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.

5 files changed, 119 insertions, 0 deletions

diff --git a/biology/profit/DESCR b/biology/profit/DESCR
new file mode 100644
index 00000000000..6614adffd68
--- /dev/null
+++ b/biology/profit/DESCR
@@ -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 --git a/biology/profit/Makefile b/biology/profit/Makefile
new file mode 100644
index 00000000000..08ac873321a
--- /dev/null
+++ b/biology/profit/Makefile
@@ -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
+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 --git a/biology/profit/PLIST b/biology/profit/PLIST
new file mode 100644
index 00000000000..e0e1b1507a2
--- /dev/null
+++ b/biology/profit/PLIST
@@ -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 --git a/biology/profit/distinfo b/biology/profit/distinfo
new file mode 100644
index 00000000000..7ae7455e987
--- /dev/null
+++ b/biology/profit/distinfo
@@ -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 --git a/biology/profit/patches/patch-aa b/biology/profit/patches/patch-aa
new file mode 100644
index 00000000000..ed4347a0954
--- /dev/null
+++ b/biology/profit/patches/patch-aa
@@ -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)