Changes in src/molecule_graph.cpp [94d5ac6:3aa8a5]

File:

• src/molecule_graph.cpp (modified) (8 diffs)

src/molecule_graph.cpp

@@ -48 +48 @@
 #include "Element/element.hpp"
 #include "Graph/BondGraph.hpp"
+#include "Graph/ListOfLocalAtoms.hpp"
 #include "Helpers/defs.hpp"
 #include "Helpers/helpers.hpp"
@@ -61 +62 @@
  * Calls this routine in each MoleculeLeafClass::next subgraph if it's not NULL.
  * \param *reference reference molecule with the bond structure to be copied
- * \param **&ListOfLocalAtoms Lookup table for this subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
- * \param FreeList true - ***ListOfLocalAtoms is free'd before return, false - it is not
+ * \param ListOfLocalAtoms Lookup table for this subgraph and index of each atom in \a *reference, may be NULL on start, then it is filled
+ * \param FreeList true - ListOfLocalAtoms is free'd before return, false - it is not
  * \return true - success, false - failure
  */
-bool molecule::FillBondStructureFromReference(const molecule * const reference, atom **&ListOfLocalAtoms, bool FreeList)
+bool molecule::FillBondStructureFromReference(const molecule * const reference, ListOfLocalAtoms_t &ListOfLocalAtoms, bool FreeList)
 {
   bool status = true;
@@ -91 +92 @@
           ++Runner) {
         atom * const OtherAtom = (*Runner)->GetOtherAtom((*iter)->GetTrueFather());
-        atom * const OtherWalker = ListOfLocalAtoms[OtherAtom->getNr()]; // local copy of current bond partner of walker
+        const ListOfLocalAtoms_t::const_iterator localiter = ListOfLocalAtoms.find(OtherAtom->getNr());
+        ASSERT( localiter != ListOfLocalAtoms.end(),
+            "molecule::FillBondStructureFromReference() - could not find id"
+            +toString(OtherAtom->getNr())+" in ListOfLocalAtoms.");
+        atom * const OtherWalker = localiter->second; // local copy of current bond partner of walker
         if (OtherWalker != NULL) {
           if (OtherWalker->getNr() > (*iter)->getNr())
@@ -103 +108 @@
   }
 
-  if ((FreeList) && (ListOfLocalAtoms != NULL)) {
+  if ((FreeList) && (!ListOfLocalAtoms.empty())) {
     // free the index lookup list
-    delete[](ListOfLocalAtoms);
+    ListOfLocalAtoms.clear();
   }
   LOG(1, "End of FillBondStructureFromReference.");
@@ -146 +151 @@
 }
 
-
-/** Storing the bond structure of a molecule to file.
- * Simply stores Atom::Nr and then the Atom::Nr of all bond partners per line.
- * \param &filename name of file
- * \param path path to file, defaults to empty
- * \return true - file written successfully, false - writing failed
- */
-bool molecule::StoreAdjacencyToFile(std::string filename, std::string path)
-{
-  ofstream AdjacencyFile;
-  string line;
-  bool status = true;
-
-  if (path != "")
-    line = path + "/" + filename;
-  else
-    line = filename;
-  AdjacencyFile.open(line.c_str(), ios::out);
-  LOG(1, "Saving adjacency list ... ");
-  if (AdjacencyFile.good()) {
-    AdjacencyFile << "m\tn" << endl;
-    for_each(begin(),end(),bind2nd(mem_fun(&atom::OutputAdjacency),&AdjacencyFile));
-    AdjacencyFile.close();
-    LOG(1, "\t... done.");
-  } else {
-    LOG(1, "\t... failed to open file " << line << ".");
-    status = false;
-  }
-
-  return status;
-}
-;
 
 /** Storing the bond structure of a molecule to file.
@@ -227 +200 @@
 
 /** Fills a lookup list of father's Atom::nr -> atom for each subgraph.
- * \param **&ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
+ * \param ListOfLocalAtoms Lookup table for each subgraph and index of each atom in global molecule, may be NULL on start, then it is filled
  * \param GlobalAtomCount number of atoms in the complete molecule
  * \return true - success, false - failure (ListOfLocalAtoms != NULL)
  */
-bool molecule::FillListOfLocalAtoms(atom **&ListOfLocalAtoms, const int GlobalAtomCount)
+bool molecule::FillListOfLocalAtoms(ListOfLocalAtoms_t &ListOfLocalAtoms, const int GlobalAtomCount)
 {
   bool status = true;
 
-  if (ListOfLocalAtoms == NULL) { // allocate and fill list of this fragment/subgraph
+  if (ListOfLocalAtoms.empty()) { // allocate and fill list of this fragment/subgraph
     status = status && CreateFatherLookupTable(ListOfLocalAtoms, GlobalAtomCount);
   } else
@@ -251 +224 @@
  * \return true - success, false - failure
  */
-bool molecule::CreateFatherLookupTable(atom **&LookupTable, int count)
+bool molecule::CreateFatherLookupTable(ListOfLocalAtoms_t &LookupTable, int count)
 {
   bool status = true;
   int AtomNo;
 
-  if (LookupTable != NULL) {
-    ELOG(1, "Pointer for Lookup table is not NULL! Aborting ...");
+  if (!LookupTable.empty()) {
+    ELOG(1, "Pointer for Lookup table is not empty! Aborting ...");
     return false;
   }
@@ -273 +246 @@
 
   // allocate and fill
-  LookupTable = new atom *[count+1];
-  if (LookupTable == NULL) {
-    ELOG(0, "LookupTable memory allocation failed!");
-    performCriticalExit();
-    status = false;
-  } else {
-    for (int i=0;i<=count;i++)
-      LookupTable[i] = NULL;
-    for (molecule::iterator iter = begin(); iter != end(); ++iter) {
-      AtomNo = (*iter)->GetTrueFather()->getNr();
-      if ((AtomNo >= 0) && (AtomNo <= count)) {
-        LOG(3, "DEBUG: Setting LookupTable[" << AtomNo << "] to " << *(*iter));
-        LookupTable[AtomNo] = (*iter);
-      } else {
-        ELOG(1, "Walker " << *(*iter) << " exceeded range of nuclear ids [0, " << count << "].");
-        status = false;
-        break;
-      }
+  for (int i=0;i<=count;i++)
+    LookupTable[i] = NULL;
+  for (molecule::iterator iter = begin(); iter != end(); ++iter) {
+    AtomNo = (*iter)->GetTrueFather()->getNr();
+    if ((AtomNo >= 0) && (AtomNo <= count)) {
+      LOG(3, "DEBUG: Setting LookupTable[" << AtomNo << "] to " << *(*iter));
+      LookupTable[AtomNo] = (*iter);
+    } else {
+      ELOG(1, "Walker " << *(*iter) << " exceeded range of nuclear ids [0, " << count << "].");
+      status = false;
+      break;
     }
   }