Mods to fix problem w/ base class method computeBornRadii() being called when PyOpenMM is run

6b18ecfa · Mark Friedrichs · 8ab02ff2 · 6b18ecfa · 6b18ecfa · 6b18ecfa
Commit 6b18ecfa authored Jul 27, 2011 by Mark Friedrichs
6 changed files
--- a/platforms/reference/src/gbsa/CpuImplicitSolvent.cpp
+++ b/platforms/reference/src/gbsa/CpuImplicitSolvent.cpp
@@ -521,7 +521,7 @@ vector<RealOpenMM>& CpuImplicitSolvent::getBornRadiiTemp( void ){
   @param obcChain            output array of Obc chain derivatives
   --------------------------------------------------------------------------------------- */
+/*
 void CpuImplicitSolvent::computeBornRadii( vector<RealVec>& atomCoordinates, vector<RealOpenMM>& bornRadii ){
   // ---------------------------------------------------------------------------------------
@@ -534,7 +534,7 @@ void CpuImplicitSolvent::computeBornRadii( vector<RealVec>& atomCoordinates, vec
   message << methodName;
   message << " Error: calling from base class.";
   SimTKOpenMMLog::printError( message );
-}
+} */
 /**---------------------------------------------------------------------------------------

--- a/platforms/reference/src/gbsa/CpuImplicitSolvent.h
+++ b/platforms/reference/src/gbsa/CpuImplicitSolvent.h
@@ -334,7 +334,7 @@ class OPENMM_EXPORT CpuImplicitSolvent {
         --------------------------------------------------------------------------------------- */
-      virtual void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii );
+      virtual void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii ) = 0;
      /**---------------------------------------------------------------------------------------

--- a/plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
+++ b/plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
@@ -310,6 +310,10 @@ void CpuGBVISoftcore::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadiu
 #define GBVISoftcoreDebug 0
+void CpuGBVISoftcore::computeBornRadii( vector<RealVec>& atomCoordinates, vector<RealOpenMM>& bornRadii ){
+    return computeBornRadii( atomCoordinates, bornRadii, NULL );
+}
 void CpuGBVISoftcore::computeBornRadii( vector<RealVec>& atomCoordinates, vector<RealOpenMM>& bornRadii, RealOpenMM* switchDeriviative ){
   // ---------------------------------------------------------------------------------------

--- a/plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.h
+++ b/plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.h
@@ -113,6 +113,7 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
      void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii,
                            RealOpenMM* switchDeriviative = NULL );
+      void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<RealOpenMM>& bornRadii );
      /**---------------------------------------------------------------------------------------

--- a/plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.cpp
+++ b/plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.cpp
@@ -207,7 +207,7 @@ vector<RealOpenMM>& CpuObcSoftcore::getObcChainTemp( void ){
   --------------------------------------------------------------------------------------- */
-void CpuObcSoftcore::computeBornRadii( vector<RealVec>& atomCoordinates, RealOpenMM* bornRadii ){
+void CpuObcSoftcore::computeBornRadii( vector<RealVec>& atomCoordinates,  std::vector<RealOpenMM>& bornRadii ){
   // ---------------------------------------------------------------------------------------

--- a/plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.h
+++ b/plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.h
@@ -124,7 +124,7 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
         --------------------------------------------------------------------------------------- */
-      void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM* bornRadii );
+      void computeBornRadii( std::vector<OpenMM::RealVec>& atomCoordinates,  std::vector<RealOpenMM>& bornRadii );
      /**---------------------------------------------------------------------------------------