8 files changed, 0 insertions, 117 deletions
diff --git a/biology/align/DESCR b/biology/align/DESCR
deleted file mode 100644
index 54c1751e372..00000000000
--- a/biology/align/DESCR
+++ /dev/null
@@ -1,11 +0,0 @@
-Given a GCG multiple sequence alignment file (a GCG MSF file), which a 
-includes a sequence of known structure, the program pdbalign maps the 
-sequence variability onto the known structure. The central premise is 
-of course, that for a closely related family of proteins (sequence ID 
-> 40%) the 3-D structures will not be significantly different.pdbdist 
-calculates the distance from each atom in the pdb file to each atom in 
-the ligand and records the minimum in the temperature field for that 
-atom record.distalign reads the output from pdbdist and also the 
-original GCG MSF file and produces an MSF file annotated with a 
-measure of sequence variability and the distance of the residue at 
-that position (of the sequence of known structure) from the ligand. 
diff --git a/biology/align/Makefile b/biology/align/Makefile
deleted file mode 100644
index 852b47e858a..00000000000
--- a/biology/align/Makefile
+++ /dev/null
@@ -1,19 +0,0 @@
-# $NetBSD: Makefile,v 1.1.1.1 2003/09/26 03:10:20 jschauma Exp $
-#
-
-DISTNAME=		pdbalign
-PKGNAME=		pdbalign-20030812
-WRKSRC=			${WRKDIR}
-CATEGORIES=		biology
-MASTER_SITES=		ftp://ftp.ebi.ac.uk/pub/software/unix/pdbalign/
-
-MAINTAINER=		hdp@cs.nmsu.edu
-HOMEPAGE=               #empty
-COMMENT=		Prediction of Protein Secondary Structure and Active Sites
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/pdbalign ${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/distalign ${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/pdbdist ${PREFIX}/bin
-
-.include "../../mk/bsd.pkg.mk"
diff --git a/biology/align/PLIST b/biology/align/PLIST
deleted file mode 100644
index ac8a9b9b24f..00000000000
--- a/biology/align/PLIST
+++ /dev/null
@@ -1,4 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/26 03:10:20 jschauma Exp $
-bin/distalign
-bin/pdbalign
-bin/pdbdist
diff --git a/biology/align/distinfo b/biology/align/distinfo
deleted file mode 100644
index 84be3e80d3a..00000000000
--- a/biology/align/distinfo
+++ /dev/null
@@ -1,8 +0,0 @@
-$NetBSD: distinfo,v 1.1.1.1 2003/09/26 03:10:20 jschauma Exp $
-
-SHA1 (pdbalign.tar.gz) = 83f8e393fe98cb877bc90e804911b1819a18c1d3
-Size (pdbalign.tar.gz) = 10457 bytes
-SHA1 (patch-aa) = 77293faa3e81fd6cdb093d378b14128208d3f845
-SHA1 (patch-ab) = 9795a6a0174811a5e4d922e1ba69e24ced97dc61
-SHA1 (patch-ac) = 1c2d621c0be9c4aa78b1d931e2b972d94173e327
-SHA1 (patch-ad) = a123bdff11fdb5f2a69d41edfb8234f2a488d12d
diff --git a/biology/align/patches/patch-aa b/biology/align/patches/patch-aa
deleted file mode 100644
index a6d8baac0ad..00000000000
--- a/biology/align/patches/patch-aa
+++ /dev/null
@@ -1,27 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 2003/09/26 03:10:20 jschauma Exp $
-
---- Makefile.orig	Wed Aug 13 13:36:33 2003
-+++ Makefile
-@@ -0,0 +1,22 @@
-+CFLAGS+= -c
-+LDFLAGS = -lm
-+
-+all: pdbalign distalign pdbdist
-+
-+pdbalign: pdbalign.o
-+	$(CC) $(LDFLAGS) -o pdbalign pdbalign.o
-+
-+distalign: distalign.o
-+	$(CC) $(LDFLAGS) -o distalign distalign.o
-+
-+pdbdist:pdbdist.o
-+	$(CC) $(LDFLAGS) -o pdbdist pdbdist.o
-+
-+pdbalign.o: 
-+	$(CC) $(CFLAGS) -o pdbalign.o pdbalign.c
-+
-+distalign.o: 
-+	$(CC) $(CFLAGS) -o distalign.o distalign.c
-+
-+pdbdist.o:
-+	$(CC) $(CFLAGS) -o pdbdist.o pdbdist.c
diff --git a/biology/align/patches/patch-ab b/biology/align/patches/patch-ab
deleted file mode 100644
index a50af45a9e6..00000000000
--- a/biology/align/patches/patch-ab
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 2003/09/26 03:10:20 jschauma Exp $
-
---- distalign.c.orig	Fri Jan 26 17:53:41 1996
-+++ distalign.c
-@@ -1019,9 +1019,9 @@ int main( argc, argv )
-     exit(0);
- }
- 
--Dr. Mansoor Saqi                    Email mass15599@ggr.co.uk
-+/*Dr. Mansoor Saqi                    Email mass15599@ggr.co.uk
- Bioinformatics Group                Phone +44 (0)81 966 2417
- Dept. of Biomolecular Structure
- Glaxo Group Research
--Greenford, Middlx, UK.
-+Greenford, Middlx, UK. */
- 
diff --git a/biology/align/patches/patch-ac b/biology/align/patches/patch-ac
deleted file mode 100644
index c39ed22b2b7..00000000000
--- a/biology/align/patches/patch-ac
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD: patch-ac,v 1.1.1.1 2003/09/26 03:10:20 jschauma Exp $
-
---- pdbalign.c.orig	Fri Jan 26 17:53:57 1996
-+++ pdbalign.c
-@@ -841,9 +841,9 @@ int main( argc, argv )
-     exit(0);
- }
- 
--Dr. Mansoor Saqi                    Email mass15599@ggr.co.uk
-+/*Dr. Mansoor Saqi                    Email mass15599@ggr.co.uk
- Bioinformatics Group                Phone +44 (0)81 966 2417
- Dept. of Biomolecular Structure
- Glaxo Group Research
- Greenford, Middlx, UK.
--
-+*/
diff --git a/biology/align/patches/patch-ad b/biology/align/patches/patch-ad
deleted file mode 100644
index 86fccbc0b0c..00000000000
--- a/biology/align/patches/patch-ad
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD: patch-ad,v 1.1.1.1 2003/09/26 03:10:20 jschauma Exp $
-
---- pdbdist.c.orig	Fri Jan 26 17:54:11 1996
-+++ pdbdist.c
-@@ -628,9 +628,9 @@ int main( argc, argv )
-     return(0);
- }
- 
--Dr. Mansoor Saqi                    Email mass15599@ggr.co.uk
-+/*Dr. Mansoor Saqi                    Email mass15599@ggr.co.uk
- Bioinformatics Group                Phone +44 (0)81 966 2417
- Dept. of Biomolecular Structure
- Glaxo Group Research
--Greenford, Middlx, UK.
-+Greenford, Middlx, UK.*/
-