Changes in src/molecule_fragmentation.cpp [c743f8:83f176]

File:

• src/molecule_fragmentation.cpp (modified) (7 diffs)

src/molecule_fragmentation.cpp

@@ +1 @@
+/*
+ * Project: MoleCuilder
+ * Description: creates and alters molecular systems
+ * Copyright (C)  2010 University of Bonn. All rights reserved.
+ * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
+ */
+
 /*
  * molecule_fragmentation.cpp
@@ -456 +463 @@
       for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
     #ifdef ADDHYDROGEN
-        if ((*iter)->getType()->Z != 1) // skip hydrogen
+        if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
     #endif
         {
@@ -476 +483 @@
     for(molecule::const_iterator iter = begin(); iter != end(); ++iter) {
   #ifdef ADDHYDROGEN
-      if ((*iter)->getType()->Z != 1) // skip hydrogen
+      if ((*iter)->getType()->getAtomicNumber() != 1) // skip hydrogen
   #endif
       {
@@ -803 +810 @@
   DoLog(1) && (Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl);
   if (file.good()) {
-    for_each(atoms.begin(),atoms.end(),bind2nd(mem_fun(&atom::OutputOrder), &file));
+    ActOnAllAtoms( &atom::OutputOrder, &file );
     file.close();
     DoLog(1) && (Log() << Verbose(1) << "done." << endl);
@@ -885 +892 @@
   for (KeySet::iterator runner = Leaf->begin(); runner != Leaf->end(); runner++) {
     Runner = FindAtom((*runner));
-    if (Runner->getType()->Z != 1) { // skip all those added hydrogens when re-filling snake stack
+    if (Runner->getType()->getAtomicNumber() != 1) { // skip all those added hydrogens when re-filling snake stack
       if (ShortestPathList[(*runner)] > SP) {  // remove the oldest one with longest shortest path
         SP = ShortestPathList[(*runner)];
@@ -974 +981 @@
     ++iter;
 #ifdef ADDHYDROGEN
-    while ((iter != Leaf->end()) && ((*iter)->getType()->Z == 1)){ // skip added hydrogen
+    while ((iter != Leaf->end()) && ((*iter)->getType()->getAtomicNumber() == 1)){ // skip added hydrogen
       iter++;
     }
@@ -1352 +1359 @@
         if ((RestrictedKeySet.find(OtherWalker->nr) != RestrictedKeySet.end())
   #ifdef ADDHYDROGEN
-         && (OtherWalker->getType()->Z != 1)
+         && (OtherWalker->getType()->getAtomicNumber() != 1)
   #endif
                                                               ) {  // skip hydrogens and restrict to fragment