Changeset df0520 for molecuilder/src/molecule.cpp

Timestamp:

Nov 2, 2009, 12:50:57 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

8bc524

Parents:

245826

Message:

Small changes.

• VolumeOfConvexEnvelope() - setprecision corrected
• BUGFIX: PrepareClustersinWater() - IsAngstroem was set to NULL instead of true
• config::Load(), ..LoadOld() - get MoleculeListClass instead of molecule
• config::TestSyntax() - removed unncessary molecule parameter
• ParseCommandLineOptions() - no mol is created anymore, this is done when parsing in config::Load(), mol is set to first active instead
• config.cpp: Lots of ^{M (dos EOL) removed}
• have const molecule * const ref now: MoleculeLeafClass::FillBondStructureFromReference(), molecule::PickLocalBackEdges(), DepthFirstSearchAnalysis_CheckForaNewComponent(), DepthFirstSearchAnalysis_ProbeAlongUnusedBond()
• are const member functions now - necessary due to periodentafel being a const pointer: molecule::ResetAllBondsToUnused(), molecule::FindNextUnused(), molecule::SetNextComponentNumber(), molecule::CyclicStructureAnalysis(), CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(), molecule::OutputGraphInfoPerBond(), molecule::OutputGraphInfoPerAtom(), molecule::CyclicBondAnalysis(), molecule::CyclicStructureAnalysis(), molecule::GetColor(), molecule::CorrectBondDegree(), molecule::OutputBondsList()
• in molecule NoNonHydrogen, NoNonBonds and NoCyclicBonds are mutable
• molecule constructor rewritten with respect to ticket #4 (shorten constructors)

File:

• molecuilder/src/molecule.cpp (modified) (4 diffs)

molecuilder/src/molecule.cpp

@@ -26 +26 @@
  * Initialises molecule list with correctly referenced start and end, and sets molecule::last_atom to zero.
  */
-molecule::molecule(periodentafel *teil)
+molecule::molecule(const periodentafel * const teil) : elemente(teil), start(new atom), end(new atom), 
+  first(new bond(start, end, 1, -1)), last(new bond(start, end, 1, -1)), MDSteps(0), AtomCount(0), 
+  BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0), NoCyclicBonds(0), BondDistance(0.), 
+  ActiveFlag(false), IndexNr(-1), last_atom(0), InternalPointer(start)
 {
   // init atom chain list
-  start = new atom;
-  end = new atom;
   start->father = NULL;
   end->father = NULL;
   link(start,end);
-  InternalPointer = start;
+
   // init bond chain list
-  first = new bond(start, end, 1, -1);
-  last = new bond(start, end, 1, -1);
   link(first,last);
+
   // other stuff
-  MDSteps = 0;
-  last_atom = 0;
-  elemente = teil;
-  AtomCount = 0;
-  BondCount = 0;
-  NoNonBonds = 0;
-  NoNonHydrogen = 0;
-  NoCyclicBonds = 0;
-  ElementCount = 0;
   for(int i=MAX_ELEMENTS;i--;)
     ElementsInMolecule[i] = 0;
@@ -54 +45 @@
   cell_size[1] = cell_size[3] = cell_size[4]= 0.;
   strcpy(name,"none");
-  IndexNr  = -1;
-  ActiveFlag = false;
 };
 
@@ -555 +544 @@
 };
 
-/** Remove bond from bond chain list.
+/** Remove bond from bond chain list and from the both atom::ListOfBonds.
  * \todo Function not implemented yet
  * \param *pointer bond pointer
@@ -563 +552 @@
 {
   //cerr << Verbose(1) << "molecule::RemoveBond: Function not implemented yet." << endl;
+  pointer->leftatom->RegisterBond(pointer);
+  pointer->rightatom->RegisterBond(pointer);
   removewithoutcheck(pointer);
   return true;