Changeset df0520 for molecuilder/src/molecule_graph.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_graph.cpp (modified) (17 diffs)

molecuilder/src/molecule_graph.cpp

@@ -190 +190 @@
  * \param output stream
  */
-void molecule::OutputBondsList(ofstream *out)
+void molecule::OutputBondsList(ofstream *out) const
 {
   *out << Verbose(1) << endl << "From contents of bond chain list:";
@@ -210 +210 @@
  * \return number of bonds that could not be corrected
  */
-int molecule::CorrectBondDegree(ofstream *out)
+int molecule::CorrectBondDegree(ofstream *out) const
 {
   int No = 0;
@@ -265 +265 @@
  * \return string of the flag
  */
-string molecule::GetColor(enum Shading color)
+string molecule::GetColor(enum Shading color) const
 {
   switch (color) {
@@ -314 +314 @@
  * \param &DFS DFS accounting data
  */
-void DepthFirstSearchAnalysis_ProbeAlongUnusedBond(ofstream *out, molecule *mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS)
+void DepthFirstSearchAnalysis_ProbeAlongUnusedBond(ofstream *out, const molecule * const mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS)
 {
   atom *OtherAtom = NULL;
@@ -357 +357 @@
  * \param &DFS DFS accounting data
  */
-void DepthFirstSearchAnalysis_CheckForaNewComponent(ofstream *out, molecule *mol, atom *&Walker, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
+void DepthFirstSearchAnalysis_CheckForaNewComponent(ofstream *out, const molecule * const mol, atom *&Walker, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
 {
   atom *OtherAtom = NULL;
@@ -403 +403 @@
  * \param &DFS DFS accounting data
  */
-void DepthFirstSearchAnalysis_CleanRootStackDownTillWalker(ofstream *out, molecule *mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
+void DepthFirstSearchAnalysis_CleanRootStackDownTillWalker(ofstream *out, const molecule * const mol, atom *&Walker, bond *&Binder, struct DFSAccounting &DFS, MoleculeLeafClass *&LeafWalker)
 {
   atom *OtherAtom = NULL;
@@ -467 +467 @@
  * \return list of each disconnected subgraph as an individual molecule class structure
  */
-MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack)
+MoleculeLeafClass * molecule::DepthFirstSearchAnalysis(ofstream *out, class StackClass<bond *> *&BackEdgeStack) const
 {
   struct DFSAccounting DFS;
@@ -548 +548 @@
 /** Scans through all bonds and set bond::Cyclic to true where atom::LowpointNr of both ends is equal: LP criterion.
  */
-void molecule::CyclicBondAnalysis()
+void molecule::CyclicBondAnalysis() const
 {
   NoCyclicBonds = 0;
@@ -565 +565 @@
  * \param *out output stream
  */
-void molecule::OutputGraphInfoPerAtom(ofstream *out)
+void molecule::OutputGraphInfoPerAtom(ofstream *out) const
 {
   *out << Verbose(1) << "Final graph info for each atom is:" << endl;
@@ -575 +575 @@
  * \param *out output stream
  */
-void molecule::OutputGraphInfoPerBond(ofstream *out)
+void molecule::OutputGraphInfoPerBond(ofstream *out) const
 {
   *out << Verbose(1) << "Final graph info for each bond is:" << endl;
@@ -829 +829 @@
  * \param *mol molecule with atoms
  */
-void CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(ofstream *out, int *&MinimumRingSize, int &MinRingSize, int &NumCycles, molecule *mol)
+void CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(ofstream *out, int *&MinimumRingSize, int &MinRingSize, int &NumCycles, const molecule * const mol)
 {
   atom *Root = NULL;
@@ -864 +864 @@
  * \todo BFS from the not-same-LP to find back to starting point of tributary cycle over more than one bond
  */
-void molecule::CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> * BackEdgeStack, int *&MinimumRingSize)
+void molecule::CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> * BackEdgeStack, int *&MinimumRingSize) const
 {
   struct BFSAccounting BFS;
@@ -900 +900 @@
 
   CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(out, MinimumRingSize, MinRingSize, NumCycles, this);
-
-}
-;
+};
 
 /** Sets the next component number.
@@ -909 +907 @@
  * \param nr number to use
  */
-void molecule::SetNextComponentNumber(atom *vertex, int nr)
+void molecule::SetNextComponentNumber(atom *vertex, int nr) const
 {
   size_t i = 0;
@@ -931 +929 @@
  * \return bond class or NULL
  */
-bond * molecule::FindNextUnused(atom *vertex)
+bond * molecule::FindNextUnused(atom *vertex) const
 {
   for (BondList::const_iterator Runner = vertex->ListOfBonds.begin(); Runner != vertex->ListOfBonds.end(); (++Runner))
@@ -943 +941 @@
  * \return true - success, false - -failure
  */
-void molecule::ResetAllBondsToUnused()
+void molecule::ResetAllBondsToUnused() const
 {
   bond *Binder = first;
@@ -1103 +1101 @@
  * \return true - everything ok, false - ReferenceStack was empty
  */
-bool molecule::PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack)
+bool molecule::PickLocalBackEdges(ofstream *out, atom **ListOfLocalAtoms, class StackClass<bond *> *&ReferenceStack, class StackClass<bond *> *&LocalStack) const
 {
   bool status = true;