Changes in src/molecule.hpp [4bb63c:d74077]

File:

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

src/molecule.hpp

@@ -29 +29 @@
 #include "Patterns/Cacheable.hpp"
 #include "Formula.hpp"
-#include "AtomSet.hpp"
 
 #include "Descriptors/MoleculeDescriptor_impl.hpp"
@@ -85 +84 @@
 
   public:
-    typedef ATOMSET(std::list) atomSet;
+    typedef std::list<atom*> atomSet;
     typedef std::set<atomId_t> atomIdSet;
     typedef ObservedIterator<atomSet> iterator;
@@ -165 +164 @@
   bool IsEnd() const ;
 
-  // templates for allowing global manipulation of all vectors
-  template <typename res> void ActOnAllVectors( res (Vector::*f)() ) const;
-  template <typename res> void ActOnAllVectors( res (Vector::*f)() const) const;
-  template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T), T t ) const;
-  template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T) const, T t ) const;
-  template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&), T &t ) const;
-  template <typename res, typename T> void ActOnAllVectors( res (Vector::*f)(T&) const, T &t ) const;
-  template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U), T t, U u ) const;
-  template <typename res, typename T, typename U> void ActOnAllVectors( res (Vector::*f)(T, U) const, T t, U u ) const;
-  template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V), T t, U u, V v) const;
-  template <typename res, typename T, typename U, typename V> void ActOnAllVectors( res (Vector::*f)(T, U, V) const, T t, U u, V v) const;
-
   // templates for allowing global manipulation of molecule with each atom as single argument
   template <typename res> void ActWithEachAtom( res (molecule::*f)(atom *) ) const;
@@ -270 +257 @@
   void Scale(const double ** const factor);
   void DeterminePeriodicCenter(Vector &center);
-  Vector * DetermineCenterOfGravity() const;
+  Vector * DetermineCenterOfGravity();
   Vector * DetermineCenterOfAll() const;
   Vector * DetermineCenterOfBox() const;
@@ -278 +265 @@
   bool VerletForceIntegration(char *file, config &configuration, const size_t offset);
   void Thermostats(config &configuration, double ActualTemp, int Thermostat);
+  void PrincipalAxisSystem(bool DoRotate);
   double VolumeOfConvexEnvelope(bool IsAngstroem);
 
@@ -340 +328 @@
 
   // Output routines.
-  bool Output(std::ostream * const output);
+  bool Output(ofstream * const output);
   bool OutputTrajectories(ofstream * const output);
   void OutputListOfBonds() const;