use templated functions to create grids (#136)

* replace CreateGridX with a templated function

* remove statements with no effect

* lint

include/RbtBaseIdxSF.h

@@ -16,10 +16,15 @@
 #ifndef _RBTBASEIDXSF_H_
 #define _RBTBASEIDXSF_H_
 
+#include <type_traits>
+
+#include "RbtBaseGrid.h"
 #include "RbtBaseSF.h"
+#include "RbtDockingSite.h"
 #include "RbtInteractionGrid.h"
 #include "RbtNonBondedGrid.h"
 #include "RbtNonBondedHHSGrid.h"
+#include "RbtWorkSpace.h"
 
 class RbtBaseIdxSF: public virtual RbtBaseSF {
  public:
@@ -47,9 +52,8 @@ class RbtBaseIdxSF: public virtual RbtBaseSF {
     ///////////////////
     RbtBaseIdxSF();
 
-    RbtInteractionGridPtr CreateInteractionGrid() const;
-    RbtNonBondedGridPtr CreateNonBondedGrid() const;
-    RbtNonBondedHHSGridPtr CreateNonBondedHHSGrid() const;
+    template <class T>
+    SmartPtr<T> CreateGrid() const;
     RbtDouble GetMaxError() const;
     // DM 12 Apr 2002
     // Returns the maximum range of the scoring function,
@@ -81,4 +85,23 @@ class RbtBaseIdxSF: public virtual RbtBaseSF {
     RbtDouble m_border;
 };
 
+template <class T>
+SmartPtr<T> RbtBaseIdxSF::CreateGrid() const {
+    // Create a grid covering the docking site
+    static_assert(std::is_base_of<RbtBaseGrid, T>::value, "T must inherit from RbtBaseGrid");
+    RbtDockingSitePtr spDS = GetWorkSpace()->GetDockingSite();
+    if (spDS.Null()) return SmartPtr<T>();
+
+    // Extend grid by _BORDER, mainly to allow for the possibility of polar hydrogens
+    // falling outside of the docking site
+    RbtCoord minCoord = spDS->GetMinCoord() - m_border;
+    RbtCoord maxCoord = spDS->GetMaxCoord() + m_border;
+    RbtVector recepExtent = maxCoord - minCoord;
+    RbtVector gridStep(m_gridStep, m_gridStep, m_gridStep);
+    RbtUInt nX = int(recepExtent.x / gridStep.x) + 1;
+    RbtUInt nY = int(recepExtent.y / gridStep.y) + 1;
+    RbtUInt nZ = int(recepExtent.z / gridStep.z) + 1;
+    return SmartPtr<T>(new T(minCoord, gridStep, nX, nY, nZ));
+}
+
 #endif  //_RBTBASEIDXSF_H_

src/lib/RbtAromIdxSF.cxx

@@ -94,8 +94,8 @@ void RbtAromIdxSF::SetupReceptor() {
     ClearReceptor();
     if (GetReceptor().Null()) return;
 
-    m_spAromGrid = CreateInteractionGrid();
-    m_spGuanGrid = CreateInteractionGrid();
+    m_spAromGrid = CreateGrid<RbtInteractionGrid>();
+    m_spGuanGrid = CreateGrid<RbtInteractionGrid>();
 
     RbtDouble idxIncr = GetParameter(_INCR);  // vdw Radius increment for indexing
     RbtDouble maxError = GetMaxError();

src/lib/RbtBaseIdxSF.cxx

@@ -39,59 +39,6 @@ RbtDouble RbtBaseIdxSF::GetBorder() const { return m_border; }
 
 void RbtBaseIdxSF::SetBorder(RbtDouble border) { SetParameter(_BORDER, border); }
 
-// DM 10 Apr 2002
-// I know, I know, grids should be templated to avoid the need for two different CreateGrid methods...
-RbtInteractionGridPtr RbtBaseIdxSF::CreateInteractionGrid() const {
-    // Create a grid covering the docking site
-    RbtDockingSitePtr spDS = GetWorkSpace()->GetDockingSite();
-    if (spDS.Null()) return RbtInteractionGridPtr();
-
-    // Extend grid by _BORDER, mainly to allow for the possibility of polar hydrogens
-    // falling outside of the docking site
-    RbtCoord minCoord = spDS->GetMinCoord() - m_border;
-    RbtCoord maxCoord = spDS->GetMaxCoord() + m_border;
-    RbtVector recepExtent = maxCoord - minCoord;
-    RbtVector gridStep(m_gridStep, m_gridStep, m_gridStep);
-    RbtUInt nX = int(recepExtent.x / gridStep.x) + 1;
-    RbtUInt nY = int(recepExtent.y / gridStep.y) + 1;
-    RbtUInt nZ = int(recepExtent.z / gridStep.z) + 1;
-    return RbtInteractionGridPtr(new RbtInteractionGrid(minCoord, gridStep, nX, nY, nZ));
-}
-
-RbtNonBondedGridPtr RbtBaseIdxSF::CreateNonBondedGrid() const {
-    // Create a grid covering the docking site
-    RbtDockingSitePtr spDS = GetWorkSpace()->GetDockingSite();
-    if (spDS.Null()) return RbtInteractionGridPtr();
-
-    // Extend grid by _BORDER, mainly to allow for the possibility of polar hydrogens
-    // falling outside of the docking site
-    RbtCoord minCoord = spDS->GetMinCoord() - m_border;
-    RbtCoord maxCoord = spDS->GetMaxCoord() + m_border;
-    RbtVector recepExtent = maxCoord - minCoord;
-    RbtVector gridStep(m_gridStep, m_gridStep, m_gridStep);
-    RbtUInt nX = int(recepExtent.x / gridStep.x) + 1;
-    RbtUInt nY = int(recepExtent.y / gridStep.y) + 1;
-    RbtUInt nZ = int(recepExtent.z / gridStep.z) + 1;
-    return RbtNonBondedGridPtr(new RbtNonBondedGrid(minCoord, gridStep, nX, nY, nZ));
-}
-
-RbtNonBondedHHSGridPtr RbtBaseIdxSF::CreateNonBondedHHSGrid() const {
-    // Create a grid covering the docking site
-    RbtDockingSitePtr spDS = GetWorkSpace()->GetDockingSite();
-    if (spDS.Null()) return RbtNonBondedHHSGridPtr();
-
-    // Extend grid by _BORDER, mainly to allow for the possibility of polar hydrogens
-    // falling outside of the docking site
-    RbtCoord minCoord = spDS->GetMinCoord() - m_border;
-    RbtCoord maxCoord = spDS->GetMaxCoord() + m_border;
-    RbtVector recepExtent = maxCoord - minCoord;
-    RbtVector gridStep(m_gridStep, m_gridStep, m_gridStep);
-    RbtUInt nX = int(recepExtent.x / gridStep.x) + 1;
-    RbtUInt nY = int(recepExtent.y / gridStep.y) + 1;
-    RbtUInt nZ = int(recepExtent.z / gridStep.z) + 1;
-    return RbtNonBondedHHSGridPtr(new RbtNonBondedHHSGrid(minCoord, gridStep, nX, nY, nZ));
-}
-
 RbtDouble RbtBaseIdxSF::GetMaxError() const {
     // maxError is half a grid diagonal. This is the tolerance we have to allow when indexing the receptor atoms on the
     // grid When retrieving the nearest neighbours to a ligand atom, we do the lookup on the nearest grid point to the

src/lib/RbtNmrSF.cxx

@@ -48,7 +48,7 @@ void RbtNmrSF::SetupReceptor() {
     RbtInt iTrace = GetTrace();
 
     // Create indexed grid for STD restraints penalty function
-    m_spGrid = CreateNonBondedGrid();
+    m_spGrid = CreateGrid<RbtNonBondedGrid>();
     // Fixed distance range used for indexing the relevant receptor atoms
     RbtDouble range = GetRange() + GetMaxError();
     RbtDockingSitePtr spDS = GetWorkSpace()->GetDockingSite();

src/lib/RbtPMFIdxSF.cxx

@@ -172,7 +172,7 @@ void RbtPMFIdxSF::SetupReceptor() {
         cout << _CT << "WARNING: no receptor defined. " << endl;
         return;
     } else {  // load PMFs from table files
-        theSurround = CreateNonBondedGrid();
+        theSurround = CreateGrid<RbtNonBondedGrid>();
         RbtDockingSitePtr spDS = GetWorkSpace()->GetDockingSite();
         RbtDouble range = GetRange() + GetMaxError();
         RbtAtomList atomList = spDS->GetAtomList(GetReceptor()->GetAtomList(), 0.0, GetCorrectedRange());

src/lib/RbtPolarIdxSF.cxx

@@ -109,9 +109,9 @@ void RbtPolarIdxSF::SetupReceptor() {
     RbtInt nCoords = GetReceptor()->GetNumSavedCoords() - 1;
     if (nCoords > 0) {
         RbtAtomList atomList = GetReceptor()->GetAtomList();
-        m_spPosGrid = CreateInteractionGrid();
+        m_spPosGrid = CreateGrid<RbtInteractionGrid>();
         m_recepPosList = CreateDonorInteractionCenters(atomList);
-        m_spNegGrid = CreateInteractionGrid();
+        m_spNegGrid = CreateGrid<RbtInteractionGrid>();
         m_recepNegList = CreateAcceptorInteractionCenters(atomList);
         for (RbtInt i = 1; i <= nCoords; i++) {
             if (iTrace > 0) {
@@ -133,8 +133,8 @@ void RbtPolarIdxSF::SetupReceptor() {
         }
     } else {
         RbtAtomList atomList = spDS->GetAtomList(GetReceptor()->GetAtomList(), 0.0, GetCorrectedRange());
-        m_spPosGrid = CreateInteractionGrid();
-        m_spNegGrid = CreateInteractionGrid();
+        m_spPosGrid = CreateGrid<RbtInteractionGrid>();
+        m_spNegGrid = CreateGrid<RbtInteractionGrid>();
         m_recepPosList = CreateDonorInteractionCenters(atomList);
         m_recepNegList = CreateAcceptorInteractionCenters(atomList);
 

src/lib/RbtPsfFileSink.cxx

@@ -117,7 +117,6 @@ void RbtPsfFileSink::Render() {
             bIter++;
             ostr << setw(8) << (*bIter)->GetAtom1Ptr()->GetAtomId() << setw(8) << (*bIter)->GetAtom2Ptr()->GetAtomId();
             bIter++;
-            ostr;
             AddLine(ostr.str());
         }
         // Remaining bonds on final incomplete line
@@ -127,7 +126,6 @@ void RbtPsfFileSink::Render() {
                 ostr << setw(8) << (*bIter)->GetAtom1Ptr()->GetAtomId() << setw(8)
                      << (*bIter)->GetAtom2Ptr()->GetAtomId();
             }
-            ostr;
             AddLine(ostr.str());
         }
 

src/lib/RbtSAIdxSF.cxx

@@ -66,7 +66,7 @@ void RbtSAIdxSF::SetupReceptor() {
     // and that they don't move very far (up to 2A)
     m_bFlexRec = GetReceptor()->isFlexible();
     RbtDouble flexDist = 2.0;
-    theIdxGrid = CreateNonBondedHHSGrid();
+    theIdxGrid = CreateGrid<RbtNonBondedHHSGrid>();
     RbtDouble idxIncr = GetParameter(_INCR).Double() + GetMaxError();
     RbtDouble flexIncr = idxIncr + flexDist;
 

src/lib/RbtVdwIdxSF.cxx

@@ -109,7 +109,7 @@ void RbtVdwIdxSF::SetupReceptor() {
     m_bFlexRec = GetReceptor()->isFlexible();
 
     m_recAtomList = GetReceptor()->GetAtomList();
-    m_spGrid = CreateNonBondedGrid();
+    m_spGrid = CreateGrid<RbtNonBondedGrid>();
     RbtDouble maxError = GetMaxError();
     RbtDouble flexDist = 2.0;
     RbtDockingSitePtr spDS = GetWorkSpace()->GetDockingSite();
@@ -242,7 +242,7 @@ void RbtVdwIdxSF::SetupSolvent() {
     // The interaction map can be partitioned in advance, based on the maximum displacement
     // of any of the tethered atoms
     if (!m_solventFixTethAtomList.empty()) {
-        m_spSolventGrid = CreateNonBondedGrid();
+        m_spSolventGrid = CreateGrid<RbtNonBondedGrid>();
         RbtDouble maxError = GetMaxError();
         RbtDouble maxFlexDist = 0.0;
         for (RbtAtomRListConstIter iter = m_solventFixTethAtomList.begin(); iter != m_solventFixTethAtomList.end();