diff options
| -rw-r--r-- | biology/pdbalign/DESCR | 11 | ||||
| -rw-r--r-- | biology/pdbalign/Makefile | 19 | ||||
| -rw-r--r-- | biology/pdbalign/PLIST | 4 | ||||
| -rw-r--r-- | biology/pdbalign/distinfo | 8 | ||||
| -rw-r--r-- | biology/pdbalign/patches/patch-aa | 27 | ||||
| -rw-r--r-- | biology/pdbalign/patches/patch-ab | 16 | ||||
| -rw-r--r-- | biology/pdbalign/patches/patch-ac | 16 | ||||
| -rw-r--r-- | biology/pdbalign/patches/patch-ad | 16 |
8 files changed, 117 insertions, 0 deletions
diff --git a/biology/pdbalign/DESCR b/biology/pdbalign/DESCR new file mode 100644 index 00000000000..54c1751e372 --- /dev/null +++ b/biology/pdbalign/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/pdbalign/Makefile b/biology/pdbalign/Makefile new file mode 100644 index 00000000000..0cba27571cd --- /dev/null +++ b/biology/pdbalign/Makefile @@ -0,0 +1,19 @@ +# $NetBSD: Makefile,v 1.1.1.1 2003/09/26 03:15:28 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/pdbalign/PLIST b/biology/pdbalign/PLIST new file mode 100644 index 00000000000..cc275c016eb --- /dev/null +++ b/biology/pdbalign/PLIST @@ -0,0 +1,4 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/26 03:15:28 jschauma Exp $ +bin/distalign +bin/pdbalign +bin/pdbdist diff --git a/biology/pdbalign/distinfo b/biology/pdbalign/distinfo new file mode 100644 index 00000000000..893441a1dbe --- /dev/null +++ b/biology/pdbalign/distinfo @@ -0,0 +1,8 @@ +$NetBSD: distinfo,v 1.1.1.1 2003/09/26 03:15:28 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/pdbalign/patches/patch-aa b/biology/pdbalign/patches/patch-aa new file mode 100644 index 00000000000..cd47ad57a82 --- /dev/null +++ b/biology/pdbalign/patches/patch-aa @@ -0,0 +1,27 @@ +$NetBSD: patch-aa,v 1.1.1.1 2003/09/26 03:15:28 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) $(CFLAGS) -o pdbdist.o pdbdist.c diff --git a/biology/pdbalign/patches/patch-ab b/biology/pdbalign/patches/patch-ab new file mode 100644 index 00000000000..e08ab288d4b --- /dev/null +++ b/biology/pdbalign/patches/patch-ab @@ -0,0 +1,16 @@ +$NetBSD: patch-ab,v 1.1.1.1 2003/09/26 03:15:28 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/pdbalign/patches/patch-ac b/biology/pdbalign/patches/patch-ac new file mode 100644 index 00000000000..43f5d83508b --- /dev/null +++ b/biology/pdbalign/patches/patch-ac @@ -0,0 +1,16 @@ +$NetBSD: patch-ac,v 1.1.1.1 2003/09/26 03:15:28 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/pdbalign/patches/patch-ad b/biology/pdbalign/patches/patch-ad new file mode 100644 index 00000000000..be9f804b9f1 --- /dev/null +++ b/biology/pdbalign/patches/patch-ad @@ -0,0 +1,16 @@ +$NetBSD: patch-ad,v 1.1.1.1 2003/09/26 03:15:28 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.*/ + |