName = field + atom.atomSerial;
           break;
         case anum:
           strAtomicNumbers += field + " "; // for MO slater basis calc

Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2010-04-28 21:00:16 UTC (rev 12965)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollection.java	2010-04-28 21:11:13 UTC (rev 12966)
@@ -1067,14 +1067,14 @@
 
   boolean haveMappedSerials;
   void mapMostRecentAtomSerialNumber() {
-    // from ?? 
-    if (atomCount == 0) 
+    // from ??
+    if (atomCount == 0)
       return;
-      int index = atomCount - 1;
-      int atomSerial = atoms[index].atomSerial;
-      if (atomSerial != Integer.MIN_VALUE)
-        atomSymbolicMap.put(new Integer(atomSerial), new Integer(index));
-      haveMappedSerials = true;
+    int index = atomCount - 1;
+    int atomSerial = atoms[index].atomSerial;
+    if (atomSerial != Integer.MIN_VALUE)
+      atomSymbolicMap.put(new Integer(atomSerial), new Integer(index));
+    haveMappedSerials = true;
   }
 
   public void createAtomSerialMap() {


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