[Jmol-commits] SF.net SVN: jmol:[15771] trunk/Jmol/src/org/jmol/modelset

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

Revision: 15771
          http://jmol.svn.sourceforge.net/jmol/?rev=15771&view=rev
Author:   hansonr
Date:     2011-07-14 16:08:45 +0000 (Thu, 14 Jul 2011)

Log Message:
-----------
pdbAddHydrogens with appendNew problem

Modified Paths:
--------------
    trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
    trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
    trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
    trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java

Modified: trunk/Jmol/src/org/jmol/modelset/AtomCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/AtomCollection.java	2011-07-14 08:48:22 UTC (rev 15770)
+++ trunk/Jmol/src/org/jmol/modelset/AtomCollection.java	2011-07-14 16:08:45 UTC (rev 15771)
@@ -1040,6 +1040,10 @@
         + " set";
     int n = 0;
     boolean isDefault = (type == TAINT_COORD);
+    if (bs != null && bs.length() > atomCount) {
+      System.out.println("atomcollection check bs " + Escape.escape(bs));
+      return;
+    }
     if (bs != null)
       for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
         s.append(i + 1).append(" ").append(atoms[i].getElementSymbol()).append(

Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2011-07-14 08:48:22 UTC (rev 15770)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java	2011-07-14 16:08:45 UTC (rev 15771)
@@ -4088,6 +4088,10 @@
     for (int i = i0; i < atomCount; i++) {
       atoms[i] = atoms[map[i]];
       atoms[i].index = i;
+      Model m = models[atoms[i].modelIndex];
+      if (m.firstAtomIndex == map[i])
+        m.firstAtomIndex = i;
+      m.bsAtoms.set(i);
     }
     if (vibrationVectors != null)
       for (int i  = i0; i < atomCount; i++)

Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java	2011-07-14 08:48:22 UTC (rev 15770)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java	2011-07-14 16:08:45 UTC (rev 15771)
@@ -1388,13 +1388,19 @@
       int[] mapNewToOld = new int[modelSet.atomCount
           - bsDeletedAtoms.cardinality()];
       int n = baseAtomIndex;
-      for (int i = baseAtomIndex; i < modelSet.atomCount; i++)
+      Model[] models = modelSet.models;
+      Atom[] atoms = modelSet.atoms;
+      for (int i = baseAtomIndex; i < modelSet.atomCount; i++) {
+        models[atoms[i].modelIndex].bsAtoms.clear(i);
+        models[atoms[i].modelIndex].bsAtomsDeleted.clear(i);
         if (bsDeletedAtoms.get(i)) {
           mapOldToNew[i] = n - 1;
+          models[atoms[i].modelIndex].atomCount--;
         } else {
           mapNewToOld[n] = i;
           mapOldToNew[i] = n++;
         }
+      }
       modelSet.modelSetAuxiliaryInfo.put("bsDeletedAtoms", bsDeletedAtoms);
       // adjust group pointers
       for (int i = baseGroupIndex; i < groups.length; i++) {

Modified: trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java	2011-07-14 08:48:22 UTC (rev 15770)
+++ trunk/Jmol/src/org/jmol/modelsetbio/Resolver.java	2011-07-14 16:08:45 UTC (rev 15771)
@@ -529,7 +529,7 @@
         continue;
       }
       String value = htBondMap.get(key);
-      Logger.info(key + " was not used; order=" + value);
+      Logger.info("bond " + key + " was not used; order=" + value);
       if (htBondMap.get(key).equals("1")) {
         htKeysUsed.put(key, Boolean.TRUE);
         continue; // that's ok


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