Adun is a new extendible molecular simulation program that also

includes data management and analysis capabilities.

WWW: http://diana.imim.es/Adun
Submitted by:	Gürkan Sengün
Reviewed by:	dinoex

9 files changed, 606 insertions, 0 deletions

diff --git a/biology/adun/Makefile b/biology/adun/Makefile
new file mode 100644
index 000000000000..20bc9d3a6a78
--- /dev/null
+++ b/biology/adun/Makefile
@@ -0,0 +1,44 @@
+# New ports collection makefile for:    adun
+# Date created:         4 Sep 2006
+# Whom:                 gurkan@linuks.mine.nu
+#
+# $FreeBSD$
+#
+
+PORTNAME=	adun
+PORTVERSION=	0.6
+CATEGORIES=	biology
+MASTER_SITES=	http://download.gna.org/adun/
+DISTNAME=	Adun${PORTVERSION}
+
+MAINTAINER=	gurkan@linuks.mine.nu
+COMMENT=	Molecular Simulator for GNUstep
+
+LIB_DEPENDS+=	gsl.9:${PORTSDIR}/math/gsl
+
+WRKSRC=		${WRKDIR}/Adun/
+USE_GMAKE=	yes
+USE_GNUSTEP=	yes
+USE_GNUSTEP_PREFIX=	yes
+USE_GNUSTEP_BACK=	yes
+USE_GNUSTEP_BUILD=	yes
+USE_GNUSTEP_INSTALL=	yes
+MAKEFILE=	GNUmakefile
+NO_FILTER_SHLIBS=	yes
+
+post-patch:
+	${CP} ${WRKSRC}/MolTalk/Defs/Linux_i686.def \
+		${WRKSRC}/MolTalk/Defs/i386.def
+	${REINPLACE_CMD} -e 's|^GNUSTEP_INSTALLATION_DIR|#GNUSTEP_INSTALLATION_DIR|' \
+		${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
+	${REINPLACE_CMD} -e 's|HOME|${PREFIX}|' \
+		${WRKSRC}/Plugins/Analyse/GNUmakefile \
+		${WRKSRC}/Plugins/Results/GNUmakefile
+
+.include <bsd.port.mk>
diff --git a/biology/adun/distinfo b/biology/adun/distinfo
new file mode 100644
index 000000000000..8258acfa9228
--- /dev/null
+++ b/biology/adun/distinfo
@@ -0,0 +1,3 @@
+MD5 (Adun0.6.tar.gz) = 34e35b5314095cef93fc17d40a7701a5
+SHA256 (Adun0.6.tar.gz) = 94acf265be17b86368e2d8c62cd2872e90a8d953ac520756af3272d2593e1203
+SIZE (Adun0.6.tar.gz) = 781286
diff --git a/biology/adun/files/patch-AdunLinkedList.m b/biology/adun/files/patch-AdunLinkedList.m
new file mode 100644
index 000000000000..165fbbf6fcb0
--- /dev/null
+++ b/biology/adun/files/patch-AdunLinkedList.m
@@ -0,0 +1,14 @@
+--- 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
new file mode 100644
index 000000000000..e88031346f82
--- /dev/null
+++ b/biology/adun/files/patch-AdunMemoryManager.h
@@ -0,0 +1,22 @@
+--- 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
new file mode 100644
index 000000000000..c1d7235482b7
--- /dev/null
+++ b/biology/adun/files/patch-AdunMemoryManager.m
@@ -0,0 +1,266 @@
+--- 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
new file mode 100644
index 000000000000..e9ab0c8dc869
--- /dev/null
+++ b/biology/adun/files/patch-GNUmakefile
@@ -0,0 +1,17 @@
+--- 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
new file mode 100644
index 000000000000..fff8726b3ebb
--- /dev/null
+++ b/biology/adun/files/patch-main.m
@@ -0,0 +1,23 @@
+--- 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-descr b/biology/adun/pkg-descr
new file mode 100644
index 000000000000..d497e1a28ba6
--- /dev/null
+++ b/biology/adun/pkg-descr
@@ -0,0 +1,4 @@
+Adun is a new extendible molecular simulation program that also
+includes data management and analysis capabilities.
+
+WWW: http://diana.imim.es/Adun
diff --git a/biology/adun/pkg-plist b/biology/adun/pkg-plist
new file mode 100644
index 000000000000..59e303a442a9
--- /dev/null
+++ b/biology/adun/pkg-plist
@@ -0,0 +1,213 @@
+Local/Applications/UL.app/Resources/EnzymixParameters.ffml
+Local/Applications/UL.app/Resources/EnzymixTopology.ffml
+Local/Applications/UL.app/Resources/H2O.pdb
+Local/Applications/UL.app/Resources/Info-gnustep.plist
+Local/Applications/UL.app/Resources/Options.gorm/data.classes
+Local/Applications/UL.app/Resources/Options.gorm/data.info
+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/data.classes
+Local/Applications/UL.app/Resources/ProgressPanel.gorm/data.info
+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
+Local/Applications/UL.app/Resources/Results.gorm/objects.gorm
+Local/Applications/UL.app/Resources/System.gorm/data.classes
+Local/Applications/UL.app/Resources/System.gorm/data.info
+Local/Applications/UL.app/Resources/System.gorm/objects.gorm
+Local/Applications/UL.app/Resources/Template.gorm/data.classes
+Local/Applications/UL.app/Resources/Template.gorm/data.info
+Local/Applications/UL.app/Resources/Template.gorm/objects.gorm
+Local/Applications/UL.app/Resources/UL.desktop
+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/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/library_paths.openapp
+Local/Applications/UL.app/stamp.make
+Local/Library/Frameworks/AdunKernel.framework/Headers
+Local/Library/Frameworks/AdunKernel.framework/Resources
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/AdunKernel
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdCommandInterface.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdController.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdCoreCommand.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdCreation.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdDataSources.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdDelegation.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdEndSimulationCommand.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdFlushEnergiesCommand.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdFrameworkFunctions.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdGridDelegate.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdKeyValueObserving.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdListMemoryManagement.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdReloadCommand.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdServerInterface.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdStatusCommand.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdUpdating.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunBondedTopology.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunBoundaryImplementor.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunController.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunCore.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunDataMatrix.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunDataSet.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunDataSource.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunDefinitions.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunDynamics.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunEnvironment.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunForceField.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunForceFieldManager.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunForceFieldTerm.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunGrid.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunIOManager.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunInteractionSystem.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunKernel.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunLinkedList.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunMemoryManager.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunModelObject.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunNonBondedListHandler.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunNonBondedTopology.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunNonbondedCalculator.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunObject.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunRelationship.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunSimulator.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunState.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunSystem.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunSystemComponent.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunSystemNode.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/AdunTimer.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/CellListHandler.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/EnzymixForceField.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/GRFNonbondedCalculator.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/NewtonianSimulator.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/PureNonBondedCalculator.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/RemoteProcessAccess.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/SCAAS.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/ShiftedNonBondedCalculator.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/SimpleListHandler.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/SphericalBox.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Headers/ULIndexSetConversions.h
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Resources/Info-gnustep.plist
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/Resources/ScriptingInfo.plist
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/libAdunKernel.so
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/libAdunKernel.so.%%MAJORLIBVERSION%%
+Local/Library/Frameworks/AdunKernel.framework/Versions/A/libAdunKernel.so.%%LIBVERSION%%
+Local/Library/Frameworks/AdunKernel.framework/Versions/Current
+Local/Library/Headers/AdunKernel
+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
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+@dirrm Local/Tools/Resources/AdunCore
+@dirrm Local/Tools/Resources
+@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
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+@dirrm Local/Library/Frameworks/AdunKernel.framework
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+@dirrm Local/Applications/UL.app/Resources
+@dirrm Local/Applications/UL.app