- Stagify

- Fix build

8 files changed, 124 insertions, 3 deletions

diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile
index 6654c2a53793..959ddb6f4669 100644
--- a/biology/protomol/Makefile
+++ b/biology/protomol/Makefile
@@ -30,7 +30,6 @@ WRKSRC=		${WRKDIR}/${PORTNAME}
 OPTIONS_DEFINE=	GLUT
 OPTIONS_DEFAULT=	GLUT
 
-NO_STAGE=	yes
 .include <bsd.port.options.mk>
 
 .if ${PORT_OPTIONS:MGLUT}
@@ -42,9 +41,9 @@ CONFIGURE_ARGS+=	--with-glut=no
 
 .if ${PORT_OPTIONS:MEXAMPLES}
 post-install:
-	@${MKDIR} ${EXAMPLESDIR}
+	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	cd ${WRKSRC}/examples && ${FIND} . | ${EGREP} -v '\.cvsignore' | \
-		${CPIO} -pdmu -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
+		${CPIO} -pdmu -R ${SHAREOWN}:${SHAREGRP} ${STAGEDIR}${EXAMPLESDIR}
 .endif
 
 .include <bsd.port.mk>
diff --git a/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGDihedralSystemForce.h b/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGDihedralSystemForce.h
new file mode 100644
index 000000000000..8366cef4e66f
--- /dev/null
+++ b/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGDihedralSystemForce.h
@@ -0,0 +1,20 @@
+--- applications/iSGProtomol-app/forces/iSGDihedralSystemForce.h.orig	2005-05-07 18:40:20.000000000 +0400
++++ applications/iSGProtomol-app/forces/iSGDihedralSystemForce.h	2014-08-22 20:49:51.000000000 +0400
+@@ -71,7 +71,7 @@
+       (dynamic_cast<const SemiGenericTopology<TBoundaryConditions>& >(*topo)).boundaryConditions;
+ 
+     for (unsigned int i = 0; i < topo->dihedrals.size(); i++) 
+-      calcTorsion(boundary,topo->dihedrals[i], positions, forces,
++      this->calcTorsion(boundary,topo->dihedrals[i], positions, forces,
+       (*energies)[ScalarStructure::DIHEDRAL],
+       (*energies)[ScalarStructure::DIHEDRAL_DELTAMU],
+       energies);
+@@ -95,7 +95,7 @@
+ 	  to = n;
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++)
+-	  calcTorsion(boundary, topo->dihedrals[j], positions, forces,
++	  this->calcTorsion(boundary, topo->dihedrals[j], positions, forces,
+           (*energies)[ScalarStructure::DIHEDRAL],
+           (*energies)[ScalarStructure::DIHEDRAL_DELTAMU],
+           energies);
diff --git a/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGImproperSystemForce.h b/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGImproperSystemForce.h
new file mode 100644
index 000000000000..5280623c79e2
--- /dev/null
+++ b/biology/protomol/files/patch-applications__iSGProtomol-app__forces__iSGImproperSystemForce.h
@@ -0,0 +1,20 @@
+--- applications/iSGProtomol-app/forces/iSGImproperSystemForce.h.orig	2005-05-07 18:40:20.000000000 +0400
++++ applications/iSGProtomol-app/forces/iSGImproperSystemForce.h	2014-08-22 20:50:15.000000000 +0400
+@@ -67,7 +67,7 @@
+     const TBoundaryConditions &boundary = 
+       (dynamic_cast<const SemiGenericTopology<TBoundaryConditions>& >(*topo)).boundaryConditions;
+     for (unsigned int i = 0; i < topo->impropers.size(); i++)
+-      calcTorsion(boundary,topo->impropers[i], positions, forces,
++      this->calcTorsion(boundary,topo->impropers[i], positions, forces,
+       (*energies)[ScalarStructure::IMPROPER],
+       (*energies)[ScalarStructure::IMPROPER_DELTAMU],
+       energies);
+@@ -91,7 +91,7 @@
+ 	  to = n;
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++)
+-	  calcTorsion(boundary, topo->impropers[j], positions, forces,
++	  this->calcTorsion(boundary, topo->impropers[j], positions, forces,
+           (*energies)[ScalarStructure::IMPROPER],
+           (*energies)[ScalarStructure::IMPROPER_DELTAMU],
+           energies);
diff --git a/biology/protomol/files/patch-framework__forces__DihedralSystemForce.h b/biology/protomol/files/patch-framework__forces__DihedralSystemForce.h
new file mode 100644
index 000000000000..7dfa5a39e731
--- /dev/null
+++ b/biology/protomol/files/patch-framework__forces__DihedralSystemForce.h
@@ -0,0 +1,20 @@
+--- framework/forces/DihedralSystemForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/DihedralSystemForce.h	2014-08-22 20:41:24.000000000 +0400
+@@ -72,7 +72,7 @@
+     const TBoundaryConditions &boundary = 
+       (dynamic_cast<const SemiGenericTopology<TBoundaryConditions>& >(*topo)).boundaryConditions;
+     for (unsigned int i = 0; i < topo->dihedrals.size(); i++) 
+-      calcTorsion(boundary,topo->dihedrals[i], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
++      this->calcTorsion(boundary,topo->dihedrals[i], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
+   }
+   template<class TBoundaryConditions> 
+   inline void DihedralSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* topo,
+@@ -93,7 +93,7 @@
+ 	  to = n;
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++)
+-	  calcTorsion(boundary, topo->dihedrals[j], positions, forces, (*energies)[ScalarStructure::DIHEDRAL],energies);
++	  this->calcTorsion(boundary, topo->dihedrals[j], positions, forces, (*energies)[ScalarStructure::DIHEDRAL],energies);
+       }
+     }
+   }
diff --git a/biology/protomol/files/patch-framework__forces__HarmDihedralSystemForce.h b/biology/protomol/files/patch-framework__forces__HarmDihedralSystemForce.h
new file mode 100644
index 000000000000..73f842f29728
--- /dev/null
+++ b/biology/protomol/files/patch-framework__forces__HarmDihedralSystemForce.h
@@ -0,0 +1,20 @@
+--- framework/forces/HarmDihedralSystemForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/HarmDihedralSystemForce.h	2014-08-22 20:42:13.000000000 +0400
+@@ -119,7 +119,7 @@
+       {
+ 	if (static_cast<int>(i) != myDihedral) {
+ 	  if(computeOthers) {
+-	    calcTorsion(boundary,topo->dihedrals[i], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
++	    this->calcTorsion(boundary,topo->dihedrals[i], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
+ 	  }
+ 	}
+ 	else {
+@@ -149,7 +149,7 @@
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++){
+ 	  if (j != myDihedral) {
+-	    calcTorsion(boundary,topo->dihedrals[j], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
++	    this->calcTorsion(boundary,topo->dihedrals[j], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
+ 	  }
+ 	  else {
+ 	    harmCalcTorsion(topo,boundary,topo->dihedrals[j], positions, forces,(*energies)[ScalarStructure::DIHEDRAL],energies);
diff --git a/biology/protomol/files/patch-framework__forces__ImproperSystemForce.h b/biology/protomol/files/patch-framework__forces__ImproperSystemForce.h
new file mode 100644
index 000000000000..907ade97189e
--- /dev/null
+++ b/biology/protomol/files/patch-framework__forces__ImproperSystemForce.h
@@ -0,0 +1,20 @@
+--- framework/forces/ImproperSystemForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/ImproperSystemForce.h	2014-08-22 20:52:46.000000000 +0400
+@@ -69,7 +69,7 @@
+     const TBoundaryConditions &boundary = 
+       (dynamic_cast<const SemiGenericTopology<TBoundaryConditions>& >(*topo)).boundaryConditions;
+     for (unsigned int i = 0; i < topo->impropers.size(); i++)
+-      calcTorsion(boundary,topo->impropers[i], positions, forces, (*energies)[ScalarStructure::IMPROPER],energies);
++      this->calcTorsion(boundary,topo->impropers[i], positions, forces, (*energies)[ScalarStructure::IMPROPER],energies);
+   }
+   template<class TBoundaryConditions> 
+   inline void ImproperSystemForce<TBoundaryConditions>::parallelEvaluate(const GenericTopology* topo,
+@@ -90,7 +90,7 @@
+ 	  to = n;
+ 	int from = (n*i)/count;
+ 	for (int j = from; j < to; j++)
+-	  calcTorsion(boundary, topo->impropers[j], positions, forces, (*energies)[ScalarStructure::IMPROPER],energies);
++	  this->calcTorsion(boundary, topo->impropers[j], positions, forces, (*energies)[ScalarStructure::IMPROPER],energies);
+       }
+     }
+   }
diff --git a/biology/protomol/files/patch-framework__forces__NonbondedCutoffMollyForce.h b/biology/protomol/files/patch-framework__forces__NonbondedCutoffMollyForce.h
new file mode 100644
index 000000000000..ef782ed94635
--- /dev/null
+++ b/biology/protomol/files/patch-framework__forces__NonbondedCutoffMollyForce.h
@@ -0,0 +1,11 @@
+--- framework/forces/NonbondedCutoffMollyForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/NonbondedCutoffMollyForce.h	2014-08-22 20:42:42.000000000 +0400
+@@ -70,7 +70,7 @@
+     this->enumerator.initialize(realTopo, this->myCutoff);
+ 
+     unsigned int n = realTopo->cellLists.size();
+-    unsigned int count = numberOfBlocks(realTopo,positions);
++    unsigned int count = this->numberOfBlocks(realTopo,positions);
+ 
+     for(unsigned int i = 0;i<count;i++){
+       unsigned int l = (n*(i+1))/count - (n*i)/count;
diff --git a/biology/protomol/files/patch-framework__forces__NonbondedCutoffSystemForce.h b/biology/protomol/files/patch-framework__forces__NonbondedCutoffSystemForce.h
new file mode 100644
index 000000000000..3868f719e668
--- /dev/null
+++ b/biology/protomol/files/patch-framework__forces__NonbondedCutoffSystemForce.h
@@ -0,0 +1,11 @@
+--- framework/forces/NonbondedCutoffSystemForce.h.orig	2005-05-07 18:40:24.000000000 +0400
++++ framework/forces/NonbondedCutoffSystemForce.h	2014-08-22 20:39:47.000000000 +0400
+@@ -76,7 +76,7 @@
+     this->enumerator.initialize(realTopo, this->myCutoff);
+ 
+     unsigned int n = realTopo->cellLists.size();
+-    unsigned int count = numberOfBlocks(realTopo,positions);
++    unsigned int count = this->numberOfBlocks(realTopo,positions);
+ 
+     for(unsigned int i = 0;i<count;i++){
+       unsigned int l = (n*(i+1))/count - (n*i)/count;