8 files changed, 85 insertions, 412 deletions

diff --git a/biology/adun/Makefile b/biology/adun/Makefile
deleted file mode 100644
index 2c6b89eba116..000000000000
--- a/biology/adun/Makefile
+++ /dev/null
@@ -1,66 +0,0 @@
-# New ports collection makefile for:    adun
-# Date created:         4 Sep 2006
-# Whom:                 gurkan@phys.ethz.ch
-#
-# $FreeBSD$
-#
-
-PORTNAME=	adun
-PORTVERSION=	0.81
-PORTREVISION=	2
-CATEGORIES=	biology gnustep
-MASTER_SITES=	http://download.gna.org/adun/
-DISTNAME=	Adun-${PORTVERSION}
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Molecular Simulator for GNUstep
-
-LIB_DEPENDS+=	gsl:${PORTSDIR}/math/gsl
-
-LICENSE=	GPLv2
-
-USE_GNUSTEP=	yes
-USE_GNUSTEP_BACK=	yes
-USE_GNUSTEP_BUILD=	yes
-USE_GNUSTEP_INSTALL=	yes
-USE_GNUSTEP_LDCONFIG=	${GNUSTEP_LOCAL_LIBRARIES}
-
-DEFAULT_LIBVERSION2=	0.13
-DEFAULT_LIBVERSION3=	3.0.1
-DEFAULT_LIBVERSION4=	0.6
-DEFAULT_LIBVERSION5=	0.1
-PLIST_SUB+=	LIBVERSION2=${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=${DEFAULT_LIBVERSION5:C/([0-9]).*/\1/1}
-ADDITIONAL_CPPFLAGS=	-D__FREEBSD__
-ADDITIONAL_INCLUDE_DIRS=	-I${WRKSRC}/Kernel -I${WRKSRC}
-ADDITIONAL_LIB_DIRS=	-L${WRKSRC}/Kernel/AdunKernel/AdunKernel.framework -L${WRKSRC}/MolTalk/MolTalk.framework -L${WRKSRC}/Kernel/Base/obj
-ADDITIONAL_LDFLAGS=	-rpath-link=${WRKSRC}/Kernel/AdunKernel/AdunKernel.framework:${WRKSRC}/MolTalk/MolTalk.framework:${WRKSRC}/Kernel/Base/obj
-
-MAKE_ENV+=	GSL_LIB_DIR=${LOCALBASE}/lib
-MAKE_ENV+=	GSL_INCLUDE_DIR=${LOCALBASE}/include
-MAKE_ENV+=	KERNEL_COMPILER="${CC}"
-
-post-patch:
-	${REINPLACE_CMD} -e 's|^GNUSTEP_INSTALLATION_DOMAIN|#GNUSTEP_INSTALLATION_DOMAIN|' \
-		${WRKSRC}/GNUmakefile \
-		${WRKSRC}/Tools/AdunShell/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/ULFramework/GNUmakefile
-	${REINPLACE_CMD} -e 's|GNUSTEP_HOME./..GNUSTEP_USER_DIR_TOOLS|GNUSTEP_LOCAL_TOOLS|' \
-		${WRKSRC}/GNUmakefile.postamble
-	${REINPLACE_CMD} -e 's|<wait.h>|<sys/wait.h>|' \
-		${WRKSRC}/UL/AdunServer/AdServer.m
-
-.include <bsd.port.mk>
diff --git a/biology/adun/distinfo b/biology/adun/distinfo
deleted file mode 100644
index 076035ee140c..000000000000
--- a/biology/adun/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (Adun-0.81.tar.gz) = 7c6c8cdf334cdad9f877705bc6eece7c4ee89d49801d606b8069d1645b734c9f
-SIZE (Adun-0.81.tar.gz) = 4554395
diff --git a/biology/adun/files/patch-AdLinkedList.h b/biology/adun/files/patch-AdLinkedList.h
deleted file mode 100644
index 62ce6dcba44f..000000000000
--- a/biology/adun/files/patch-AdLinkedList.h
+++ /dev/null
@@ -1,12 +0,0 @@
---- 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/pkg-descr b/biology/adun/pkg-descr
deleted file mode 100644
index 9e3a558e5b7e..000000000000
--- a/biology/adun/pkg-descr
+++ /dev/null
@@ -1,6 +0,0 @@
-Adun is a new extendible molecular simulation program that also
-includes data management and analysis capabilities.
-
-LICENSE: GPL2 or later
-
-WWW: http://diana.imim.es/Adun
diff --git a/biology/adun/pkg-plist b/biology/adun/pkg-plist
deleted file mode 100644
index 82dde3984c9b..000000000000
--- a/biology/adun/pkg-plist
+++ /dev/null
@@ -1,310 +0,0 @@
-GNUstep/Local/Applications/UL.app/Resources/Converter.gorm/classes.nib
-GNUstep/Local/Applications/UL.app/Resources/Converter.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/Converter.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/Converter.gorm/info.nib
-GNUstep/Local/Applications/UL.app/Resources/Converter.gorm/keyedobjects.nib
-GNUstep/Local/Applications/UL.app/Resources/Converter.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/CreateAttributePanel.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/CreateAttributePanel.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/CreateAttributePanel.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/DatabasePanel.gorm/classes.nib
-GNUstep/Local/Applications/UL.app/Resources/DatabasePanel.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/DatabasePanel.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/DatabasePanel.gorm/info.nib
-GNUstep/Local/Applications/UL.app/Resources/DatabasePanel.gorm/keyedobjects.nib
-GNUstep/Local/Applications/UL.app/Resources/DatabasePanel.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/ExportPanel.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/ExportPanel.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/ExportPanel.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/H2O.pdb
-GNUstep/Local/Applications/UL.app/Resources/Info-gnustep.plist
-GNUstep/Local/Applications/UL.app/Resources/Options.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/Options.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/Options.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/Preferences.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/Preferences.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/Preferences.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/ProgressPanel.gorm/classes.nib
-GNUstep/Local/Applications/UL.app/Resources/ProgressPanel.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/ProgressPanel.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/ProgressPanel.gorm/info.nib
-GNUstep/Local/Applications/UL.app/Resources/ProgressPanel.gorm/keyedobjects.nib
-GNUstep/Local/Applications/UL.app/Resources/ProgressPanel.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/QuickStartFiles/1BK2
-GNUstep/Local/Applications/UL.app/Resources/QuickStartFiles/ContainerTemplate
-GNUstep/Local/Applications/UL.app/Resources/QuickStartFiles/ExplicitSolventTemplate
-GNUstep/Local/Applications/UL.app/Resources/QuickStartFiles/GDP
-GNUstep/Local/Applications/UL.app/Resources/QuickStartFiles/GasPhaseTemplate
-GNUstep/Local/Applications/UL.app/Resources/QuickStartFiles/H2O
-GNUstep/Local/Applications/UL.app/Resources/Results.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/Results.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/Results.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/System.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/System.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/System.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/Template.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/Template.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/Template.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/UL.desktop
-GNUstep/Local/Applications/UL.app/Resources/UL.gorm/data.classes
-GNUstep/Local/Applications/UL.app/Resources/UL.gorm/data.info
-GNUstep/Local/Applications/UL.app/Resources/UL.gorm/objects.gorm
-GNUstep/Local/Applications/UL.app/Resources/apply.png
-GNUstep/Local/Applications/UL.app/Resources/dataset-close.png
-GNUstep/Local/Applications/UL.app/Resources/defaultOptions.plist
-GNUstep/Local/Applications/UL.app/Resources/document-save.png
-GNUstep/Local/Applications/UL.app/Resources/export.png
-GNUstep/Local/Applications/UL.app/Resources/icon.tiff
-GNUstep/Local/Applications/UL.app/Resources/reload.png
-GNUstep/Local/Applications/UL.app/Resources/splash.tiff
-GNUstep/Local/Applications/UL.app/UL
-GNUstep/Local/Applications/UL.app/stamp.make
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/AdunKernel
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Headers
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Resources
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/AdunKernel
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdCommandInterface.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdController.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdCoreAdditions.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdCoreCommand.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdDataSources.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdEndSimulationCommand.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdForceFieldTerm.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdFrameworkFunctions.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdGridDelegate.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdIndexSetConversions.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdMatrixModification.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdMemento.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdServerInterface.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdStatusCommand.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunAmberForceField.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunBerendsenThermostat.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunCellListHandler.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunCharmmForceField.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunCheckpointManager.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunConfigurationGenerator.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunContainerDataSource.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunController.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunCore.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunCuboidBox.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDataMatrix.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDataSet.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDataSource.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDefinitions.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunDynamics.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunElementSelection.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunEllipsoidBox.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunEnzymixForceField.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunFileSystemSimulationStorage.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunForceField.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunForceFieldCollection.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunGRFNonbondedTerm.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunGrid.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunHarmonicConstraintTerm.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunIOManager.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunInteractionSystem.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunKernel.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunLangevinThermostat.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunLinkedList.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunListHandler.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMatrixStructureCoder.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMemoryManager.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMinimiser.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunModelObject.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMolecularMechanicsForceField.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMoleculeCavity.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunMultithreadedNonbondedTerm.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunNonbondedTerm.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunPureNonbondedTerm.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSCAAS.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunShiftedNonbondedTerm.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSimpleListHandler.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSimulationData.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSimulator.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSmoothedGBTerm.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSphericalBox.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSystem.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunSystemCollection.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunTemplateProcessor.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunTimer.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers/AdunTrajectory.h
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Resources/Info-gnustep.plist
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Resources/OptimisedCoefficients.plist
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Resources/PBBornRadii.plist
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Resources/ScriptingInfo.plist
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/libAdunKernel.so
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/libAdunKernel.so.%%MAJORLIBVERSION2%%
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/libAdunKernel.so.%%LIBVERSION2%%
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/Current
-GNUstep/Local/Library/Frameworks/AdunKernel.framework/libAdunKernel.so
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Headers
-GNUstep/Local/Library/Frameworks/MolTalk.framework/MolTalk
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Resources
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTAlPos.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTAtom.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTAtomFactory.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTChain.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTChainFactory.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTCompressedFileStream.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTCoordinates.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTFileStream.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTMatrix.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTMatrix44.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTMatrix53.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTPairwiseSequenceAlignment.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTPairwiseStrxAlignment.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTQuaternion.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTResidue.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTResidueFactory.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTSelection.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTStream.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTString.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTStructure.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTStructureFactory.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTSubstitutionMatrix.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MTVector.h
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers/MolTalk.h
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-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/libMolTalk.so.%%LIBVERSION3%%
-GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/Current
-GNUstep/Local/Library/Frameworks/MolTalk.framework/libMolTalk.so
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Headers
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-GNUstep/Local/Library/Frameworks/ULFramework.framework/ULFramework
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/PDBConfigurationBuilder.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULAnalysisManager.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULAnalysisPlugin.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULConfigurationBuilder.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULConfigurationPlugin.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULDatabaseIndex.h
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-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULFileSystemDatabaseBackend.h
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-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULIOManager.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULInteractionsBuilder.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULMenuExtensions.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULMerger.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULMergerDelegate.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULProcess.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULProcessManager.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULServerInterface.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULServerManager.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULSimpleMergerDelegate.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULSystem.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULSystemBuilder.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULSystemController.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULTemplate.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers/ULTopologyFrameBuilder.h
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Amber/AmberParameters.ffml
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Amber/AmberTopology.ffml
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Charmm27/Charmm27Parameters.ffml
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Charmm27/Charmm27Topology.ffml
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Enzymix/EnzymixParameters.ffml
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Enzymix/EnzymixTopology.ffml
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/ForceFields.plist
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/Info-gnustep.plist
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ScriptingInfo.plist
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/Version
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-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/pdbBuilderOptions.plist
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/pdbNameMap.plist
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/ULFramework
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/libULFramework.so
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/libULFramework.so.%%MAJORLIBVERSION4%%
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/libULFramework.so.%%LIBVERSION4%%
-GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/Current
-GNUstep/Local/Library/Frameworks/ULFramework.framework/libULFramework.so
-GNUstep/Local/Library/Headers/AdunKernel
-GNUstep/Local/Library/Headers/Base/AdBaseFunctions.h
-GNUstep/Local/Library/Headers/Base/AdForceFieldFunctions.h
-GNUstep/Local/Library/Headers/Base/AdGeneralizedBornFunctions.h
-GNUstep/Local/Library/Headers/Base/AdLinkedList.h
-GNUstep/Local/Library/Headers/Base/AdMatrix.h
-GNUstep/Local/Library/Headers/Base/AdQuadratureFunctions.h
-GNUstep/Local/Library/Headers/Base/AdQuaternion.h
-GNUstep/Local/Library/Headers/Base/AdSorter.h
-GNUstep/Local/Library/Headers/Base/AdVector.h
-GNUstep/Local/Library/Headers/Base/AdVolumeFunctions.h
-GNUstep/Local/Library/Headers/MolTalk
-GNUstep/Local/Library/Headers/ULFramework
-GNUstep/Local/Library/Headers/XMLLib/ULAtomListNode.h
-GNUstep/Local/Library/Headers/XMLLib/ULClassNode.h
-GNUstep/Local/Library/Headers/XMLLib/ULConnectivityNode.h
-GNUstep/Local/Library/Headers/XMLLib/ULInteractionNode.h
-GNUstep/Local/Library/Headers/XMLLib/ULMolecularLibraryNode.h
-GNUstep/Local/Library/Headers/XMLLib/ULMolecularLibraryTree.h
-GNUstep/Local/Library/Headers/XMLLib/ULMoleculeClassNode.h
-GNUstep/Local/Library/Headers/XMLLib/ULMoleculeNode.h
-GNUstep/Local/Library/Headers/XMLLib/ULParameterNode.h
-GNUstep/Local/Library/Headers/XMLLib/ULParameterTree.h
-GNUstep/Local/Library/Headers/XMLLib/ULTopologyNode.h
-GNUstep/Local/Library/Headers/XMLLib/XMLDocumentRoot.h
-GNUstep/Local/Library/Headers/XMLLib/XMLLib.h
-GNUstep/Local/Library/Headers/XMLLib/XMLNode.h
-GNUstep/Local/Library/Libraries/libAdunKernel.so
-GNUstep/Local/Library/Libraries/libAdunKernel.so.%%MAJORLIBVERSION2%%
-GNUstep/Local/Library/Libraries/libAdunKernel.so.%%LIBVERSION2%%
-GNUstep/Local/Library/Libraries/libULFramework.so
-GNUstep/Local/Library/Libraries/libULFramework.so.%%MAJORLIBVERSION4%%
-GNUstep/Local/Library/Libraries/libULFramework.so.%%LIBVERSION4%%
-GNUstep/Local/Library/Libraries/libXMLLib.so
-GNUstep/Local/Library/Libraries/libXMLLib.so.%%MAJORLIBVERSION5%%
-GNUstep/Local/Library/Libraries/libXMLLib.so.%%LIBVERSION5%%
-GNUstep/Local/Library/Libraries/libadun_base.so
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-GNUstep/Local/Library/Libraries/libadun_base.so.%%LIBVERSION%%
-GNUstep/Local/Library/Libraries/libMolTalk.so
-GNUstep/Local/Library/Libraries/libMolTalk.so.%%MAJORLIBVERSION3%%
-GNUstep/Local/Library/Libraries/libMolTalk.so.%%LIBVERSION3%%
-GNUstep/Local/Tools/AdunCore
-GNUstep/Local/Tools/AdunServer
-GNUstep/Local/Tools/InstallPlugin.py
-GNUstep/Local/Tools/UL
-@dirrmtry GNUstep/Local/Library/Tools/Resources/AdunCore
-@dirrmtry GNUstep/Local/Library/Tools/Resources
-@dirrmtry GNUstep/Local/Library/Tools
-@dirrm GNUstep/Local/Library/Headers/XMLLib
-@dirrmtry GNUstep/Local/Library/Headers/Framework/Protocols
-@dirrmtry GNUstep/Local/Library/Headers/Framework
-@dirrm GNUstep/Local/Library/Headers/Base
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Enzymix
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Charmm27
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields/Amber
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources/ForceFields
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Resources
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%/Headers
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions/%%MAJORLIBVERSION4%%
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework/Versions
-@dirrm GNUstep/Local/Library/Frameworks/ULFramework.framework
-@dirrm GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Resources
-@dirrm GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%/Headers
-@dirrm GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions/%%MAJORLIBVERSION3%%
-@dirrm GNUstep/Local/Library/Frameworks/MolTalk.framework/Versions
-@dirrm GNUstep/Local/Library/Frameworks/MolTalk.framework
-@dirrm GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Resources
-@dirrm GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%/Headers
-@dirrm GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions/%%MAJORLIBVERSION2%%
-@dirrm GNUstep/Local/Library/Frameworks/AdunKernel.framework/Versions
-@dirrm GNUstep/Local/Library/Frameworks/AdunKernel.framework
-@dirrm GNUstep/Local/Applications/UL.app/Resources/UL.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/Template.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/System.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/Results.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/QuickStartFiles
-@dirrm GNUstep/Local/Applications/UL.app/Resources/ProgressPanel.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/Preferences.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/Options.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/ExportPanel.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/DatabasePanel.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/CreateAttributePanel.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources/Converter.gorm
-@dirrm GNUstep/Local/Applications/UL.app/Resources
-@dirrm GNUstep/Local/Applications/UL.app
diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile
index 5f2b0572cd7f..f8852192aa08 100644
--- a/biology/biococoa/Makefile
+++ b/biology/biococoa/Makefile
@@ -1,14 +1,15 @@
 # $FreeBSD$
 
 PORTNAME=	biococoa
-PORTVERSION=	1.6.0
-PORTREVISION=	2
+PORTVERSION=	2.2.1
+PORTREVISION=	0
 CATEGORIES=	biology gnustep
-MASTER_SITES=	${MASTER_SITE_DEBIAN}
+MASTER_SITES=	http://bioinformatics.org/biococoa/downloads/ ${MASTER_SITE_DEBIAN}
 MASTER_SITE_SUBDIR=	pool/main/b/biococoa.app
-DISTNAME=	biococoa.app_${PORTVERSION}.orig
+DISTNAME=	biococoa-${PORTVERSION}-src
+EXTRACT_SUFX=	.tgz
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	theraven@FreeBSD.org
 COMMENT=	Bioinformatics framework
 
 LICENSE=	LGPL21
@@ -18,6 +19,6 @@ USE_GNUSTEP_BACK=	yes
 USE_GNUSTEP_BUILD=	yes
 USE_GNUSTEP_INSTALL=	yes
 
-WRKSRC=		${WRKDIR}/biococoa
+WRKSRC=		${WRKDIR}/biococoa-${PORTVERSION}
 
 .include <bsd.port.mk>
diff --git a/biology/biococoa/distinfo b/biology/biococoa/distinfo
index 24ea23186a0d..4e46bf63bf24 100644
--- a/biology/biococoa/distinfo
+++ b/biology/biococoa/distinfo
@@ -1,2 +1,2 @@
-SHA256 (biococoa.app_1.6.0.orig.tar.gz) = dc9afef09686699532a5fa918de18778ae1bd3fea3a66d4bc9158b35f11d1931
-SIZE (biococoa.app_1.6.0.orig.tar.gz) = 22089
+SHA256 (biococoa-2.2.1-src.tgz) = f13855e83bd40fb6a16a6d0d04fb669a1b36fcbaea9484a5c894277467a9ae0d
+SIZE (biococoa-2.2.1-src.tgz) = 368512
diff --git a/biology/biococoa/pkg-plist b/biology/biococoa/pkg-plist
index 79f13f5f033f..af00d4f3f9fc 100644
--- a/biology/biococoa/pkg-plist
+++ b/biology/biococoa/pkg-plist
@@ -1,8 +1,76 @@
-GNUstep/Local/Applications/BioCocoa.app/BioCocoa
-GNUstep/Local/Applications/BioCocoa.app/Resources/BioCocoa.desktop
-GNUstep/Local/Applications/BioCocoa.app/Resources/Info-gnustep.plist
-GNUstep/Local/Applications/BioCocoa.app/Resources/biococoa.tiff
-GNUstep/Local/Applications/BioCocoa.app/stamp.make
-GNUstep/Local/Tools/BioCocoa
-@dirrm GNUstep/Local/Applications/BioCocoa.app/Resources
-@dirrm GNUstep/Local/Applications/BioCocoa.app
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/BioCocoa
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/BioCocoa
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCAminoAcid.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCAnnotation.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCAtom.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCachedFastaFile.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCachedSequenceFile.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCChain.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCodon.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCodonDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCCodonRNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCDataMatrix.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCFoundation.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCFoundationDefines.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCGeneticCode.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCMCP.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCNucleotide.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCNucleotideDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCNucleotideRNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCPairwiseAlignment.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCParseSOFT.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCPlatform.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCPreferences.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCProteinStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCResidue.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSample.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCScoreMatrix.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSecondaryStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequence.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceAlignment.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceArray.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceCodon.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceReader.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceStructure.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceTool.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSequenceWriter.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSeries.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCStringDefinitions.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSuffixArray.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSymbol.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCSymbolSet.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolComplement.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolDigest.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolHydropathyCalculator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolMassCalculator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolSequenceFinder.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolSymbolCounter.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolTranslator.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCToolTranslatorDNA.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCUtilData.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers/BCUtilStrings.h
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Resources/Info-gnustep.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Resources/aminoacids.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Resources/nucleotides.plist
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/libBioCocoa.so
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/libBioCocoa.so.%%MAJORVERSION%%
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/libBioCocoa.so.%%VERSION%%
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/libBioCocoa.so
+GNUstep/Local/Library/Libraries/libBioCocoa.so
+GNUstep/Local/Library/Libraries/libBioCocoa.so.%%MAJORVERSION%%
+GNUstep/Local/Library/Libraries/libBioCocoa.so.%%VERSION%%
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Headers
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Resources
+GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/Current
+GNUstep/Local/Library/Headers/BioCocoa
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework
+@dirrm GNUstep/Local/Library/Headers/BioCocoa
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/Current
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Resources
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%/Headers
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions/%%MAJORVERSION%%
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Versions
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Resources
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework/Headers
+@dirrm GNUstep/Local/Library/Frameworks/BioCocoa.framework