Changes in src/molecule.hpp [f17e1c:c27778]

File:

• src/molecule.hpp (modified) (8 diffs)

src/molecule.hpp

@@ -7 +7 @@
 #define MOLECULES_HPP_
 
+using namespace std;
+
 /*********************************************** includes ***********************************/
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+// GSL headers
+#include <gsl/gsl_eigen.h>
+#include <gsl/gsl_heapsort.h>
+#include <gsl/gsl_linalg.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_multimin.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_randist.h>
 
 //// STL headers
@@ -24 +31 @@
 #include "types.hpp"
 #include "graph.hpp"
+#include "stackclass.hpp"
 #include "tesselation.hpp"
 #include "Patterns/Observer.hpp"
 #include "Patterns/ObservedIterator.hpp"
 #include "Patterns/Cacheable.hpp"
-#include "Formula.hpp"
 
 #include "Descriptors/MoleculeDescriptor_impl.hpp"
@@ -46 +53 @@
 class periodentafel;
 class Vector;
-class Shape;
-template <class> class StackClass;
 
 /******************************** Some definitions for easier reading **********************************/
@@ -98 +103 @@
     //int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
     int BondCount;          //!< number of atoms, brought up-to-date by CountBonds()
+    int ElementCount;       //!< how many unique elements are therein
+    int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
     mutable int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
     mutable int NoNonBonds;     //!< number of non-hydrogen bonds in molecule
@@ -108 +115 @@
 
   private:
-    Formula formula;
+    Cacheable<string> formula;
     Cacheable<int>    AtomCount;
     moleculeId_t id;
@@ -134 +141 @@
   void setId(moleculeId_t);
   void setName(const std::string);
-  const Formula &getFormula();
-  unsigned int getElementCount();
-  bool hasElement(const element*) const;
-  bool hasElement(atomicNumber_t) const;
-  bool hasElement(const std::string&) const;
-
+  const std::string getFormula();
+  std::string calcFormula();
 
   iterator begin();
@@ -257 +260 @@
 
   /// Count and change present atoms' coordination.
+  void CountElements();
   bool CenterInBox();
   bool BoundInBox();
@@ -312 +316 @@
 
   molecule *CopyMolecule();
-  molecule* CopyMoleculeFromSubRegion(const Shape&) const;
+  molecule* CopyMoleculeFromSubRegion(const Vector offset, const double *parallelepiped) const;
 
   /// Fragment molecule by two different approaches: