[pkgsrc/trunk]: pkgsrc/biology/align Initial import of pdbalign-20030812, one...

[jschauma <jschauma%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/5ff997bf3be6
branches:  trunk
changeset: 462059:5ff997bf3be6
user:      jschauma <jschauma%pkgsrc.org@localhost>
date:      Fri Sep 26 03:10:20 2003 +0000

description:
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.

diffstat:

 biology/align/DESCR            |  11 +++++++++++
 biology/align/Makefile         |  19 +++++++++++++++++++
 biology/align/PLIST            |   4 ++++
 biology/align/distinfo         |   8 ++++++++
 biology/align/patches/patch-aa |  27 +++++++++++++++++++++++++++
 biology/align/patches/patch-ab |  16 ++++++++++++++++
 biology/align/patches/patch-ac |  16 ++++++++++++++++
 biology/align/patches/patch-ad |  16 ++++++++++++++++
 8 files changed, 117 insertions(+), 0 deletions(-)

diffs (149 lines):

diff -r cc69a13bca49 -r 5ff997bf3be6 biology/align/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/align/DESCR       Fri Sep 26 03:10:20 2003 +0000
@@ -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 -r cc69a13bca49 -r 5ff997bf3be6 biology/align/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/align/Makefile    Fri Sep 26 03:10:20 2003 +0000
@@ -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@localhost
+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 -r cc69a13bca49 -r 5ff997bf3be6 biology/align/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/align/PLIST       Fri Sep 26 03:10:20 2003 +0000
@@ -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 -r cc69a13bca49 -r 5ff997bf3be6 biology/align/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/align/distinfo    Fri Sep 26 03:10:20 2003 +0000
@@ -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 -r cc69a13bca49 -r 5ff997bf3be6 biology/align/patches/patch-aa
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/align/patches/patch-aa    Fri Sep 26 03:10:20 2003 +0000
@@ -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) $(CFLAGS) -o pdbdist.o pdbdist.c
diff -r cc69a13bca49 -r 5ff997bf3be6 biology/align/patches/patch-ab
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/align/patches/patch-ab    Fri Sep 26 03:10:20 2003 +0000
@@ -0,0 +1,16 @@
+$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@localhost
++/*Dr. Mansoor Saqi                    Email mass15599%ggr.co.uk@localhost
+ Bioinformatics Group                Phone +44 (0)81 966 2417
+ Dept. of Biomolecular Structure
+ Glaxo Group Research
+-Greenford, Middlx, UK.
++Greenford, Middlx, UK. */
+ 
diff -r cc69a13bca49 -r 5ff997bf3be6 biology/align/patches/patch-ac
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/align/patches/patch-ac    Fri Sep 26 03:10:20 2003 +0000
@@ -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@localhost
++/*Dr. Mansoor Saqi                    Email mass15599%ggr.co.uk@localhost
+ Bioinformatics Group                Phone +44 (0)81 966 2417
+ Dept. of Biomolecular Structure
+ Glaxo Group Research
+ Greenford, Middlx, UK.
+-
++*/
diff -r cc69a13bca49 -r 5ff997bf3be6 biology/align/patches/patch-ad
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/align/patches/patch-ad    Fri Sep 26 03:10:20 2003 +0000
@@ -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@localhost
++/*Dr. Mansoor Saqi                    Email mass15599%ggr.co.uk@localhost
+ Bioinformatics Group                Phone +44 (0)81 966 2417
+ Dept. of Biomolecular Structure
+ Glaxo Group Research
+-Greenford, Middlx, UK.
++Greenford, Middlx, UK.*/
+