A bunch of changes

The big one is I started using the
mathkernel generated energy functions.
I swapped the old _Stretch_termCode.cc out for the new
stretch_energy, stretch_gradient, stretch_hessian functions.

The energyStretch.cc file is pretty messy right now.  I'll clean it up
when I add the nonbond code.

Author: Christian Schafmeisterr

include/cando/chem/energyComponent.h

@@ -50,6 +50,8 @@ This is an open source license for the CANDO software from Temple University, bu
 #include <cando/chem/scoringFunction.h>
 #include <cando/chem/residue.h>
 
+#define SIZE_T size_t
+
 		//
 		// SCALE FACTOR FOR ELECTROSTIC INTERACTIONS???
 		//

include/cando/chem/energyFunction.h

@@ -97,6 +97,12 @@ FORWARD(BoundingBox);
 
 core::T_sp specializeKeepInteractionFactory( core::T_sp keepInteractionFactory, core::T_sp aclass );
 
+bool skipInteraction_EnergyNonbond( core::T_sp keepInteractionFunction,
+                                   Atom_sp atomA,
+                                   Atom_sp atomB,
+                                   core::T_sp ti3A,
+                                   core::T_sp ti3B );
+
 bool skipInteraction( core::T_sp keepInteractionFunction,
                       Atom_sp atomA = unbound<Atom_O>(),
                       Atom_sp atomB = unbound<Atom_O>(),

include/cando/chem/energyNonbond.h

@@ -273,6 +273,7 @@ class EnergyNonbond_O : public EnergyComponent_O
   core::List_sp nonbondTermsAsAList();
 
   void setNonbondExcludedAtomInfo(AtomTable_sp atom_table, core::SimpleVector_int32_t_sp excluded_atoms_list, core::SimpleVector_int32_t_sp number_excluded_atoms);
+  void checkEnergyNonbond();
   EnergyNonbond_sp copyFilter(core::T_sp keepInteractionFactory);
  public:
   EnergyNonbond_O( const EnergyNonbond_O& ss ); //!< Copy constructor

include/cando/chem/scoringFunction.h

@@ -250,8 +250,10 @@ class ScoringFunction_O : public core::CxxObject_O
                                                        core::T_sp activeAtomMask,
                                                        core::T_sp debugInteractions=nil<core::T_O>(),
                                                        bool disableRestraints=false);
+#if 0
   virtual double	evaluateEnergyForceFullHessianForDebugging(core::T_sp energyScale, core::T_sp activeAtomMask, core::T_sp debugInteractions,
                                                                    bool disableRestraints);
+  #endif
 
   void evaluateFiniteDifferenceForce(NVector_sp pos, core::T_sp energyScale, NVector_sp force, double delta=0.00001, core::T_sp activeAtomMask=nil<core::T_O>() );
 #if 0

include/cando/main/extension.h

@@ -51,6 +51,8 @@ typedef int32_t vecint;
 #define NVECTOR_sp_TYPE core::SimpleVector_float_sp
 #endif
 
+#define DOUBLE vecreal
+
 #if NUM_REAL == VECREAL_DOUBLE
 typedef double num_real;
 typedef int64_t num_int;