diff options
author | Maho Nakata <maho@FreeBSD.org> | 2008-03-07 02:38:09 +0000 |
---|---|---|
committer | Maho Nakata <maho@FreeBSD.org> | 2008-03-07 02:38:09 +0000 |
commit | 89a3cd0f56e3b66427011fb2c658c733b7054476 (patch) | |
tree | 5bff3c99498032b00045df7dcc0bcbed77c6d2bf /biology/pymol | |
parent | - Update to 1.4.9.5 (diff) |
Update to 1.0r2.
Notes
Notes:
svn path=/head/; revision=208552
Diffstat (limited to 'biology/pymol')
-rw-r--r-- | biology/pymol/Makefile | 49 | ||||
-rw-r--r-- | biology/pymol/distinfo | 6 | ||||
-rw-r--r-- | biology/pymol/files/patch-Rules.make | 71 | ||||
-rw-r--r-- | biology/pymol/files/patch-setup+pymol+com+linux-rh7x | 27 | ||||
-rw-r--r-- | biology/pymol/files/patch-setup.py | 19 | ||||
-rw-r--r-- | biology/pymol/pkg-plist | 1419 |
6 files changed, 636 insertions, 955 deletions
diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile index dc1d75cfe776..d053e5b0e62e 100644 --- a/biology/pymol/Makefile +++ b/biology/pymol/Makefile @@ -5,13 +5,9 @@ # $FreeBSD$ PORTNAME= pymol -PORTVERSION= 0.99rc6 -PORTREVISION= 2 +PORTVERSION= 1.0r2 CATEGORIES= biology python -MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} -MASTER_SITE_SUBDIR= pymol -DISTNAME= pymol-${PORTVERSION:S/./_/}-src -EXTRACT_SUFX= .tgz +MASTER_SITES= ${MASTER_SITE_LOCAL:S|%SUBDIR%|maho/pymol|} MAINTAINER= maho@FreeBSD.org COMMENT= Free and Open-Source molecular modeling system @@ -26,42 +22,15 @@ WRKSRC= ${WRKDIR}/pymol-${PORTVERSION} USE_GMAKE= yes USE_PYTHON= yes -.include <bsd.port.pre.mk> +pre-build: + @${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+" ${WRKSRC}/setup.py -.if ${ARCH} == "ia64" -BROKEN= Does not build on ${ARCH} -.endif - -.if ${ARCH} == "sparc64" || ${ARCH} == "amd64" || ${ARCH} == "ia64" -PICFLAG?= -fPIC -.else -PICFLAG?= -fpic -.endif - -pre-patch: - @${CP} ${WRKSRC}/setup/Rules.linux ${WRKSRC}/Rules.make - -post-patch: - @${CP} ${WRKSRC}/setup/pymol.com.linux-rh7x ${WRKSRC}/pymol - @${REINPLACE_CMD} -e 's,@PREFIX@,${PREFIX},g' -e 's,@LOCALBASE@,${LOCALBASE},g' ${WRKSRC}/pymol - ${REINPLACE_CMD} -e 's,@PYTHON_VERSION@,${PYTHON_VERSION},g' \ - -e 's,@LOCALBASE@,${LOCALBASE},g' \ - -e 's,@X11BASE@,${X11BASE},g' \ - -e 's,@CFLAGS@,${CFLAGS},g' \ - -e 's,@CC@,${CC},g' \ - -e 's,@PICFLAG@,${PICFLAG},g' ${WRKSRC}/Rules.make +do-build: + @cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} build do-install: + @(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} install \ + ; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup2.py install) @${INSTALL_SCRIPT} ${WRKSRC}/pymol ${PREFIX}/bin/pymol - @${MKDIR} ${PREFIX}/share/pymol - @${TAR} -C ${WRKSRC} -chf - data modules test | \ - ${TAR} -xf - -C ${PREFIX}/share/pymol -.if !defined(NOPORTDOCS) - @${MKDIR} ${EXAMPLESDIR} - @${TAR} -C ${WRKSRC}/examples --exclude package -chf - . | \ - ${TAR} -xf - -C ${EXAMPLESDIR} -.endif - @${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py ${PREFIX}/share/pymol/modules - @${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py ${PREFIX}/share/pymol/modules -.include <bsd.port.post.mk> +.include <bsd.port.mk> diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo index a7292cf0ce50..5bf879c618ae 100644 --- a/biology/pymol/distinfo +++ b/biology/pymol/distinfo @@ -1,3 +1,3 @@ -MD5 (pymol-0_99rc6-src.tgz) = cb29385ab523f648d4db47a222b1d03e -SHA256 (pymol-0_99rc6-src.tgz) = d56bebc1316fd3442c54dee5bc4b2979041943bf50a9b34b44839595fd1b9a59 -SIZE (pymol-0_99rc6-src.tgz) = 4198816 +MD5 (pymol-1.0r2.tar.gz) = 196bd9a8f7de6e7c9e77eacd463ce140 +SHA256 (pymol-1.0r2.tar.gz) = 876d1422c4fd9a8bb792ac38e960afb4cc59b54e0e0d26bf44daaeaff122b16f +SIZE (pymol-1.0r2.tar.gz) = 7636761 diff --git a/biology/pymol/files/patch-Rules.make b/biology/pymol/files/patch-Rules.make deleted file mode 100644 index 7091e92ddf73..000000000000 --- a/biology/pymol/files/patch-Rules.make +++ /dev/null @@ -1,71 +0,0 @@ ---- Rules.make.orig Sun Sep 17 20:42:52 2006 -+++ Rules.make Sun Sep 17 20:48:26 2006 -@@ -4,27 +4,27 @@ - # - #- Building ---------------------------------------------------------- - #--- Tell "make" how to get to PyMOL --PYMOL_PATH = ${HOME}/pymol -+PYMOL_PATH = @LOCALBASE@ - #--------------------------------------------------------------------- - # - #- Dependencies ------------------------------------------------------ - #--- X-windows --XLIB_DIR = -L/usr/X11R6/lib --XINC_DIR = -I/usr/X11R6/include -+XLIB_DIR = -L@X11BASE@/lib -+XINC_DIR = -I@X11BASE@/include - #--- Python --PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python -+PYTHON_EXE = $(PYMOL_PATH)/bin/python - PYTHON_LIB = - PYTHON_LIB_DIR = --PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.3 \ -- -I$(PYMOL_PATH)/ext/include/python2.3/Numeric -+PYTHON_INC_DIR = -I$(PYMOL_PATH)/include/@PYTHON_VERSION@ \ -+ -I$(PYMOL_PATH)/include/@PYTHON_VERSION@/Numeric - #--- Other external dependencies --EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include --EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib -+EXT_INC_DIR = -I$(PYMOL_PATH)/include -+EXT_LIB_DIR = -L$(PYMOL_PATH)/lib - #--------------------------------------------------------------------- - # - #- Build for LINUX as an importable module --------------------------- - #--- System libraries --LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -ldl -lpng -lXmu $(ZLIB) -lm -+LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -lpng -lXmu $(ZLIB) -lm - #--- PyMOL configuration - DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_PYMOL_INLINE - #--- How we build shared libraries -@@ -32,19 +32,19 @@ - #--- What are we trying to build? - DEST = -o modules/pymol/_cmd.so - #--- Gcc Options for Linux --CCOPT1 = -march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes -+CCOPT1 = @PICFLAG@ @CFLAGS@ #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes - #--- libraries for PyOpenGL - PYOGL_LIB = -lglut -lGL -lGLU -lXmu -lXi - #--------------------------------------------------------------------- - # - #- Choose One -------------------------------------------------------- - #--- GCC Optimized --CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer -finline-limit=10000 -+#CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer -finline-limit=10000 - #--- GCC Profiling - #CCOPT2 = -pg -O3 -funroll-loops - #--- Debugging - #CCOPT2 = -g -D_MemoryDebug_ON --CCOPT2 = -g -+CCOPT2 = #-g - #--------------------------------------------------------------------- - # - #- Choose One -------------------------------------------------------- -@@ -70,7 +70,7 @@ - # No changes normally required below here - #--------------------------------------------------------------------- - --CC = cc -+CC = @CC@ - - LIB_DIRS = $(EXT_LIB_DIR) $(PYTHON_LIB_DIR) $(XLIB_DIR) - diff --git a/biology/pymol/files/patch-setup+pymol+com+linux-rh7x b/biology/pymol/files/patch-setup+pymol+com+linux-rh7x deleted file mode 100644 index c1273c309745..000000000000 --- a/biology/pymol/files/patch-setup+pymol+com+linux-rh7x +++ /dev/null @@ -1,27 +0,0 @@ ---- setup/pymol.com.linux-rh7x Sun Nov 20 02:46:39 2005 -+++ setup/pymol.com.linux-rh7x Sat Jul 1 13:28:49 2006 -@@ -5,7 +5,7 @@ - # ============================================================== - # Set PYMOL_PATH to point at the correct location on your system - # --PYMOL_PATH=/usr/local/pymol -+PYMOL_PATH=@LOCALBASE@/share/pymol - export PYMOL_PATH - # - # ============================================================== -@@ -13,13 +13,13 @@ - # - # python modules - # --if [ "$PYTHONPATH" == "" ]; then -+if [ "$PYTHONPATH" = "" ]; then - PYTHONPATH=${PYMOL_PATH}/modules - else - PYTHONPATH=${PYMOL_PATH}/modules:${PYTHONPATH} - fi - export PYTHONPATH - # --/usr/bin/python $PYMOL_PATH/modules/pymol/__init__.py "$@" -+@LOCALBASE@/bin/python $PYMOL_PATH/modules/pymol/__init__.py "$@" - - diff --git a/biology/pymol/files/patch-setup.py b/biology/pymol/files/patch-setup.py new file mode 100644 index 000000000000..08bb35418fee --- /dev/null +++ b/biology/pymol/files/patch-setup.py @@ -0,0 +1,19 @@ +--- setup.py.orig 2007-07-03 07:11:15.000000000 +0900 ++++ setup.py 2008-03-06 17:59:33.000000000 +0900 +@@ -88,6 +88,8 @@ + "layer0","layer1","layer2", + "layer3","layer4","layer5", + "/usr/include/freetype2", ++ "%%LOCALBASE%%/include", ++ "%%LOCALBASE%%/include/freetype2", + # "/users/warren/ext/include", + # VMD plugin support + # "contrib/uiuc/plugins/include", +@@ -98,6 +100,7 @@ + pyogl_libs = ["GL","GLU","glut"] + lib_dirs=[ + "/usr/X11R6/lib", ++ "%%LOCALBASE%%/lib", + # "/users/warren/pymol/ext/lib" + ] + def_macros=[("_PYMOL_MODULE",None), diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist index 269b5262b20a..7300fff42a06 100644 --- a/biology/pymol/pkg-plist +++ b/biology/pymol/pkg-plist @@ -1,815 +1,606 @@ bin/pymol -share/pymol/data/chempy/fragments/ace.pkl -share/pymol/data/chempy/fragments/acetylene.pkl -share/pymol/data/chempy/fragments/ala.pkl -share/pymol/data/chempy/fragments/arg.pkl -share/pymol/data/chempy/fragments/asn.pkl -share/pymol/data/chempy/fragments/asp.pkl -share/pymol/data/chempy/fragments/benzene.pkl -share/pymol/data/chempy/fragments/butane.pkl -share/pymol/data/chempy/fragments/ct_ala.pkl -share/pymol/data/chempy/fragments/ct_arg.pkl -share/pymol/data/chempy/fragments/ct_asn.pkl -share/pymol/data/chempy/fragments/ct_asp.pkl -share/pymol/data/chempy/fragments/ct_cys.pkl -share/pymol/data/chempy/fragments/ct_gln.pkl -share/pymol/data/chempy/fragments/ct_glu.pkl -share/pymol/data/chempy/fragments/ct_gly.pkl -share/pymol/data/chempy/fragments/ct_hid.pkl -share/pymol/data/chempy/fragments/ct_hie.pkl -share/pymol/data/chempy/fragments/ct_hip.pkl -share/pymol/data/chempy/fragments/ct_his.pkl -share/pymol/data/chempy/fragments/ct_ile.pkl -share/pymol/data/chempy/fragments/ct_leu.pkl -share/pymol/data/chempy/fragments/ct_lys.pkl -share/pymol/data/chempy/fragments/ct_met.pkl -share/pymol/data/chempy/fragments/ct_phe.pkl -share/pymol/data/chempy/fragments/ct_pro.pkl -share/pymol/data/chempy/fragments/ct_ser.pkl -share/pymol/data/chempy/fragments/ct_thr.pkl -share/pymol/data/chempy/fragments/ct_trp.pkl -share/pymol/data/chempy/fragments/ct_tyr.pkl -share/pymol/data/chempy/fragments/ct_val.pkl -share/pymol/data/chempy/fragments/cyclobutane.pkl -share/pymol/data/chempy/fragments/cycloheptane.pkl -share/pymol/data/chempy/fragments/cyclohexane.pkl -share/pymol/data/chempy/fragments/cyclopentadiene.pkl -share/pymol/data/chempy/fragments/cyclopentane.pkl -share/pymol/data/chempy/fragments/cys.pkl -share/pymol/data/chempy/fragments/ethylene.pkl -share/pymol/data/chempy/fragments/formaldehyde.pkl -share/pymol/data/chempy/fragments/formamide.pkl -share/pymol/data/chempy/fragments/gln.pkl -share/pymol/data/chempy/fragments/glu.pkl -share/pymol/data/chempy/fragments/gly.pkl -share/pymol/data/chempy/fragments/hid.pkl -share/pymol/data/chempy/fragments/hie.pkl -share/pymol/data/chempy/fragments/hip.pkl -share/pymol/data/chempy/fragments/his.pkl -share/pymol/data/chempy/fragments/ile.pkl -share/pymol/data/chempy/fragments/leu.pkl -share/pymol/data/chempy/fragments/lys.pkl -share/pymol/data/chempy/fragments/met.pkl -share/pymol/data/chempy/fragments/methane.pkl -share/pymol/data/chempy/fragments/nme.pkl -share/pymol/data/chempy/fragments/nt_ala.pkl -share/pymol/data/chempy/fragments/nt_arg.pkl -share/pymol/data/chempy/fragments/nt_asn.pkl -share/pymol/data/chempy/fragments/nt_asp.pkl -share/pymol/data/chempy/fragments/nt_cys.pkl -share/pymol/data/chempy/fragments/nt_gln.pkl -share/pymol/data/chempy/fragments/nt_glu.pkl -share/pymol/data/chempy/fragments/nt_gly.pkl -share/pymol/data/chempy/fragments/nt_hid.pkl -share/pymol/data/chempy/fragments/nt_hie.pkl -share/pymol/data/chempy/fragments/nt_hip.pkl -share/pymol/data/chempy/fragments/nt_his.pkl -share/pymol/data/chempy/fragments/nt_ile.pkl -share/pymol/data/chempy/fragments/nt_leu.pkl -share/pymol/data/chempy/fragments/nt_lys.pkl -share/pymol/data/chempy/fragments/nt_met.pkl -share/pymol/data/chempy/fragments/nt_phe.pkl -share/pymol/data/chempy/fragments/nt_pro.pkl -share/pymol/data/chempy/fragments/nt_ser.pkl -share/pymol/data/chempy/fragments/nt_thr.pkl -share/pymol/data/chempy/fragments/nt_trp.pkl -share/pymol/data/chempy/fragments/nt_tyr.pkl -share/pymol/data/chempy/fragments/nt_val.pkl -share/pymol/data/chempy/fragments/peptide.pkl -share/pymol/data/chempy/fragments/phe.pkl -share/pymol/data/chempy/fragments/pro.pkl -share/pymol/data/chempy/fragments/realtime.pkl -share/pymol/data/chempy/fragments/ser.pkl -share/pymol/data/chempy/fragments/sulfone.pkl -share/pymol/data/chempy/fragments/thr.pkl -share/pymol/data/chempy/fragments/trp.pkl -share/pymol/data/chempy/fragments/tyr.pkl -share/pymol/data/chempy/fragments/val.pkl -share/pymol/data/chempy/sidechains/generate1.py -share/pymol/data/chempy/sidechains/generate2.py 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-share/pymol/data/demo/il2.pdb -share/pymol/data/demo/pept.pdb -share/pymol/data/demo/pept.pkl -share/pymol/data/pmg_tk/bitmaps/builder/aro5.gif -share/pymol/data/pmg_tk/bitmaps/builder/aro5.xbm -share/pymol/data/pmg_tk/bitmaps/builder/aro6.gif -share/pymol/data/pmg_tk/bitmaps/builder/aro6.xbm -share/pymol/data/pmg_tk/bitmaps/builder/cyc4.gif -share/pymol/data/pmg_tk/bitmaps/builder/cyc4.xbm -share/pymol/data/pmg_tk/bitmaps/builder/cyc5.gif -share/pymol/data/pmg_tk/bitmaps/builder/cyc5.xbm -share/pymol/data/pmg_tk/bitmaps/builder/cyc6.gif -share/pymol/data/pmg_tk/bitmaps/builder/cyc6.xbm -share/pymol/data/pmg_tk/bitmaps/builder/cyc7.gif -share/pymol/data/pmg_tk/bitmaps/builder/cyc7.xbm -share/pymol/data/pymol/cmyk.png -share/pymol/data/pymol/matrices/BLOSUM62 -share/pymol/data/pymol/splash.png -share/pymol/data/tut/1hpv.pdb -share/pymol/modules/chempy/__init__.py -share/pymol/modules/chempy/__init__.pyc -share/pymol/modules/chempy/__init__.pyo -share/pymol/modules/chempy/arc.py -share/pymol/modules/chempy/arc.pyc -share/pymol/modules/chempy/arc.pyo -share/pymol/modules/chempy/bmin/__init__.py -share/pymol/modules/chempy/bmin/__init__.pyc -share/pymol/modules/chempy/bmin/__init__.pyo -share/pymol/modules/chempy/bmin/commands.py -share/pymol/modules/chempy/bmin/commands.pyc -share/pymol/modules/chempy/bmin/commands.pyo -share/pymol/modules/chempy/bmin/realtime.py -share/pymol/modules/chempy/bmin/realtime.pyc -share/pymol/modules/chempy/bmin/realtime.pyo -share/pymol/modules/chempy/bmin/state.py -share/pymol/modules/chempy/bmin/state.pyc -share/pymol/modules/chempy/bmin/state.pyo -share/pymol/modules/chempy/bmin/util.py -share/pymol/modules/chempy/bmin/util.pyc -share/pymol/modules/chempy/bmin/util.pyo -share/pymol/modules/chempy/bond_amber.py -share/pymol/modules/chempy/bond_amber.pyc -share/pymol/modules/chempy/bond_amber.pyo -share/pymol/modules/chempy/bond_mmff.py -share/pymol/modules/chempy/bond_mmff.pyc -share/pymol/modules/chempy/bond_mmff.pyo -share/pymol/modules/chempy/bonds.py -share/pymol/modules/chempy/bonds.pyc -share/pymol/modules/chempy/bonds.pyo -share/pymol/modules/chempy/brick.py -share/pymol/modules/chempy/brick.pyc -share/pymol/modules/chempy/brick.pyo -share/pymol/modules/chempy/cc1.py -share/pymol/modules/chempy/cc1.pyc -share/pymol/modules/chempy/cc1.pyo -share/pymol/modules/chempy/cex.py -share/pymol/modules/chempy/cex.pyc -share/pymol/modules/chempy/cex.pyo -share/pymol/modules/chempy/champ/__init__.py -share/pymol/modules/chempy/champ/__init__.pyc -share/pymol/modules/chempy/champ/__init__.pyo -share/pymol/modules/chempy/champ/_champ.so -share/pymol/modules/chempy/champ/amber99.py -share/pymol/modules/chempy/champ/amber99.pyc -share/pymol/modules/chempy/champ/amber99.pyo -share/pymol/modules/chempy/champ/assign.py -share/pymol/modules/chempy/champ/assign.pyc -share/pymol/modules/chempy/champ/assign.pyo -share/pymol/modules/chempy/champ/formal_charges.py -share/pymol/modules/chempy/champ/formal_charges.pyc 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