Changeset 1de701 for molecuilder/src/molecule.cpp

Timestamp:

May 8, 2010, 12:47:57 PM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

Children:

0341a9

Parents:

25e17e9

Message:

FIX: Memory corruption in particleInfo class

File:

• molecuilder/src/molecule.cpp (modified) (9 diffs)

molecuilder/src/molecule.cpp

@@ -135 +135 @@
       if (pointer->type->Z != 1)
         NoNonHydrogen++;
-      if (pointer->Name == NULL) {
-        Free(&pointer->Name);
-        pointer->Name = Malloc<char>(6, "molecule::AddAtom: *pointer->Name");
-        sprintf(pointer->Name, "%2s%02d", pointer->type->symbol, pointer->nr+1);
+      if(pointer->getName() == "Unknown"){
+        stringstream sstr;
+        sstr << pointer->type->symbol << pointer->nr+1;
+        pointer->setName(sstr.str());
       }
     }
@@ -157 +157 @@
   if (pointer != NULL) {
     atom *walker = pointer->clone();
-    walker->Name = Malloc<char>(strlen(pointer->Name) + 1, "atom::atom: *Name");
-    strcpy (walker->Name, pointer->Name);
+    stringstream sstr;
+    sstr << pointer->getName();
+    walker->setName(sstr.str());
     walker->nr = last_atom++;  // increase number within molecule
     add(walker, end);
@@ -252 +253 @@
   BondRescale = TopOrigin->type->HBondDistance[TopBond->BondDegree-1];
   if (BondRescale == -1) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!" << endl);
     return false;
     BondRescale = bondlength;
@@ -295 +296 @@
             SecondOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
           } else {
-            DoeLog(2) && (eLog()<< Verbose(2) << "Detected more than four bonds for atom " << TopOrigin->Name);
+            DoeLog(2) && (eLog()<< Verbose(2) << "Detected more than four bonds for atom " << TopOrigin->getName());
           }
         }
@@ -339 +340 @@
       bondangle = TopOrigin->type->HBondAngle[1];
       if (bondangle == -1) {
-        DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl);
+        DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!" << endl);
         return false;
         bondangle = 0;
@@ -616 +617 @@
     add(Binder, last);
   } else {
-    DoeLog(1) && (eLog()<< Verbose(1) << "Could not add bond between " << atom1->Name << " and " << atom2->Name << " as one or both are not present in the molecule." << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "Could not add bond between " << atom1->getName() << " and " << atom2->getName() << " as one or both are not present in the molecule." << endl);
   }
   return Binder;
@@ -695 +696 @@
     AtomCount--;
   } else
-    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
   if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
     ElementCount--;
@@ -713 +714 @@
     ElementsInMolecule[pointer->type->Z]--; // decrease number of atom of this element
   else
-    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
+    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
   if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
     ElementCount--;
@@ -915 +916 @@
         if (Walker->type->Z != 1) // count non-hydrogen atoms whilst at it
           NoNonHydrogen++;
-        Free(&Walker->Name);
-        Walker->Name = Malloc<char>(6, "molecule::CountAtoms: *walker->Name");
-        sprintf(Walker->Name, "%2s%02d", Walker->type->symbol, Walker->nr+1);
-        DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << Walker->nr << " " << Walker->Name << "." << endl);
+        stringstream sstr;
+        sstr << Walker->type->symbol << Walker->nr+1;
+        Walker->setName(sstr.str());
+        DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << Walker->nr << " " << Walker->getName() << "." << endl);
         i++;
       }