Changes in src/molecule_graph.cpp [952f38:83f176]

File:

• src/molecule_graph.cpp (modified) (4 diffs)

src/molecule_graph.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_graph.cpp
@@ -6 +13 @@
  */
 
+// include config.h
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -184 +192 @@
                           //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
                           (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
-                          const double distance = domain.periodicDistanceSquared(OtherWalker->x,Walker->x);
+                          const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
                           const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
 //                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;
@@ -737 +745 @@
         OtherAtom = (*Runner)->GetOtherAtom(Walker);
 #ifdef ADDHYDROGEN
-        if (OtherAtom->type->Z != 1) {
+        if (OtherAtom->getType()->getAtomicNumber() != 1) {
 #endif
         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);