From 315c2f1194384d384782ee550ba519a7189439c1 Mon Sep 17 00:00:00 2001 From: jschauma Date: Fri, 26 Sep 2003 03:10:20 +0000 Subject: 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. --- 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(+) create mode 100644 biology/align/DESCR create mode 100644 biology/align/Makefile create mode 100644 biology/align/PLIST create mode 100644 biology/align/distinfo create mode 100644 biology/align/patches/patch-aa create mode 100644 biology/align/patches/patch-ab create mode 100644 biology/align/patches/patch-ac create mode 100644 biology/align/patches/patch-ad (limited to 'biology') 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.*/ + -- cgit v1.2.3