Changeset 245826 for molecuilder/src/config.cpp

Timestamp:

Oct 30, 2009, 4:09:29 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

df0520

Parents:

b84ab4

Message:

BondGraph is initialized within config::Load(), as it has to happen after parsing options and before loading molecule. And various fixes.

• FIX: BondGraph::LoadBondLengthTable() - scans into TempContainer, which is later given over to BondLengthMatrix or NULL'd if parsing failed.
• BondGraph::ConstructBondGraph() adapted to above, uses both bonds functions depending on present BondLengthMatrix.
• FIX: BondGraph::GetBondLength() - checks whether BondLengthMatrix is NULL.
• config::Load() and ..LoadOld() get additionally the BondLengthFilename and allocates and parses BondGraph.
• builder.cpp ParseCommandLineOptions() has been adapted to above changes.
• FIX: molecule::CreateAdjacencyList() checks whether bonddistance is > 1. (otherwise quite useless and yielding too many cells).

File:

• molecuilder/src/config.cpp (modified) (5 diffs)

molecuilder/src/config.cpp

@@ -831 +831 @@
 /** Initializes config file structure by loading elements from a give file.
  * \param *file input file stream being the opened config file
+ * \param BondGraphFileName file name of the bond length table file, if string is left blank, no table is parsed.
  * \param *periode pointer to a periodentafel class with all elements
  * \param *mol pointer to molecule containing all atoms of the molecule
  */
-void config::Load(const char * const filename, const periodentafel * const periode, molecule * const &mol)
+void config::Load(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol)
 {
   ifstream *file = new ifstream(filename);
@@ -860 +861 @@
   /* Namen einlesen */
 
+  // 1. parse in options
   ParseForParameter(verbose,FileBuffer, "mainname", 0, 1, 1, string_type, (config::mainname), 1, critical);
   ParseForParameter(verbose,FileBuffer, "defaultpath", 0, 1, 1, string_type, (config::defaultpath), 1, critical);
@@ -1040 +1042 @@
     config::StructOpt = 0;
 
+  // 2. parse the bond graph file if given
+  BG = new BondGraph(IsAngstroem);
+  if (BG->LoadBondLengthTable((ofstream *)&cout, BondGraphFileName)) {
+    cout << Verbose(0) << "Bond length table loaded successfully." << endl;
+  } else {
+    cout << Verbose(0) << "Bond length table loading failed." << endl;
+  }
+
+  // 3. parse the molecule in
   LoadMolecule(mol, FileBuffer, periode, FastParsing);
+
+  // 4. dissect the molecule into connected subgraphs
+  BG->ConstructBondGraph((ofstream *)&cout, mol);
 
   delete(FileBuffer);
@@ -1047 +1061 @@
 /** Initializes config file structure by loading elements from a give file with old pcp syntax.
  * \param *file input file stream being the opened config file with old pcp syntax
+ * \param BondGraphFileName file name of the bond length table file, if string is left blank, no table is parsed.
  * \param *periode pointer to a periodentafel class with all elements
  * \param *mol pointer to molecule containing all atoms of the molecule
  */
-void config::LoadOld(const char * const filename, const periodentafel * const periode, molecule * const &mol)
+void config::LoadOld(const char * const filename, const string &BondGraphFileName, const periodentafel * const periode, molecule * const &mol)
 {
   ifstream *file = new ifstream(filename);
@@ -1207 +1222 @@
   config::StructOpt = 0;
 
+
+  // 2. parse the bond graph file if given
+  BG = new BondGraph(IsAngstroem);
+  if (BG->LoadBondLengthTable((ofstream *)&cout, BondGraphFileName)) {
+    cout << Verbose(0) << "Bond length table loaded successfully." << endl;
+  } else {
+    cout << Verbose(0) << "Bond length table loading failed." << endl;
+  }
+
   // Routine from builder.cpp
-
 
   for (i=MAX_ELEMENTS;i--;)