- update to 0.8.2

- take maintainership
Approved by:	maintainer

9 files changed, 205 insertions, 456 deletions

diff --git a/biology/adun/Makefile b/biology/adun/Makefile
index 14e889492e17..23c364e64767 100644
--- a/biology/adun/Makefile
+++ b/biology/adun/Makefile
@@ -6,13 +6,12 @@
 #
 
 PORTNAME=	adun
-PORTVERSION=	0.6
-PORTREVISION=	3
+PORTVERSION=	0.8.2
 CATEGORIES=	biology gnustep
 MASTER_SITES=	http://download.gna.org/adun/
-DISTNAME=	Adun${PORTVERSION}
+DISTNAME=	Adun-${PORTVERSION}
 
-MAINTAINER=	gurkan@phys.ethz.ch
+MAINTAINER=	dinoex@FreeBSD.org
 COMMENT=	Molecular Simulator for GNUstep
 
 LIB_DEPENDS+=	gsl.12:${PORTSDIR}/math/gsl
@@ -24,22 +23,34 @@ USE_GNUSTEP_BUILD=	yes
 USE_GNUSTEP_INSTALL=	yes
 USE_GNUSTEP_LDCONFIG=	${GNUSTEP_LOCAL_LIBRARIES}
 
-WRKSRC=		${WRKDIR}/Adun
-DEFAULT_LIBVERSION2=	0.0
+DEFAULT_LIBVERSION2=	0.11
+DEFAULT_LIBVERSION3=	3.0.1
+DEFAULT_LIBVERSION4=	0.6
+DEFAULT_LIBVERSION5=	0.1
 PLIST_SUB+=	LIBVERSION2=${DEFAULT_LIBVERSION2}
 PLIST_SUB+=	MAJORLIBVERSION2=${DEFAULT_LIBVERSION2:C/([0-9]).*/\1/1}
+PLIST_SUB+=	LIBVERSION3=${DEFAULT_LIBVERSION3}
+PLIST_SUB+=	MAJORLIBVERSION3=${DEFAULT_LIBVERSION3:C/([0-9]).*/\1/1}
+PLIST_SUB+=	LIBVERSION4=${DEFAULT_LIBVERSION4}
+PLIST_SUB+=	MAJORLIBVERSION4=${DEFAULT_LIBVERSION4:C/([0-9]).*/\1/1}
+PLIST_SUB+=	LIBVERSION5=${DEFAULT_LIBVERSION5}
+PLIST_SUB+=	MAJORLIBVERSION5=${DEFAULT_LIBVERSION5:C/([0-9]).*/\1/1}
+ADDITIONAL_CFLAGS=	-D__FREEBSD__
+ADDITIONAL_OBJCFLAGS=	-D__FREEBSD__
 
 post-patch:
-	${REINPLACE_CMD} -e 's|include Defs/|-include Defs/|' \
-		${WRKSRC}/MolTalk/GNUmakefile.preamble
-	${REINPLACE_CMD} -e 's|^GNUSTEP_INSTALLATION_DIR|#GNUSTEP_INSTALLATION_DIR|' \
+	${REINPLACE_CMD} -e 's|^GNUSTEP_INSTALLATION_DOMAIN|#GNUSTEP_INSTALLATION_DOMAIN|' \
+		${WRKSRC}/GNUmakefile \
 		${WRKSRC}/Tools/GNUmakefile \
 		${WRKSRC}/Tools/ResultsConverter/GNUmakefile \
 		${WRKSRC}/MolTalk/GNUmakefile.preamble \
 		${WRKSRC}/Kernel/GNUmakefile \
 		${WRKSRC}/Kernel/AdunKernel/GNUmakefile \
 		${WRKSRC}/UL/GNUmakefile \
-		${WRKSRC}/UL/AdunServer/GNUmakefile
+		${WRKSRC}/UL/AdunServer/GNUmakefile \
+		${WRKSRC}/UL/ULFramework/GNUmakefile
+	${REINPLACE_CMD} -e 's|GNUSTEP_HOME./..GNUSTEP_USER_DIR_TOOLS|GNUSTEP_LOCAL_TOOLS|' \
+		${WRKSRC}/GNUmakefile.postamble
 
 .include <bsd.port.pre.mk>
 
diff --git a/biology/adun/distinfo b/biology/adun/distinfo
index 8258acfa9228..723528cd81fc 100644
--- a/biology/adun/distinfo
+++ b/biology/adun/distinfo
@@ -1,3 +1,3 @@
-MD5 (Adun0.6.tar.gz) = 34e35b5314095cef93fc17d40a7701a5
-SHA256 (Adun0.6.tar.gz) = 94acf265be17b86368e2d8c62cd2872e90a8d953ac520756af3272d2593e1203
-SIZE (Adun0.6.tar.gz) = 781286
+MD5 (Adun-0.8.2.tar.gz) = 7b6866bcce8632c849043105213be591
+SHA256 (Adun-0.8.2.tar.gz) = 7086a8adab7e4716683fa6a02ac70b7da705a9862a40fbcdb2ac5d110f045898
+SIZE (Adun-0.8.2.tar.gz) = 998386
diff --git a/biology/adun/files/patch-AdLinkedList.h b/biology/adun/files/patch-AdLinkedList.h
new file mode 100644
index 000000000000..62ce6dcba44f
--- /dev/null
+++ b/biology/adun/files/patch-AdLinkedList.h
@@ -0,0 +1,12 @@
+--- Kernel/Base/AdLinkedList.h.orig	2006-11-02 14:42:45.000000000 +0100
++++ Kernel/Base/AdLinkedList.h	2008-04-29 09:14:45.000000000 +0200
+@@ -25,6 +25,9 @@
+ 
+ #include <stdio.h>
+ #include <stdlib.h>
++#ifdef __FreeBSD__
++#include <sys/types.h>
++#endif
+ 
+ //! \brief Element for the linked lists.
+ /**
diff --git a/biology/adun/files/patch-AdunLinkedList.m b/biology/adun/files/patch-AdunLinkedList.m
deleted file mode 100644
index 165fbbf6fcb0..000000000000
--- a/biology/adun/files/patch-AdunLinkedList.m
+++ /dev/null
@@ -1,14 +0,0 @@
---- Kernel/AdunKernel/Framework/AdunLinkedList.m.orig	Tue Jun 13 12:16:44 2006
-+++ Kernel/AdunKernel/Framework/AdunLinkedList.m	Sun Nov  5 13:34:01 2006
-@@ -109,7 +109,11 @@
- 	NSDebugLLog(@"AdListMemoryManagement", @"Creating New Block - There are now %d blocks", block_no);
- 	//On 64 bit machines we should align on a 64 bit boundary
- 
-+#ifndef __FreeBSD__
- 	posix_memalign((void**)&listPointer, 32, BLOCKSIZE*sizeof(ListElement));
-+#else
-+	listPointer = malloc(BLOCKSIZE*sizeof(ListElement));
-+#endif
- 	blocks[block_no-1] = listPointer;
- 
- 	return blocks[block_no-1];
diff --git a/biology/adun/files/patch-AdunMemoryManager.h b/biology/adun/files/patch-AdunMemoryManager.h
deleted file mode 100644
index e88031346f82..000000000000
--- a/biology/adun/files/patch-AdunMemoryManager.h
+++ /dev/null
@@ -1,22 +0,0 @@
---- Kernel/AdunKernel/Headers/AdunKernel/AdunMemoryManager.h.orig	Tue Jun 13 12:16:44 2006
-+++ Kernel/AdunKernel/Headers/AdunKernel/AdunMemoryManager.h	Sun Nov  5 13:16:58 2006
-@@ -24,7 +24,9 @@
- #define _ADUNIOMANAGER_
- 
- #include <stdlib.h>
-+#ifndef __FreeBSD__
- #include <malloc.h>
-+#endif
- #include "Base/InterTable.h"
- #include "AdunKernel/AdunDefinitions.h"
- #include "AdunKernel/AdunObject.h"
-@@ -38,7 +40,9 @@
- 
- @interface AdMemoryManager: AdObject 
- {
-+#ifndef __FreeBSD__
- 	struct mallinfo mem_struct;
-+#endif
- 	BOOL MEMORY_STATS;
- }
- 
diff --git a/biology/adun/files/patch-AdunMemoryManager.m b/biology/adun/files/patch-AdunMemoryManager.m
deleted file mode 100644
index c1d7235482b7..000000000000
--- a/biology/adun/files/patch-AdunMemoryManager.m
+++ /dev/null
@@ -1,266 +0,0 @@
---- Kernel/AdunKernel/Framework/AdunMemoryManager.m.orig	Tue Jun 13 12:16:44 2006
-+++ Kernel/AdunKernel/Framework/AdunMemoryManager.m	Sun Nov  5 13:15:25 2006
-@@ -68,6 +68,7 @@
- 	NSError* error;
- 	NSMutableDictionary* errorDict;
- 
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -77,6 +78,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	//The return value of malloc(0) is implementation dependant
- 	//It can return NULL in which case it is indistinguisable from
-@@ -133,6 +135,7 @@
- 	
- 	memset(array, 0, size);
- 	
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -143,6 +146,7 @@
- 			mem_struct.fordblks); 
- 		fflush(stderr);
- 	}
-+#endif
- 
- 
- 	return array;
-@@ -154,6 +158,7 @@
- 	double *array;
- 	AdMatrix *matrix;
- 
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -163,6 +168,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	matrix = (AdMatrix*)malloc(sizeof(AdMatrix));
- 	matrix->no_rows = no_rows;
-@@ -172,6 +178,7 @@
- 	for(i=0, j=0; i < no_rows; i++, j = j + no_columns)
- 			matrix->matrix[i] = array + j;
- 
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -181,6 +188,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON,
- 		 	mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	return matrix;
- }
-@@ -191,6 +199,7 @@
- 	int *array;
- 	IntMatrix *matrix;
- 
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -200,6 +209,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	matrix = (IntMatrix*)malloc(sizeof(IntMatrix));
- 	matrix->no_rows = no_rows;
-@@ -209,6 +219,7 @@
- 	for(i=0, j=0; i < no_rows; i++, j = j + no_columns)
- 			matrix->matrix[i] = array + j;
- 
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -220,6 +231,7 @@
- 	}
- 
- 	return matrix;
-+#endif
- }
- 
- - (InterTable*) allocateInterTableWithRows: (int) no_rows withColumns: (int) no_columns
-@@ -228,6 +240,7 @@
- 	double *array;
- 	InterTable *table;
- 	
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -237,6 +250,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON,
- 			 mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	table = (InterTable*)malloc(sizeof(InterTable));
- 	table->no_interactions = no_rows;
-@@ -248,6 +262,7 @@
- 	for(i=0, j=0; i < no_rows; i++, j = j + no_columns)
- 			table->table[i] = array + j;
- 	
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -257,12 +272,14 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	return table;
- }
- 
- - (void) freeArray: (void*)array
- {	
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -272,9 +289,11 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	free(array);
- 
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -284,6 +303,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- }
- 
- /** Do not use this method to free matrices not allocated by one of the
-@@ -297,6 +317,7 @@
- 	free(matrix[0]); 	//frees the number array	
- 	free(matrix);		//frees the index array	
- 
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -306,6 +327,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- }
- 
-@@ -313,6 +335,7 @@
- {
- 	//matrices are allocated as arrays
- 	//with another array of indexes
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -322,6 +345,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	if(matrix->no_rows != 0)
- 	{
-@@ -330,6 +354,7 @@
- 	}
- 	free(matrix);
- 	
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -339,10 +364,12 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- }
- 
- - (void) freeIntMatrix: (IntMatrix*) matrix 
- {
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -352,6 +379,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	if(matrix->no_rows != 0)
- 	{
-@@ -360,6 +388,7 @@
- 	}
- 	free(matrix);
- 	
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -369,6 +398,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- }
- 
- - (void) freeInterTable: (InterTable*) matrix  
-@@ -376,6 +406,7 @@
- 	//matrices are allocated as arrays
- 	//with another array of indexes
- 	
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -385,6 +416,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- 
- 	if(matrix->no_interactions != 0)
- 	{
-@@ -394,6 +426,7 @@
- 
- 	free(matrix);
- 	
-+#ifndef __FreeBSD__
- 	if(MEMORY_STATS==YES)
- 	{
- 		mem_struct = mallinfo();
-@@ -403,6 +436,7 @@
- 			(float)mem_struct.uordblks/(float)MEM_CON, 
- 			mem_struct.fordblks); 
- 	}
-+#endif
- }
- 
- @end
diff --git a/biology/adun/files/patch-GNUmakefile b/biology/adun/files/patch-GNUmakefile
deleted file mode 100644
index e9ab0c8dc869..000000000000
--- a/biology/adun/files/patch-GNUmakefile
+++ /dev/null
@@ -1,17 +0,0 @@
---- GNUmakefile.orig	Tue Apr  4 18:23:24 2006
-+++ GNUmakefile	Sun Nov  5 13:56:03 2006
-@@ -2,12 +2,12 @@
- include $(GNUSTEP_MAKEFILES)/common.make
- 
- SUBPROJECTS =  Kernel/ MolTalk/ UL/ 
--GNUSTEP_INSTALLATION_DIR=$(HOME)/GNUstep
-+#GNUSTEP_INSTALLATION_DIR=$(HOME)/GNUstep
- 
- #Rpm
- 
- PACKAGE_NAME=Adun
--PACKAGE_VERSION=0.5
-+PACKAGE_VERSION=0.6
- 
- -include GNUmakefile.preamble
- 
diff --git a/biology/adun/files/patch-main.m b/biology/adun/files/patch-main.m
deleted file mode 100644
index fff8726b3ebb..000000000000
--- a/biology/adun/files/patch-main.m
+++ /dev/null
@@ -1,23 +0,0 @@
---- Kernel/main.m.orig	Mon Aug  7 12:17:30 2006
-+++ Kernel/main.m	Sun Nov  5 13:27:26 2006
-@@ -3,7 +3,9 @@
- #include <stdio.h>
- #include <float.h>
- #include <fenv.h>
-+#ifndef __FreeBSD__
- #include <mcheck.h>
-+#endif
- #include "AdunKernel/AdunKernel.h"
- 
- /** \mainpage
-@@ -250,8 +252,10 @@
- 
- 	if([[NSUserDefaults standardUserDefaults] boolForKey: @"TraceMemory"] == YES)
- 	{
-+#ifndef __FreeBSD__
- 		mtrace();
- 		mcheck(NULL);
-+#endif
- 	}
- 
- 	logFile = [[NSUserDefaults standardUserDefaults] stringForKey: @"LogFile"];
diff --git a/biology/adun/pkg-plist b/biology/adun/pkg-plist
index 802fdf626b2e..8afd76cf6267 100644
--- a/biology/adun/pkg-plist
+++ b/biology/adun/pkg-plist
@@ -1,5 +1,18 @@
-Local/Applications/UL.app/Resources/EnzymixParameters.ffml
-Local/Applications/UL.app/Resources/EnzymixTopology.ffml
+Local/Applications/UL.app/Resources/Converter.gorm/classes.nib
+Local/Applications/UL.app/Resources/Converter.gorm/data.classes
+Local/Applications/UL.app/Resources/Converter.gorm/data.info
+Local/Applications/UL.app/Resources/Converter.gorm/info.nib
+Local/Applications/UL.app/Resources/Converter.gorm/keyedobjects.nib
+Local/Applications/UL.app/Resources/Converter.gorm/objects.gorm
+Local/Applications/UL.app/Resources/DatabasePanel.gorm/classes.nib
+Local/Applications/UL.app/Resources/DatabasePanel.gorm/data.classes
+Local/Applications/UL.app/Resources/DatabasePanel.gorm/data.info
+Local/Applications/UL.app/Resources/DatabasePanel.gorm/info.nib
+Local/Applications/UL.app/Resources/DatabasePanel.gorm/keyedobjects.nib
+Local/Applications/UL.app/Resources/DatabasePanel.gorm/objects.gorm
+Local/Applications/UL.app/Resources/ExportPanel.gorm/data.classes
+Local/Applications/UL.app/Resources/ExportPanel.gorm/data.info
+Local/Applications/UL.app/Resources/ExportPanel.gorm/objects.gorm
 Local/Applications/UL.app/Resources/H2O.pdb
 Local/Applications/UL.app/Resources/Info-gnustep.plist
 Local/Applications/UL.app/Resources/Options.gorm/data.classes
@@ -8,8 +21,11 @@ Local/Applications/UL.app/Resources/Options.gorm/objects.gorm
 Local/Applications/UL.app/Resources/Preferences.gorm/data.classes
 Local/Applications/UL.app/Resources/Preferences.gorm/data.info
 Local/Applications/UL.app/Resources/Preferences.gorm/objects.gorm
+Local/Applications/UL.app/Resources/ProgressPanel.gorm/classes.nib
 Local/Applications/UL.app/Resources/ProgressPanel.gorm/data.classes
 Local/Applications/UL.app/Resources/ProgressPanel.gorm/data.info
+Local/Applications/UL.app/Resources/ProgressPanel.gorm/info.nib
+Local/Applications/UL.app/Resources/ProgressPanel.gorm/keyedobjects.nib
 Local/Applications/UL.app/Resources/ProgressPanel.gorm/objects.gorm
 Local/Applications/UL.app/Resources/Results.gorm/data.classes
 Local/Applications/UL.app/Resources/Results.gorm/data.info
@@ -25,12 +41,10 @@ Local/Applications/UL.app/Resources/UL.gorm/data.classes
 Local/Applications/UL.app/Resources/UL.gorm/data.info
 Local/Applications/UL.app/Resources/UL.gorm/objects.gorm
 Local/Applications/UL.app/Resources/apply.png
+Local/Applications/UL.app/Resources/dataset-close.png
 Local/Applications/UL.app/Resources/defaultOptions.plist
 Local/Applications/UL.app/Resources/document-save.png
-Local/Applications/UL.app/Resources/pdbBuilderOptions.plist
-Local/Applications/UL.app/Resources/pdbNameMap.plist
 Local/Applications/UL.app/Resources/reload.png
-Local/Applications/UL.app/Resources/resultsOptions.plist
 Local/Applications/UL.app/Resources/splash.tiff
 Local/Applications/UL.app/UL
 Local/Applications/UL.app/stamp.make
@@ -40,22 +54,24 @@ Local/Library/Frameworks/AdunKernel.framework/Resources
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/AdunKernel
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdCommandInterface.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdController.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdCoreAdditions.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdCoreCommand.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdCreation.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdDataSources.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdDelegation.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdEndSimulationCommand.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdFlushEnergiesCommand.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdForceFieldTerm.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdFrameworkFunctions.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdGridDelegate.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdKeyValueObserving.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdListMemoryManagement.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdReloadCommand.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdIndexSetConversions.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdMatrixModification.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdMemento.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdServerInterface.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdStatusCommand.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdUpdating.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunBondedTopology.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunBoundaryImplementor.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunAmberForceField.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunBerendsenThermostat.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunCellListHandler.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunCharmmForceField.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunConfigurationGenerator.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunContainerDataSource.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunController.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunCore.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDataMatrix.h
@@ -63,101 +79,138 @@ Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Head
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDataSource.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDefinitions.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDynamics.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunEnvironment.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunEllipsoidBox.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunEnzymixForceField.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunFileSystemSimulationStorage.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunForceField.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunForceFieldManager.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunForceFieldTerm.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunForceFieldCollection.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunGRFNonbondedTerm.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunGrid.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunIOManager.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunInteractionSystem.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunKernel.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunLangevinThermostat.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunLinkedList.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunListHandler.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMemoryManager.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMinimiser.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunModelObject.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunNonBondedListHandler.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunNonBondedTopology.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunNonbondedCalculator.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunObject.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunRelationship.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMolecularMechanicsForceField.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMoleculeCavity.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMultithreadedNonbondedTerm.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunNonbondedTerm.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunPureNonbondedTerm.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSCAAS.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunShiftedNonbondedTerm.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSimpleListHandler.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSimulationData.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSimulator.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunState.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSphericalBox.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSystem.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSystemComponent.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSystemNode.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSystemCollection.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunTemplateProcessor.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunTimer.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/CellListHandler.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/EnzymixForceField.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/GRFNonbondedCalculator.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/NewtonianSimulator.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/PureNonBondedCalculator.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/RemoteProcessAccess.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/SCAAS.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/ShiftedNonBondedCalculator.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/SimpleListHandler.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/SphericalBox.h
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/ULIndexSetConversions.h
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Resources/Info-gnustep.plist
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Resources/ScriptingInfo.plist
 Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/libAdunKernel.so
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/libAdunKernel.so.%%MAJORLIBVERSION%%
-Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/libAdunKernel.so.%%LIBVERSION%%
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/libAdunKernel.so.%%MAJORLIBVERSION2%%
+Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/libAdunKernel.so.%%LIBVERSION2%%
 Local/Library/Frameworks/AdunKernel.framework/Versions/Current
 Local/Library/Frameworks/AdunKernel.framework/libAdunKernel.so
+Local/Library/Frameworks/MolTalk.framework/Headers
+Local/Library/Frameworks/MolTalk.framework/MolTalk
+Local/Library/Frameworks/MolTalk.framework/Resources
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTAlPos.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTAtom.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTAtomFactory.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTChain.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTChainFactory.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTCompressedFileStream.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTCoordinates.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTFileStream.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTMatrix.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTMatrix44.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTMatrix53.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTPairwiseSequenceAlignment.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTPairwiseStrxAlignment.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTQuaternion.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTResidue.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTResidueFactory.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTSelection.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTStream.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTString.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTStructure.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTStructureFactory.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTSubstitutionMatrix.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTVector.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MolTalk.h
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/MolTalk
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Resources/Info-gnustep.plist
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Resources/ScriptingInfo.plist
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/libMolTalk.so
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/libMolTalk.so.%%MAJORLIBVERSION3%%
+Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/libMolTalk.so.%%LIBVERSION3%%
+Local/Library/Frameworks/MolTalk.framework/Versions/Current
+Local/Library/Frameworks/MolTalk.framework/libMolTalk.so
+Local/Library/Frameworks/ULFramework.framework/Headers
+Local/Library/Frameworks/ULFramework.framework/Resources
+Local/Library/Frameworks/ULFramework.framework/ULFramework
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/PDBConfigurationBuilder.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULAnalysisManager.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULAnalysisPlugin.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULConfigurationBuilder.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULConfigurationPlugin.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULDatabaseIndex.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULDatabaseInterface.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULDatabaseSimulationIndex.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULFileSystemDatabaseBackend.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULFramework.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULFrameworkDefinitions.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULFrameworkFunctions.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULIOManager.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULInteractionsBuilder.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULMenuExtensions.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULMerger.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULMergerDelegate.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULProcess.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULProcessManager.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULServerInterface.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULSimpleMergerDelegate.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULSystem.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULSystemBuilder.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULSystemController.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULTemplate.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULTopologyFrameBuilder.h
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Amber/AmberParameters.ffml
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Amber/AmberTopology.ffml
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Charmm27/Charmm27Parameters.ffml
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Charmm27/Charmm27Topology.ffml
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Enzymix/EnzymixParameters.ffml
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Enzymix/EnzymixTopology.ffml
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/ForceFields.plist
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/Info-gnustep.plist
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ScriptingInfo.plist
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/Version
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/iupacPdbMap.plist
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/objectTemplates.plist
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/pdbBuilderOptions.plist
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/pdbNameMap.plist
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/ULFramework
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/libULFramework.so
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/libULFramework.so.%%MAJORLIBVERSION4%%
+Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/libULFramework.so.%%LIBVERSION4%%
+Local/Library/Frameworks/ULFramework.framework/Versions/Current
+Local/Library/Frameworks/ULFramework.framework/libULFramework.so
 Local/Library/Headers/AdunKernel
+Local/Library/Headers/Base/AdBaseFunctions.h
 Local/Library/Headers/Base/AdForceFieldFunctions.h
 Local/Library/Headers/Base/AdLinkedList.h
 Local/Library/Headers/Base/AdMatrix.h
 Local/Library/Headers/Base/AdQuaternion.h
 Local/Library/Headers/Base/AdSorter.h
 Local/Library/Headers/Base/AdVector.h
-Local/Library/Headers/Base/InterTable.h
-Local/Library/Headers/MolTalk/Atom.oh
-Local/Library/Headers/MolTalk/Chain.oh
-Local/Library/Headers/MolTalk/ChainFactory.oh
-Local/Library/Headers/MolTalk/CompressedFileStream.oh
-Local/Library/Headers/MolTalk/Coordinates.oh
-Local/Library/Headers/MolTalk/FileStream.oh
-Local/Library/Headers/MolTalk/Matrix.oh
-Local/Library/Headers/MolTalk/Matrix44.oh
-Local/Library/Headers/MolTalk/Matrix53.oh
-Local/Library/Headers/MolTalk/MolTalk.oh
-Local/Library/Headers/MolTalk/PairwiseStrxAlignment.oh
-Local/Library/Headers/MolTalk/Residue.oh
-Local/Library/Headers/MolTalk/ResidueFactory.oh
-Local/Library/Headers/MolTalk/Selection.oh
-Local/Library/Headers/MolTalk/Stream.oh
-Local/Library/Headers/MolTalk/String.oh
-Local/Library/Headers/MolTalk/Structure.oh
-Local/Library/Headers/MolTalk/StructureFactory.oh
-Local/Library/Headers/MolTalk/Vector.oh
-Local/Library/Headers/ULFramework/PDBConfigurationBuilder.h
-Local/Library/Headers/ULFramework/ULAnalysisManager.h
-Local/Library/Headers/ULFramework/ULAnalysisPlugin.h
-Local/Library/Headers/ULFramework/ULConfigurationBuilder.h
-Local/Library/Headers/ULFramework/ULConfigurationPlugin.h
-Local/Library/Headers/ULFramework/ULDatabaseIndex.h
-Local/Library/Headers/ULFramework/ULDatabaseInterface.h
-Local/Library/Headers/ULFramework/ULDatabaseSimulationIndex.h
-Local/Library/Headers/ULFramework/ULFileSystemDatabaseBackend.h
-Local/Library/Headers/ULFramework/ULFileSystemSimulationStorage.h
-Local/Library/Headers/ULFramework/ULIOManager.h
-Local/Library/Headers/ULFramework/ULIndexSetConversions.h
-Local/Library/Headers/ULFramework/ULInteractionsBuilder.h
-Local/Library/Headers/ULFramework/ULMatrix.h
-Local/Library/Headers/ULFramework/ULMerger.h
-Local/Library/Headers/ULFramework/ULMergerDelegate.h
-Local/Library/Headers/ULFramework/ULModelController.h
-Local/Library/Headers/ULFramework/ULOptions.h
-Local/Library/Headers/ULFramework/ULOptionsController.h
-Local/Library/Headers/ULFramework/ULProcess.h
-Local/Library/Headers/ULFramework/ULProcessManager.h
-Local/Library/Headers/ULFramework/ULServerInterface.h
-Local/Library/Headers/ULFramework/ULSimpleMergerDelegate.h
-Local/Library/Headers/ULFramework/ULSimulation.h
-Local/Library/Headers/ULFramework/ULSystem.h
-Local/Library/Headers/ULFramework/ULSystemBuilder.h
-Local/Library/Headers/ULFramework/ULSystemController.h
-Local/Library/Headers/ULFramework/ULTopologyFrameBuilder.h
+Local/Library/Headers/MolTalk
+Local/Library/Headers/ULFramework
 Local/Library/Headers/XMLLib/ULAtomListNode.h
 Local/Library/Headers/XMLLib/ULClassNode.h
 Local/Library/Headers/XMLLib/ULConnectivityNode.h
@@ -173,33 +226,45 @@ Local/Library/Headers/XMLLib/XMLDocumentRoot.h
 Local/Library/Headers/XMLLib/XMLLib.h
 Local/Library/Headers/XMLLib/XMLNode.h
 Local/Library/Libraries/libAdunKernel.so
-Local/Library/Libraries/libAdunKernel.so.%%MAJORLIBVERSION%%
-Local/Library/Libraries/libAdunKernel.so.%%LIBVERSION%%
+Local/Library/Libraries/libAdunKernel.so.%%MAJORLIBVERSION2%%
+Local/Library/Libraries/libAdunKernel.so.%%LIBVERSION2%%
 Local/Library/Libraries/libULFramework.so
-Local/Library/Libraries/libULFramework.so.%%MAJORVERSION%%
-Local/Library/Libraries/libULFramework.so.%%MAJORVERSION%%.52
+Local/Library/Libraries/libULFramework.so.%%MAJORLIBVERSION4%%
+Local/Library/Libraries/libULFramework.so.%%LIBVERSION4%%
 Local/Library/Libraries/libXMLLib.so
-Local/Library/Libraries/libXMLLib.so.%%MAJORVERSION%%
-Local/Library/Libraries/libXMLLib.so.%%MAJORVERSION%%.1
+Local/Library/Libraries/libXMLLib.so.%%MAJORLIBVERSION5%%
+Local/Library/Libraries/libXMLLib.so.%%LIBVERSION5%%
 Local/Library/Libraries/libadun_base.so
 Local/Library/Libraries/libadun_base.so.%%MAJORLIBVERSION%%
 Local/Library/Libraries/libadun_base.so.%%LIBVERSION%%
-Local/Library/Libraries/libmoltalk.so
-Local/Library/Libraries/libmoltalk.so.%%MAJORLIBVERSION%%
-Local/Library/Libraries/libmoltalk.so.%%LIBVERSION%%
-Local/Library/Tools/Resources/AdunCore/reloadOptions.plist
+Local/Library/Libraries/libMolTalk.so
+Local/Library/Libraries/libMolTalk.so.%%MAJORLIBVERSION3%%
+Local/Library/Libraries/libMolTalk.so.%%LIBVERSION3%%
 Local/Tools/AdunCore
 Local/Tools/AdunServer
+Local/Tools/InstallPlugin.py
 Local/Tools/UL
-@dirrm Local/Library/Tools/Resources/AdunCore
+@dirrmtry Local/Library/Tools/Resources/AdunCore
 @dirrmtry Local/Library/Tools/Resources
 @dirrmtry Local/Library/Tools
 @dirrm Local/Library/Headers/XMLLib
-@dirrm Local/Library/Headers/ULFramework
-@dirrm Local/Library/Headers/MolTalk
-@dirrm Local/Library/Headers/Framework/Protocols
-@dirrm Local/Library/Headers/Framework
+@dirrmtry Local/Library/Headers/Framework/Protocols
+@dirrmtry Local/Library/Headers/Framework
 @dirrm Local/Library/Headers/Base
+@dirrm Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Enzymix
+@dirrm Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Charmm27
+@dirrm Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Amber
+@dirrm Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields
+@dirrm Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources
+@dirrm Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers
+@dirrm Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%
+@dirrm Local/Library/Frameworks/ULFramework.framework/Versions
+@dirrm Local/Library/Frameworks/ULFramework.framework
+@dirrm Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Resources
+@dirrm Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers
+@dirrm Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%
+@dirrm Local/Library/Frameworks/MolTalk.framework/Versions
+@dirrm Local/Library/Frameworks/MolTalk.framework
 @dirrm Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Resources
 @dirrm Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers
 @dirrm Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%
@@ -212,5 +277,8 @@ Local/Tools/UL
 @dirrm Local/Applications/UL.app/Resources/ProgressPanel.gorm
 @dirrm Local/Applications/UL.app/Resources/Preferences.gorm
 @dirrm Local/Applications/UL.app/Resources/Options.gorm
+@dirrm Local/Applications/UL.app/Resources/ExportPanel.gorm
+@dirrm Local/Applications/UL.app/Resources/DatabasePanel.gorm
+@dirrm Local/Applications/UL.app/Resources/Converter.gorm
 @dirrm Local/Applications/UL.app/Resources
 @dirrm Local/Applications/UL.app