Initial import of pdbalign-20030812, one of the many packages provided by

brook at biology dot nmsu dot edu and his team at NMSU.


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. 

8 files changed, 117 insertions, 0 deletions

diff --git a/biology/align/DESCR b/biology/align/DESCR
new file mode 100644
index 00000000000..54c1751e372
--- /dev/null
+++ b/biology/align/DESCR
@@ -0,0 +1,11 @@
+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
new file mode 100644
index 00000000000..852b47e858a
--- /dev/null
+++ b/biology/align/Makefile
@@ -0,0 +1,19 @@
+# $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
new file mode 100644
index 00000000000..ac8a9b9b24f
--- /dev/null
+++ b/biology/align/PLIST
@@ -0,0 +1,4 @@
+@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
new file mode 100644
index 00000000000..84be3e80d3a
--- /dev/null
+++ b/biology/align/distinfo
@@ -0,0 +1,8 @@
+$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
new file mode 100644
index 00000000000..a6d8baac0ad
--- /dev/null
+++ b/biology/align/patches/patch-aa
@@ -0,0 +1,27 @@
+$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) $(CFLAGS) -o pdbdist.o pdbdist.c
diff --git a/biology/align/patches/patch-ab b/biology/align/patches/patch-ab
new file mode 100644
index 00000000000..a50af45a9e6
--- /dev/null
+++ b/biology/align/patches/patch-ab
@@ -0,0 +1,16 @@
+$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
new file mode 100644
index 00000000000..c39ed22b2b7
--- /dev/null
+++ b/biology/align/patches/patch-ac
@@ -0,0 +1,16 @@
+$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
new file mode 100644
index 00000000000..86fccbc0b0c
--- /dev/null
+++ b/biology/align/patches/patch-ad
@@ -0,0 +1,16 @@
+$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.*/
+