Changes in src/molecules.hpp [a251a3:110ceb]

File:

• src/molecules.hpp (modified) (6 diffs)

src/molecules.hpp

@@ -13 +13 @@
 #include <gsl/gsl_vector.h>
 #include <gsl/gsl_matrix.h>
+#include <gsl/gsl_eigen.h>
 #include <gsl/gsl_heapsort.h>
 
@@ -39 +40 @@
 #define KeySet set<int>
 #define NumberValuePair pair<int, double>
-#define Graph map<KeySet, NumberValuePair, KeyCompare >
-#define GraphPair pair<KeySet, NumberValuePair >
+#define Graph map <KeySet, NumberValuePair, KeyCompare >
+#define GraphPair pair <KeySet, NumberValuePair >
 #define KeySetTestPair pair<KeySet::iterator, bool>
 #define GraphTestPair pair<Graph::iterator, bool>
@@ -265 +266 @@
   void CenterEdge(ofstream *out, vector *max); 
   void CenterOrigin(ofstream *out, vector *max); 
-  void CenterGravity(ofstream *out, vector *max); 
+  void CenterGravity(ofstream *out, vector *max);
   void Translate(const vector *x);
   void Mirror(const vector *x);
   void Align(vector *n);
   void Scale(double **factor);
-  void DetermineCenterOfGravity(vector &CenterOfGravity);
+  void DetermineCenter(vector &center);
+  vector * DetermineCenterOfGravity(ofstream *out);
   void SetBoxDimension(vector *dim);
   double * ReturnFullMatrixforSymmetric(double *cell_size);
   void ScanForPeriodicCorrection(ofstream *out);
-
+        void PrincipalAxisSystem(ofstream *out, bool DoRotate);
+        double VolumeOfConvexEnvelope(ofstream *out, bool IsAngstroem);
+        
   bool CheckBounds(const vector *x) const;
   void GetAlignVector(struct lsq_params * par) const;
@@ -283 +287 @@
   
   // Graph analysis
-  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, bool ReturnStack, int *&MinimumRingSize);
+  MoleculeLeafClass * DepthFirstSearchAnalysis(ofstream *out, int *&MinimumRingSize);
   void CyclicStructureAnalysis(ofstream *out, class StackClass<bond *> *BackEdgeStack, int *&MinimumRingSize);
   bond * FindNextUnused(atom *vertex);
@@ -303 +307 @@
   bool ParseOrderAtSiteFromFile(ofstream *out, char *path);
   bool StoreOrderAtSiteFile(ofstream *out, char *path);
-  bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList, bool IsAngstroem);
+  bool ParseKeySetFile(ofstream *out, char *filename, Graph *&FragmentList);
   bool StoreKeySetFile(ofstream *out, Graph &KeySetList, char *path);
   bool StoreForcesFile(ofstream *out, MoleculeListClass *BondFragments, char *path, int *SortIndex);
@@ -392 +396 @@
     char *configpath;
     char *configname;
+    bool FastParsing;
     
     private: