diff options
-rw-r--r-- | biology/nab/Makefile | 51 | ||||
-rw-r--r-- | biology/nab/distinfo | 1 | ||||
-rw-r--r-- | biology/nab/files/Makefile | 6 | ||||
-rw-r--r-- | biology/nab/files/Makefile.doc | 5 | ||||
-rw-r--r-- | biology/nab/files/config.h | 110 | ||||
-rw-r--r-- | biology/nab/files/patch-aa | 25 | ||||
-rw-r--r-- | biology/nab/files/patch-ac | 13 | ||||
-rw-r--r-- | biology/nab/files/patch-ad | 13 | ||||
-rw-r--r-- | biology/nab/files/patch-ae | 19 | ||||
-rw-r--r-- | biology/nab/files/patch-af | 23 | ||||
-rw-r--r-- | biology/nab/files/patch-ag | 32 | ||||
-rw-r--r-- | biology/nab/files/patch-ah | 19 | ||||
-rw-r--r-- | biology/nab/files/patch-ai | 41 | ||||
-rw-r--r-- | biology/nab/pkg-comment | 1 | ||||
-rw-r--r-- | biology/nab/pkg-descr | 20 | ||||
-rw-r--r-- | biology/nab/pkg-message | 6 | ||||
-rw-r--r-- | biology/nab/pkg-plist | 281 |
17 files changed, 666 insertions, 0 deletions
diff --git a/biology/nab/Makefile b/biology/nab/Makefile new file mode 100644 index 000000000000..592421cc793b --- /dev/null +++ b/biology/nab/Makefile @@ -0,0 +1,51 @@ +# New ports collection Makefile for: nab +# Date created: Sept. 10, 2000 +# Whom: M. L. Dodson <bdodson@scms.utmb.edu> +# $FreeBSD$ + +PORTNAME= nab +PORTVERSION= 4.2 +CATEGORIES= biology +MASTER_SITES= ftp://ftp.scripps.edu/pub/case/ + +MAINTAINER= bdodson@scms.utmb.edu + +NO_WRKSUBDIR= yes +MAKE_ENV+= WRKSRC=${WRKSRC} PREFIX=${PREFIX} \ + NABHOME=${PREFIX}/share/nab ARCH= \ + INSTALL_MAN="${INSTALL_MAN}" +MAN1= nab.1 +MANCOMPRESSED= yes + +post-extract: + @${CP} ${FILESDIR}/Makefile ${WRKSRC} + @${CP} ${FILESDIR}/Makefile.doc ${WRKSRC}/doc/Makefile + @${CP} ${FILESDIR}/config.h ${WRKSRC} + +pre-install: + @-mkdir -p ${PREFIX}/share/nab +.if !defined(${NOPORTDOCS}) + @cd ${WRKSRC} && (tar cf - examples test | \ + (cd ${PREFIX}/share/nab; tar xf -)) + @-mkdir -p ${PREFIX}/share/doc/nab + ${INSTALL_MAN} ${WRKSRC}/doc/NAB.pdf ${PREFIX}/share/doc/nab +.endif + @cd ${WRKSRC} && (tar cf - dgdb reslib | \ + (cd ${PREFIX}/share/nab; tar xf -)) + @(cd ${PREFIX}/share; ${CHOWN} -R ${SHAREOWN}.${SHAREGRP} nab; \ + ${CHMOD} -R ugo+rX-w nab) + @-(cd ${PREFIX}/share/nab; ${RM} -f coords && ${LN} -s ../NDB coords) + +post-install: + @(cd ${PREFIX}/bin; \ + ${RM} -f nab && ${MV} ${PREFIX}/share/nab/bin/nab . ; \ + ${RM} -f nab2c && ${MV} ${PREFIX}/share/nab/bin/nab2c . ; \ + ${CHOWN} ${BINOWN}:${BINGRP} nab nab2c teLeap ; \ + strip nab nab2c teLeap ; \ + ${RMDIR} ${PREFIX}/share/nab/bin) + @${CAT} ${PKGMESSAGE} + +test: all + @cd ${WRKSRC}/src && make test + +.include <bsd.port.mk> diff --git a/biology/nab/distinfo b/biology/nab/distinfo new file mode 100644 index 000000000000..42f4bcadaada --- /dev/null +++ b/biology/nab/distinfo @@ -0,0 +1 @@ +MD5 (nab-4.2.tar.gz) = 5b703cc9dc514549ea97c751fa68f239 diff --git a/biology/nab/files/Makefile b/biology/nab/files/Makefile new file mode 100644 index 000000000000..79f216e09eb8 --- /dev/null +++ b/biology/nab/files/Makefile @@ -0,0 +1,6 @@ +# $FreeBSD$ +#SUBDIR=cccp cifparse src +SUBDIR=src tleap doc +MAN1=nab.1 + +.include <bsd.subdir.mk> diff --git a/biology/nab/files/Makefile.doc b/biology/nab/files/Makefile.doc new file mode 100644 index 000000000000..279a1dcd4d88 --- /dev/null +++ b/biology/nab/files/Makefile.doc @@ -0,0 +1,5 @@ +all: + +install: + gzip -nfc -9 nab.1 > nab.1.gz + ${INSTALL_MAN} ${WRKSRC}/doc/nab.1.gz ${PREFIX}/man/man1 diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h new file mode 100644 index 000000000000..d79236788f96 --- /dev/null +++ b/biology/nab/files/config.h @@ -0,0 +1,110 @@ +############################################################################### +# Configuration section: look at sections (1) to (4) below, making +# changes that seem necessary. For most UNIX systems, no changes +# should be necessary. +# +############################################################################### +# +# (1) You need to define the symbols NABHOME and ARCH, either on the +# make command line (e.g. "make ARCH=sun4 NABHOME=/thr/eigen/nab5") +# or as environment variables. +# +# NABHOME should be an absolute path to the directory above this one. +# ARCH is used to distinguish compilations for various architectures. +# +# Files created by "make install" end up in: +# $NABHOME/bin/$ARCH +# $NABHOME/lib/$ARCH +# $NABHOME/include +# +# You can choose ARCH as you wish, but it would generally +# be related to the output of the "uname" command. +# +#BINDIR=$(NABHOME)/bin/$(ARCH) +#LIBDIR=$(NABHOME)/lib/$(ARCH) +#NABHOME=/usr/local/share/nab +#ARCH= +BINDIR=$(NABHOME)/bin +LIBDIR=$(NABHOME)/lib +INCDIR=$(NABHOME)/include +# +############################################################################### +# +# +# (2) If you want to search additional libraries by default, add them +# to the FLIBS variable here. (External libraries can also be linked into +# NAB programs simply by including them on the command line; libraries +# included in FLIBS are always searched.) +# +#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a +#FLIBS=../cifparse/cifparse.a +# +# following for Sun4, Solaris 2.x +# +#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a -lF77 -lM77 -lsunmath +# +# following for HP-UX +# +#FLIBS=$(LIBDIR)/cifparse.a $(LIBDIR)/libsym.a lapack.a blas.a -lf -lvec +# +############################################################################### +# +# (3) Set AVS to 1 if you want AVS support; if so, set AVSDIR to point to +# your AVS distribution. The directories $AVSDIR/include and $AVSDIR/lib +# must exist, and CFLAGS (below) must also be modified for AVS support. +# +AVS= 0 +# +#AVSDIR= /tsri/avs/$(ARCH)/avs +#AVSINCDIR= $(AVSDIR)/include +# +# +############################################################################### +# +# (4) Modify any of the following if you need to change, e.g. to use gcc +# rather than cc, etc. +# +# +SHELL= /bin/sh +# +# Set the C compiler, etc. +# +# (For GNU: cc-->gcc; lex-->flex; yacc-->bison -y -t; +# Note: If you lexer is "really" flex, you need to set +# LEX=flex below. For example, on many linux distributions, +# /usr/bin/lex is really just a pointer to /usr/bin/flex, +# so LEX=flex is necessary. In general, gcc seems to need +# flex.) +# +CC= cc +LEX= flex +YACC= yacc +AR= ar +# +# Set the C-preprocessor. Code for the preprocessor from gcc is in +# ../cccp; it gets installed as $(NABHOME)/bin/$(ARCH)/cpp; +# this should generally *not* be changed. +# +#CPP= $(NABHOME)/bin/$(ARCH)/cpp -lang-c++ +#CPP= ../cccp/cpp -lang-c++ +CPP= cc -E -x c++ +# +# Use these CFLAGS if AVS = 0 +# Notes: for 64-bit IRIX, add "-n32" to both CFLAGS and OCFLAGS +# for RedHat Linux 5.1 (and other linuxes?) add -DHAVE_STRERROR +# +OCFLAGS= -O +CFLAGS= -DHAVE_STRERROR ${OCFLAGS} +NABFLAGS= +# +# Use these CFLAGS if AVS = 1 +# +#CFLAGS= -g -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR) +#OCFLAGS= -O -DAVS=$(AVS) -DAVSDIR='"$(AVSDIR)"' -I$(AVSINCDIR) +# +# +# For Win95, set SFX to ".exe"; for Unix,NT leave it empty: +# +#SFX=.exe +SFX= +# diff --git a/biology/nab/files/patch-aa b/biology/nab/files/patch-aa new file mode 100644 index 000000000000..c8e736e87ab8 --- /dev/null +++ b/biology/nab/files/patch-aa @@ -0,0 +1,25 @@ +*** src/Makefile.orig Fri Jan 8 16:06:59 1999 +--- src/Makefile Thu Jan 14 16:15:53 1999 +*************** +*** 7,15 **** + ./nab -c $(NABFLAGS) $< + @rm -f $*.c + +- .c.o: $< +- $(CC) -c $(CFLAGS) $< +- + NAB2COBJS= \ + nab2c.o \ + cgen.o \ +--- 7,12 ---- +*************** +*** 77,82 **** +--- 74,81 ---- + yammp.o + + #=========================================================================== ++ ++ all: system + + system: nab \ + nab2c \ diff --git a/biology/nab/files/patch-ac b/biology/nab/files/patch-ac new file mode 100644 index 000000000000..1487c52d9336 --- /dev/null +++ b/biology/nab/files/patch-ac @@ -0,0 +1,13 @@ +*** cccp/Makefile.orig Thu Jan 14 16:20:38 1999 +--- cccp/Makefile Thu Jan 14 16:21:08 1999 +*************** +*** 4,9 **** +--- 4,11 ---- + ######### no configuration should be needed beyond this line ################# + ############################################################################## + ++ all: cpp$(SFX) ++ + cpp$(SFX): cppmain.o cpplib.o cpphash.o cppalloc.o cpperror.o cppexp.o version.o \ + obstack.o alloca.o + $(CC) $(CFLAGS) -o cpp$(SFX) cppmain.o cpplib.o cpphash.o \ diff --git a/biology/nab/files/patch-ad b/biology/nab/files/patch-ad new file mode 100644 index 000000000000..f498e568a3cf --- /dev/null +++ b/biology/nab/files/patch-ad @@ -0,0 +1,13 @@ +*** cifparse/Makefile.orig Thu Jan 14 16:21:50 1999 +--- cifparse/Makefile Thu Jan 14 16:22:08 1999 +*************** +*** 11,16 **** +--- 11,18 ---- + cifp.tab.o \ + cifparse.o + ++ all: cifparse.a ++ + cifparse.a: $(CIFOBS) + -rm cifparse.a + $(AR) rv cifparse.a $(CIFOBS) diff --git a/biology/nab/files/patch-ae b/biology/nab/files/patch-ae new file mode 100644 index 000000000000..b901073e9ebb --- /dev/null +++ b/biology/nab/files/patch-ae @@ -0,0 +1,19 @@ +*** examples/program_7.nab.orig Thu Jan 14 16:53:07 1999 +--- examples/program_7.nab Thu Jan 14 16:53:24 1999 +*************** +*** 9,15 **** + cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" ); + + m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb", +! "dna", 2.25, -4.96, 36.0, 4.38, "" ); + + b = newbounds(m, ""); + allocate xyz[ 4*m.natoms ]; +--- 9,15 ---- + cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" ); + + m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb", +! "dna", 2.25, -4.96, 36.0, 3.38, "" ); + + b = newbounds(m, ""); + allocate xyz[ 4*m.natoms ]; diff --git a/biology/nab/files/patch-af b/biology/nab/files/patch-af new file mode 100644 index 000000000000..bf908f8b23a6 --- /dev/null +++ b/biology/nab/files/patch-af @@ -0,0 +1,23 @@ +*** src/reslib.c.orig Tue Apr 21 14:10:50 1998 +--- src/reslib.c Mon Feb 1 09:50:35 1999 +*************** +*** 610,618 **** + fclose( cfp ); + } + +! fclose( pfp ); + +! fclose( bfp ); + + return( rlp ); + } +--- 610,618 ---- + fclose( cfp ); + } + +! if( pfp ) {fclose( pfp );} + +! if( bfp ) {fclose( bfp );} + + return( rlp ); + } diff --git a/biology/nab/files/patch-ag b/biology/nab/files/patch-ag new file mode 100644 index 000000000000..d902077dd59d --- /dev/null +++ b/biology/nab/files/patch-ag @@ -0,0 +1,32 @@ +*** src/database.c.orig Tue Apr 21 12:17:17 1998 +--- src/database.c Tue Mar 9 09:09:06 1999 +*************** +*** 73,78 **** +--- 73,85 ---- + + #include "database.h" + ++ #if (defined(__unix__) || defined(unix)) && !defined(USG) ++ #include <sys/param.h> ++ #endif ++ ++ #if defined(BSD) ++ #include <math.h> ++ #endif + + #ifndef TRUE + #define TRUE 1 +*************** +*** 985,991 **** +--- 992,1002 ---- + + sDBRemoveLeadingSpaces( sLine ); + sDBRemoveFirstString( sLine, sHead ); ++ #if defined(linux) || defined(BSD) ++ sscanf( sHead, "%lg", dPDbl ); ++ #else + sscanf( sHead, "%lG", dPDbl ); ++ #endif + + } + diff --git a/biology/nab/files/patch-ah b/biology/nab/files/patch-ah new file mode 100644 index 000000000000..71f8da6baac6 --- /dev/null +++ b/biology/nab/files/patch-ah @@ -0,0 +1,19 @@ +*** semantics/Makefile.orig Fri Mar 10 20:08:16 2000 +--- semantics/Makefile Sun Sep 10 18:47:44 2000 +*************** +*** 43,49 **** + SYM_UPARROW_ASSIGN.rules + + checkexpr.c: $(RULES) attribute.tab parse ../src/nab.h ../src/nabgrm.y +! ./parse *.rules + + parse: parse.c + $(CC) -o parse parse.c +--- 43,49 ---- + SYM_UPARROW_ASSIGN.rules + + checkexpr.c: $(RULES) attribute.tab parse ../src/nab.h ../src/nabgrm.y +! env NABHOME=.. ./parse *.rules + + parse: parse.c + $(CC) -o parse parse.c diff --git a/biology/nab/files/patch-ai b/biology/nab/files/patch-ai new file mode 100644 index 000000000000..76cf860b0ce6 --- /dev/null +++ b/biology/nab/files/patch-ai @@ -0,0 +1,41 @@ +*** tleap/Makefile.orig Tue Jun 20 13:41:55 2000 +--- tleap/Makefile Sun Sep 10 19:38:24 2000 +*************** +*** 5,13 **** + .SUFFIXES: + .SUFFIXES: .c .o + +- .c.o: $< +- $(CC) -c $(CFLAGS) -DSYSV $< +- + # + # Absolutely necessary routines + # +--- 5,10 ---- +*************** +*** 76,81 **** +--- 73,79 ---- + OUL2P= utilLib2Pdb.o + + TLEAP_OBJ= $(OA) $(OG) $(OO) $(OL) $(OC) ++ all: teLeap$(SFX) + teLeap$(SFX): $(TLEAP_OBJ) + $(CC) -o $@ $(TLEAP_OBJ) -lm + +*************** +*** 409,415 **** + zMatrix.o: zMatrix.h + + install: teLeap$(SFX) +! mv teLeap$(SFX) $(BINDIR) + + uninstall: clean + -rm $(BINDIR)/teLeap$(SFX) +--- 407,413 ---- + zMatrix.o: zMatrix.h + + install: teLeap$(SFX) +! mv teLeap$(SFX) $(PREFIX)/bin + + uninstall: clean + -rm $(BINDIR)/teLeap$(SFX) diff --git a/biology/nab/pkg-comment b/biology/nab/pkg-comment new file mode 100644 index 000000000000..98f624d1cacd --- /dev/null +++ b/biology/nab/pkg-comment @@ -0,0 +1 @@ +This is nab (nucleic acid builder), a language for macromolecules diff --git a/biology/nab/pkg-descr b/biology/nab/pkg-descr new file mode 100644 index 000000000000..f2f95cd05b16 --- /dev/null +++ b/biology/nab/pkg-descr @@ -0,0 +1,20 @@ +This is version 4.2 of nab (nucleic acid builder), a computer language that +is intended for use in creating, describing and modifying macromolecules, +especially nucleic acids. Programs written in nab are translated into C, +which in turn is compiled into machine code. + +Further general information can be obtained from our web page: + +WWW: http://www.scripps.edu/case + +Although we have been using this code for some time now, users should be +aware that bugs may still exist. Please see the file COPYING for the usual +disclaimer of liability. Further enhancements are planned, and will be +announced on the web page. + +Please send comments and suggestions to Tom Macke (macke@scripps.edu) and/or +to Dave Case (case@scripps.edu). If you find the program useful, please +send us a note outlining your applications. + +This port to FreeBSD by M. L. Dodson, Univ. of Texas Medical Branch, Galveston +bdodson@scms.utmb.edu diff --git a/biology/nab/pkg-message b/biology/nab/pkg-message new file mode 100644 index 000000000000..349abd45952d --- /dev/null +++ b/biology/nab/pkg-message @@ -0,0 +1,6 @@ +------------------------------------------------------------------------------- +You must set the environment variable NABHOME before nab is used. This is +needed so that nab can find its residue and structure databases. This should be +NABHOME=${PREFIX}/share/nab, where ${PREFIX} was the value of the PREFIX +makefile variable when nab was built. +------------------------------------------------------------------------------- diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist new file mode 100644 index 000000000000..c0200e730db8 --- /dev/null +++ b/biology/nab/pkg-plist @@ -0,0 +1,281 @@ +bin/nab +bin/nab2c +bin/teLeap +share/doc/nab/NAB.pdf +share/nab/lib/libnab.a +share/nab/include/nabcode.h +share/nab/include/nab.h +share/nab/include/defreal.h +share/nab/include/nabtypes.h +share/nab/examples/program_1.nab +share/nab/examples/program_2.nab +share/nab/examples/program_3.nab +share/nab/examples/program_4.nab +share/nab/examples/program_5.nab +share/nab/examples/program_6.nab +share/nab/examples/program_7.nab +share/nab/examples/program_7.nab.orig +share/nab/examples/README +share/nab/examples/program_9.nab +share/nab/examples/program_10.nab +share/nab/examples/program_11.nab +share/nab/examples/program_12.nab +share/nab/examples/program_13.nab +share/nab/examples/program_14.nab +share/nab/examples/program_8.nab +share/nab/examples/test.pdb +share/nab/examples/ADE.pdb +share/nab/examples/Makefile +share/nab/examples/gcg10.pdb +share/nab/examples/rna_pseudoknot.pdb +share/nab/examples/THY.pdb +share/nab/examples/program_5.gcg.in +share/nab/examples/getbase.nab +share/nab/examples/program_4.ref +share/nab/examples/acgtacgt.pdb +share/nab/examples/program_5.tat.in +share/nab/examples/program_2.ref +share/nab/examples/program_5.cgc.in +share/nab/examples/program_5.ata.in +share/nab/examples/test.sup.pdb +share/nab/examples/gcg10.pdb.save +share/nab/dgdb/bdna.basepair.db +share/nab/dgdb/bdna.nucleotide.db +share/nab/dgdb/bdna.stack.db +share/nab/dgdb/trna.stack.db +share/nab/dgdb/arna.basepair.db +share/nab/dgdb/trna.basepair.db +share/nab/dgdb/zdna.nucleotide.db +share/nab/dgdb/adna.nucleotide.db +share/nab/dgdb/adna.basepair.db +share/nab/dgdb/adna.stack.db +share/nab/dgdb/zdna.basepair.db +share/nab/dgdb/zdna.stack.db +share/nab/dgdb/trna.nucleotide.db +share/nab/dgdb/dna.basepair.db +share/nab/dgdb/arna.nucleotide.db +share/nab/dgdb/rna.basepair.db +share/nab/dgdb/arna.stack.db +share/nab/reslib/bdna.std/bdna.std.bnd +share/nab/reslib/bdna.std/bdna.std.chi +share/nab/reslib/bdna.std/bdna.std.pdb +share/nab/reslib/bdna.std/dna.qr +share/nab/reslib/bounds.db +share/nab/reslib/protein.opls/protein.opls.bnd +share/nab/reslib/protein.opls/protein.opls.chi +share/nab/reslib/protein.opls/protein.opls.pdb +share/nab/reslib/protein.opls/protein.opls.qr +share/nab/reslib/arna.std/arna.std.bnd +share/nab/reslib/arna.std/arna.std.pdb +share/nab/reslib/adna.std.rlb +share/nab/reslib/axes/Axes.bnd +share/nab/reslib/axes/XYZ.axes +share/nab/reslib/rna.amber94/rna.amber94.3.bnd +share/nab/reslib/rna.amber94/rna.amber94.3.pdb +share/nab/reslib/rna.amber94/rna.amber94.5.qr +share/nab/reslib/rna.amber94/rna.amber94.5.bnd +share/nab/reslib/rna.amber94/rna.amber94.5.pdb +share/nab/reslib/rna.amber94/rna.amber94.qr +share/nab/reslib/rna.amber94/rna.amber94.bnd +share/nab/reslib/rna.amber94/rna.amber94.chi +share/nab/reslib/rna.amber94/rna.amber94.pdb +share/nab/reslib/rna.amber94/rna.amber94.3.qr +share/nab/reslib/rna.amber94/rna.amber94_nmr.3.qr +share/nab/reslib/rna.amber94/rna.amber94_nmr.qr +share/nab/reslib/rna.amber94/rna.amber94_nmr.5.qr +share/nab/reslib/arna.std.rlb +share/nab/reslib/protein.amber94/protein.amber94.C.bnd +share/nab/reslib/protein.amber94/protein.amber94.C.pdb +share/nab/reslib/protein.amber94/protein.amber94.C.qr +share/nab/reslib/protein.amber94/protein.amber94.N.bnd +share/nab/reslib/protein.amber94/protein.amber94.N.pdb +share/nab/reslib/protein.amber94/protein.amber94.N.qr +share/nab/reslib/protein.amber94/protein.amber94.NC.chi +share/nab/reslib/protein.amber94/protein.amber94.bnd +share/nab/reslib/protein.amber94/protein.amber94.chi 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