Libghemical port. This port installs support libraries of

science/ghemical port. From version 2.0, science/ghemical becomes
large, splitted into two parts. Update of ghemical port will
follow soon.

6 files changed, 181 insertions, 0 deletions

diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile
new file mode 100644
index 0000000..65ff217
--- /dev/null
+++ b/science/libghemical/Makefile
@@ -0,0 +1,36 @@
+# New ports collection makefile for: libghemical
+# Date created:			July 3, 2006
+# Whom:				Nakata Maho <maho@FreeBSD.org>
+#
+# $FreeBSD$
+
+PORTNAME=	libghemical
+PORTVERSION=	2.00
+CATEGORIES=	science
+MASTER_SITES=	http://www.uku.fi/~thassine/projects/download/ \
+		http://bioinformatics.org/ghemical/download/
+DISTNAME=	${PORTNAME}-${PORTVERSION}
+
+MAINTAINER=	maho@FreeBSD.org
+COMMENT=	Support libraries of science/ghemical port
+
+BUILD_DEPENDS=	${LOCALBASE}/lib/libmpqc.a:${PORTSDIR}/science/mpqc \
+		openbabel:${PORTSDIR}/science/openbabel \
+		mopac7:${PORTSDIR}/biology/mopac
+
+USE_GMAKE=	yes
+USE_GNOME=	pkgconfig
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--enable-mopac7 --enable-mpqc --enable-openbabel \
+		--with-blas="-L${LOCALBASE}/lib -lf77blas -lcblas -latlas" \
+		--with-lapack=-lalapack
+
+USE_AUTOTOOLS=	autoconf:259
+PLIST_SUB=	LIBGHEMICAL_VERSION="${PORTVERSION}"
+
+.include <bsd.port.pre.mk>
+
+pre-configure:
+	@cd ${WRKDIR}/${DISTNAME} ; ${AUTOCONF}
+
+.include <bsd.port.post.mk>
diff --git a/science/libghemical/distinfo b/science/libghemical/distinfo
new file mode 100644
index 0000000..5e9297d
--- /dev/null
+++ b/science/libghemical/distinfo
@@ -0,0 +1,3 @@
+MD5 (libghemical-2.00.tar.gz) = 19ee087b6f3c0ce816ed1722b4a5b002
+SHA256 (libghemical-2.00.tar.gz) = e873b3042df75fa1c9f37fc99f2ff14227965ed13c7680169f714ab6575d5f21
+SIZE (libghemical-2.00.tar.gz) = 629479
diff --git a/science/libghemical/files/ghemical-f2c.sh b/science/libghemical/files/ghemical-f2c.sh
new file mode 100644
index 0000000..9a1a372
--- /dev/null
+++ b/science/libghemical/files/ghemical-f2c.sh
@@ -0,0 +1,16 @@
+#
+# Make new c sources from fortran sources, restore changes,
+# made by Tommi Hassinen (3 comments are corrected additionally).
+# Should be started in miniMOPAC directory.
+
+f2c fortran/*.f
+cp fortran/*.c ./
+sed -e 's,/\* fortran/\(.*\)\.f -- translated by f2c (version 20000817),/\* \1.f -- translated by f2c (version 19991025),' \
+-e 's,dscal_,mMdscal_,g' \
+-e 's,dswap_,mMdswap_,g' \
+-e 's,daxpy_,mMdaxpy_,g' \
+-i '' *.c 
+mv etime.c etime.c.orig
+head -18 etime.c.orig > etime.c
+echo '#include <time.h>' >> etime.c
+tail +19 etime.c.orig >> etime.c
diff --git a/science/libghemical/files/patch-configure.ac b/science/libghemical/files/patch-configure.ac
new file mode 100644
index 0000000..9487ccf
--- /dev/null
+++ b/science/libghemical/files/patch-configure.ac
@@ -0,0 +1,48 @@
+--- configure.ac.orig	Mon Apr 24 19:58:14 2006
++++ configure.ac	Mon Jul  3 10:54:47 2006
+@@ -46,6 +46,16 @@
+ 		;;
+ esac
+ 
++AC_ARG_WITH(blas,
++[  --with-blas             Gives BLAS name you use(e.g., -lblas).],
++BLAS=$withval
++)
++
++AC_ARG_WITH(lapack,
++[  --with-lapack           Gives LAPACK name you use(e.g., -llapack).],
++LAPACK=$withval
++)
++
+ AC_ARG_ENABLE(mpqc,[  --enable-mpqc           compile with MPQC support],WITH_MPQC="$enableval",WITH_MPQC="no")
+ AC_ARG_ENABLE(mopac7,[  --enable-mopac7         compile with MOPAC7 support],WITH_MOPAC7="$enableval",WITH_MOPAC7="no")
+ ##removed20060208##AC_ARG_ENABLE(openbabel,[  --enable-openbabel      compile with OpenBabel support],WITH_OPENBABEL="$enableval",WITH_OPENBABEL="no")
+@@ -69,8 +79,26 @@
+ AC_CHECK_LIB([m], [acos])
+ 
+ if test $WITH_MPQC = yes; then
+-	AC_CHECK_LIB([blas], [main], , AC_MSG_ERROR([Cannot find blas library needed for MPQC support]))
+-	AC_CHECK_LIB([lapack], [main], , AC_MSG_ERROR([Cannot find lapack library needed for MPQC support]))
++
++#Blas and lapack ...actually not checked...
++BLAS=""
++ if test "$BLASNAME" = NONE; then
++   AC_MSG_ERROR([BLAS is required to complete the build])
++ else
++   HAVE_BLAS="yes"
++   BLAS="$BLASNAME"
++ fi
++ 
++ AC_SUBST(HAVE_BLAS)
++
++LAPACK=""
++if test "$LAPACKNAME" = NONE; then
++  AC_MSG_ERROR([LAPACK is required to complete the build])
++else
++  HAVE_LAPACK="yes"
++  LAPACK="$LAPACKNAME"
++fi
++
+ 	AM_PATH_SC(1.2.5, HAVE_MPQC="yes", HAVE_MPQC="no")
+ 	if test "${HAVE_MPQC}" = "yes"; then
+ 		AC_DEFINE([ENABLE_MPQC], [], [Define if you are building a version that interfaces directly with MPQC])
diff --git a/science/libghemical/pkg-descr b/science/libghemical/pkg-descr
new file mode 100644
index 0000000..a804fdc
--- /dev/null
+++ b/science/libghemical/pkg-descr
@@ -0,0 +1,3 @@
+libghemical is a support library packages for biology/ghemical
+
+WWW: http://www.uku.fi/~thassine/projects/ghemical/
diff --git a/science/libghemical/pkg-plist b/science/libghemical/pkg-plist
new file mode 100644
index 0000000..99a3ff4
--- /dev/null
+++ b/science/libghemical/pkg-plist
@@ -0,0 +1,75 @@
+include/ghemical/libghemicaldefine.h
+include/ghemical/libghemicalconfig2.h
+include/ghemical/typedef.h
+include/ghemical/v3d.h
+include/ghemical/atom.h
+include/ghemical/bond.h
+include/ghemical/constraint.h
+include/ghemical/model.h
+include/ghemical/engine.h
+include/ghemical/typerule.h
+include/ghemical/utility.h
+include/ghemical/seqbuild.h
+include/ghemical/eng1_qm.h
+include/ghemical/eng1_qm_mpqc.h
+include/ghemical/eng1_qm_mopac.h
+include/ghemical/eng1_mm.h
+include/ghemical/eng1_mm_tripos52.h
+include/ghemical/tab_mm_tripos52.h
+include/ghemical/eng1_mm_default.h
+include/ghemical/tab_mm_default.h
+include/ghemical/eng1_mm_prmfit.h
+include/ghemical/tab_mm_prmfit.h
+include/ghemical/eng1_sf.h
+include/ghemical/eng1_sf_ua.h
+include/ghemical/eng1_sf_cg.h
+include/ghemical/eng2_qm_mm.h
+include/ghemical/notice.h
+include/ghemical/conjgrad.h
+include/ghemical/intcrd.h
+include/ghemical/search.h
+include/ghemical/geomopt.h
+include/ghemical/moldyn.h
+include/ghemical/pop_ana.h
+include/ghemical/resonance.h
+@dirrm include/ghemical
+lib/libghemical.so.0
+lib/libghemical.la
+lib/libghemical.a
+lib/pkgconfig/libghemical.pc
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_amino02.in
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminoct02.in
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_aminont02.in
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/all_nuc02.in
+share/libghemical/%%LIBGHEMICAL_VERSION%%/amber/parm99.dat
+share/libghemical/%%LIBGHEMICAL_VERSION%%/builder/amino.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/builder/nucleic.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/atomtypes.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/parameters1.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/parameters2.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/parameters3.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default/parameters4.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/atomtypes.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/parameters1.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/parameters2.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/parameters3.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit/parameters4.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/atomtypes.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters1.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters2.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters3.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters4.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52/parameters5.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/loopdip.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/looptor.txt
+share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default/nonbonded.txt
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf/default
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_sf
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/tripos52
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/prmfit
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm/default
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/param_mm
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/amber
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%/builder
+@dirrm share/libghemical/%%LIBGHEMICAL_VERSION%%
+@dirrm share/libghemical