[pkgsrc/trunk]: pkgsrc/biology/profit Initial import of profit, one of the ma...

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

details:   https://anonhg.NetBSD.org/pkgsrc/rev/1519bb6d3d52
branches:  trunk
changeset: 462201:1519bb6d3d52
user:      jschauma <jschauma%pkgsrc.org@localhost>
date:      Sat Sep 27 23:18:26 2003 +0000

description:
Initial import of profit, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.

ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate
program for performing least squares fits of two protein structures. It
performs a very simple and basic function, but allows as much flexibility as
possible in performing this procedure. Thus one can specify subsets of atoms
to be considered, specify zones to be fitted by number, sequence, or by
sequence alignment.

diffstat:

 biology/profit/DESCR            |   6 ++++
 biology/profit/Makefile         |  28 ++++++++++++++++++++++
 biology/profit/PLIST            |  51 +++++++++++++++++++++++++++++++++++++++++
 biology/profit/distinfo         |   5 ++++
 biology/profit/patches/patch-aa |  29 +++++++++++++++++++++++
 5 files changed, 119 insertions(+), 0 deletions(-)

diffs (139 lines):

diff -r e62ec0468100 -r 1519bb6d3d52 biology/profit/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/profit/DESCR      Sat Sep 27 23:18:26 2003 +0000
@@ -0,0 +1,6 @@
+ProFit (pronounced Pro-Fit, not profit!) is designed to be the ultimate
+program for performing least squares fits of two protein structures. It
+performs a very simple and basic function, but allows as much flexibility as
+possible in performing this procedure. Thus one can specify subsets of atoms
+to be considered, specify zones to be fitted by number, sequence, or by
+sequence alignment. 
diff -r e62ec0468100 -r 1519bb6d3d52 biology/profit/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/profit/Makefile   Sat Sep 27 23:18:26 2003 +0000
@@ -0,0 +1,28 @@
+# $NetBSD: Makefile,v 1.1.1.1 2003/09/27 23:18:26 jschauma Exp $
+#
+
+DISTNAME=              profit
+PKGNAME=               profit-2.2
+WRKSRC=                        ${WRKDIR}/ProFitV2.2/src
+CATEGORIES=            biology
+MASTER_SITES=          http://www.rubic.rdg.ac.uk/~andrew/bioinf.org/software/profit/235216/
+
+MAINTAINER=            hdp%cs.nmsu.edu@localhost
+HOMEPAGE=              http://www.rubic.rdg.ac.uk/~andrew/bioinf.org/software/profit/index.html
+COMMENT=               Performs least squares fits of two protein structures
+
+ALL_TARGET=            ${DISTNAME}
+USE_BUILDLINK2=                YES
+
+do-install:
+       ${INSTALL_PROGRAM} ${WRKSRC}/profit ${PREFIX}/bin
+       ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/profit
+.for sufx in dvi ps tex
+       ${INSTALL_DATA} ${WRKSRC}/../doc/ProFit.${sufx}                 \
+               ${PREFIX}/share/doc/profit
+.endfor
+       ${INSTALL_DATA_DIR} ${PREFIX}/share/doc/html/profit
+       cd ${WRKSRC}/../doc/ProFit/ &&                                  \
+               ${PAX} -rw . ${PREFIX}/share/doc/html/profit/
+
+.include "../../mk/bsd.pkg.mk"
diff -r e62ec0468100 -r 1519bb6d3d52 biology/profit/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/profit/PLIST      Sat Sep 27 23:18:26 2003 +0000
@@ -0,0 +1,51 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/27 23:18:27 jschauma Exp $
+bin/profit
+share/doc/html/profit/IMG_PARAMS.db
+share/doc/html/profit/ProFit.css
+share/doc/html/profit/ProFit.html
+share/doc/html/profit/images.aux
+share/doc/html/profit/images.log
+share/doc/html/profit/images.pl
+share/doc/html/profit/images.tex
+share/doc/html/profit/img1.gif
+share/doc/html/profit/img2.gif
+share/doc/html/profit/img3.gif
+share/doc/html/profit/img4.gif
+share/doc/html/profit/index.html
+share/doc/html/profit/internals.pl
+share/doc/html/profit/l2h32434/img1.gif
+share/doc/html/profit/l2h32434/img2.gif
+share/doc/html/profit/l2h32434/img3.gif
+share/doc/html/profit/l2h32434/img4.gif
+share/doc/html/profit/labels.pl
+share/doc/html/profit/node1.html
+share/doc/html/profit/node10.html
+share/doc/html/profit/node11.html
+share/doc/html/profit/node12.html
+share/doc/html/profit/node13.html
+share/doc/html/profit/node14.html
+share/doc/html/profit/node15.html
+share/doc/html/profit/node16.html
+share/doc/html/profit/node17.html
+share/doc/html/profit/node18.html
+share/doc/html/profit/node19.html
+share/doc/html/profit/node2.html
+share/doc/html/profit/node20.html
+share/doc/html/profit/node21.html
+share/doc/html/profit/node22.html
+share/doc/html/profit/node23.html
+share/doc/html/profit/node24.html
+share/doc/html/profit/node25.html
+share/doc/html/profit/node3.html
+share/doc/html/profit/node4.html
+share/doc/html/profit/node5.html
+share/doc/html/profit/node6.html
+share/doc/html/profit/node7.html
+share/doc/html/profit/node8.html
+share/doc/html/profit/node9.html
+share/doc/profit/ProFit.dvi
+share/doc/profit/ProFit.ps
+share/doc/profit/ProFit.tex
+@dirrm share/doc/profit
+@dirrm share/doc/html/profit/l2h32434
+@dirrm share/doc/html/profit
diff -r e62ec0468100 -r 1519bb6d3d52 biology/profit/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/profit/distinfo   Sat Sep 27 23:18:26 2003 +0000
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1.1.1 2003/09/27 23:18:27 jschauma Exp $
+
+SHA1 (profit.tar.gz) = ddf74ebea7e855f5f3319fe0ca64d8a1672a7562
+Size (profit.tar.gz) = 242960 bytes
+SHA1 (patch-aa) = 3c2f745109183b38ac56799e3576997f931c93b3
diff -r e62ec0468100 -r 1519bb6d3d52 biology/profit/patches/patch-aa
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/profit/patches/patch-aa   Sat Sep 27 23:18:26 2003 +0000
@@ -0,0 +1,29 @@
+$NetBSD: patch-aa,v 1.1.1.1 2003/09/27 23:18:27 jschauma Exp $
+
+--- Makefile.orig      2002-08-06 07:56:26.000000000 -0400
++++ Makefile   2003-09-27 19:11:59.000000000 -0400
+@@ -7,7 +7,7 @@
+ #
+ # To allow decompression of gzipped PDB files on the fly, change the 
+ # COPT line to
+-COPT  = -DGUNZIP_SUPPORT -g
++COPT  = -DGUNZIP_SUPPORT
+ # COPT  = 
+ #
+ LINK1 = 
+@@ -29,11 +29,13 @@
+ bioplib/LegalAtomSpec.o bioplib/GetPDBChainLabels.o bioplib/DupePDB.o \
+ bioplib/TranslatePDB.o bioplib/AtomNameMatch.o bioplib/chindex.o
+ 
++all: profit
++
+ profit : $(OFILES) $(LFILES)
+-      $(CC) -g -o profit $(OFILES) $(LFILES) $(XMAS) -lm $(LINK2) $(XMASLIB)
++      $(CC) -o profit $(OFILES) ${LDFLAGS} $(LFILES) $(XMAS) -lm $(LINK2) $(XMASLIB)
+    
+ .c.o : $(IFILES)
+-      $(CC) $(COPT) -o $@ -c $<
++      $(CC) $(COPT) ${CFLAGS} -o $@ -c $<
+ 
+ clean :
+       /bin/rm $(OFILES) $(LFILES)