diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/pymol/Makefile | 6 | ||||
| -rw-r--r-- | biology/pymol/distinfo | 4 | ||||
| -rw-r--r-- | biology/pymol/files/patch-Rules.make | 58 | ||||
| -rw-r--r-- | biology/pymol/pkg-plist | 650 |
4 files changed, 380 insertions, 338 deletions
diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile index 5606d9289773..96f12da45b20 100644 --- a/biology/pymol/Makefile +++ b/biology/pymol/Makefile @@ -5,7 +5,7 @@ # $FreeBSD$ PORTNAME= pymol -PORTVERSION= 0.93 +PORTVERSION= 0.97 CATEGORIES= biology python MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} MASTER_SITE_SUBDIR= pymol @@ -48,6 +48,10 @@ post-patch: ${WRKSRC}/modules/pmg_tk/Demo.py @${RM} -f ${WRKSRC}/modules/pmg_tk/Demo.py.* ${REINPLACE_CMD} -e 's,@PYTHON_VERSION@,${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-install: diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo index 66d4c7893b26..8b31ff1b9c8e 100644 --- a/biology/pymol/distinfo +++ b/biology/pymol/distinfo @@ -1,2 +1,2 @@ -MD5 (pymol-0_93-src.tgz) = f3a4e6d7fb25ad97e07a9f2eead304a5 -SIZE (pymol-0_93-src.tgz) = 2352042 +MD5 (pymol-0_97-src.tgz) = e1220898cea37483ddd6f410a6fc02d2 +SIZE (pymol-0_97-src.tgz) = 2753262 diff --git a/biology/pymol/files/patch-Rules.make b/biology/pymol/files/patch-Rules.make index 930081bf6e65..98559e719a8e 100644 --- a/biology/pymol/files/patch-Rules.make +++ b/biology/pymol/files/patch-Rules.make @@ -1,26 +1,26 @@ ---- Rules.make.orig Wed Mar 17 19:40:11 2004 -+++ Rules.make Wed Mar 17 19:40:33 2004 -@@ -4,22 +4,22 @@ +--- Rules.make~ Mon Feb 7 17:02:46 2005 ++++ Rules.make Mon Feb 7 17:04:11 2005 +@@ -4,27 +4,27 @@ # #- Building ---------------------------------------------------------- #--- Tell "make" how to get to PyMOL --PYMOL_PATH = /users/warren/pymol -+PYMOL_PATH = ${LOCALBASE} +-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 ++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/python2.2 \ -- -I$(PYMOL_PATH)/ext/include/python2.2/Numeric +-PYTHON_INC_DIR = -I$(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 @@ -31,49 +31,41 @@ #--------------------------------------------------------------------- # #- Build for LINUX as an importable module --------------------------- -@@ -28,18 +28,18 @@ + #--- 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 + DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_PYMOL_INLINE #--- How we build shared libraries --BUILD = -shared -+BUILD = -shared +@@ -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 = #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes ++CCOPT1 = @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 -+CCOPT2 = #-O3 -funroll-loops -fomit-frame-pointer +-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 -@@ -69,18 +69,19 @@ + #CCOPT2 = -g -D_MemoryDebug_ON +-CCOPT2 = -g ++CCOPT2 = #-g + #--------------------------------------------------------------------- + # + #- Choose One -------------------------------------------------------- +@@ -70,7 +70,7 @@ # No changes normally required below here #--------------------------------------------------------------------- -CC = cc -+override CC := ${CC} ++CC = @CC@ LIB_DIRS = $(EXT_LIB_DIR) $(PYTHON_LIB_DIR) $(XLIB_DIR) - # Enable source files to find headers - PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \ -- -I../layer3 -I../layer4 -I../layer5 -+ -I../layer3 -I../layer4 -I../layer5 -I../modules/ - - C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \ -- $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) -+ $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) $(PYMOL_INC_DIRS) @PICFLAG@ -+ -+override CFLAGS := $(C_FLAGS) ${CFLAGS} - --CFLAGS = $(C_FLAGS) - - - diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist index d90d2476eda2..9df559b09878 100644 --- a/biology/pymol/pkg-plist +++ b/biology/pymol/pkg-plist @@ -1,397 +1,434 @@ 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share/pymol/test/inp/C0300session.pml share/pymol/test/inp/C0500misc.pml share/pymol/test/inp/C0600util.pml +share/pymol/test/inp/C0700odd.pml share/pymol/test/inp/C1000viewing.pml share/pymol/test/inp/C1010helping.pml share/pymol/test/inp/C1020querying.pml @@ -420,6 +458,7 @@ share/pymol/test/inp/C1060controlling.py share/pymol/test/inp/C1070exporting.pml share/pymol/test/inp/C1080isomore.pml share/pymol/test/inp/C1090coulomb.pml +share/pymol/test/inp/C1100do.py share/pymol/test/inp/L0010ccp4read.pml share/pymol/test/inp/L0020xplorread.pml share/pymol/test/inp/L0030isomesh.pml @@ -431,15 +470,6 @@ share/pymol/test/inp/T02.py share/pymol/test/inp/T03.py share/pymol/test/inp/T04.py share/pymol/test/inp/U01.pml -share/pymol/test/ref/C0700odd.1.pdb -share/pymol/test/ref/C0700odd.2.pdb -share/pymol/test/ref/C0700odd.3.pdb -share/pymol/test/ref/C0700odd.4.pdb -share/pymol/test/ref/C0700odd.5.pdb -share/pymol/test/ref/C0700odd.6.pdb -share/pymol/test/ref/C0700odd.7.pdb -share/pymol/test/ref/C0700odd.log -share/pymol/test/ref/C1100do.log share/pymol/test/ref/C0001quit.log share/pymol/test/ref/C0010hello.log share/pymol/test/ref/C0020pdb.log @@ -459,6 +489,7 @@ share/pymol/test/ref/C0140iterate.log share/pymol/test/ref/C0150alter.1.pdb share/pymol/test/ref/C0150alter.log share/pymol/test/ref/C0160get.log +share/pymol/test/ref/T01.log share/pymol/test/ref/C0170scene.log share/pymol/test/ref/C0200feedback.log share/pymol/test/ref/C0201extend.log @@ -466,6 +497,22 @@ share/pymol/test/ref/C0202help_python.log share/pymol/test/ref/C0300session.log share/pymol/test/ref/C0500misc.log share/pymol/test/ref/C0600util.log +share/pymol/test/ref/C0700odd.1.pdb +share/pymol/test/ref/C0700odd.2.pdb +share/pymol/test/ref/C0700odd.3.pdb +share/pymol/test/ref/C0700odd.4.pdb +share/pymol/test/ref/C0700odd.5.pdb +share/pymol/test/ref/C0700odd.6.pdb +share/pymol/test/ref/C0700odd.7.pdb +share/pymol/test/ref/C0700odd.8.pdb +share/pymol/test/ref/C0700odd.9.pdb +share/pymol/test/ref/C0700odd.A.pdb +share/pymol/test/ref/C0700odd.B.pdb +share/pymol/test/ref/C0700odd.C.pdb +share/pymol/test/ref/C0700odd.D.pdb +share/pymol/test/ref/U01.log +share/pymol/test/ref/C0700odd.E.pdb +share/pymol/test/ref/C0700odd.log share/pymol/test/ref/C1000viewing.log share/pymol/test/ref/C1010helping.log share/pymol/test/ref/C1020querying.log @@ -476,47 +523,17 @@ share/pymol/test/ref/C1060controlling.log share/pymol/test/ref/C1070exporting.log share/pymol/test/ref/C1080isomore.log share/pymol/test/ref/C1090coulomb.log +share/pymol/test/ref/C1100do.log share/pymol/test/ref/L0010ccp4read.log share/pymol/test/ref/L0020xplorread.log share/pymol/test/ref/L0030isomesh.log share/pymol/test/ref/L0040isomesh2.log share/pymol/test/ref/L0100isomisc.log share/pymol/test/ref/L0200electro.log -share/pymol/test/ref/T01.log -share/pymol/test/ref/U01.log -share/pymol/test/run -share/pymol/test/show -share/pymol/test/trim.py -share/pymol/test/vdiff -share/pymol/test/win.py -@dirrm share/pymol/test/ref -@dirrm share/pymol/test/inp -@dirrm share/pymol/test/dat -@dirrm share/pymol/test -@dirrm share/pymol/modules/pymol/wizard -@dirrm share/pymol/modules/pymol/opengl/glut -@dirrm share/pymol/modules/pymol/opengl/glu -@dirrm share/pymol/modules/pymol/opengl/gl -@dirrm share/pymol/modules/pymol/opengl -@dirrm share/pymol/modules/pymol/embed/wxpymol -@dirrm share/pymol/modules/pymol/embed/epymol -@dirrm share/pymol/modules/pymol/embed -@dirrm share/pymol/modules/pymol -@dirrm share/pymol/modules/pmg_wx -@dirrm share/pymol/modules/pmg_tk/startup -@dirrm share/pymol/modules/pmg_tk -@dirrm share/pymol/modules/chempy/tinker -@dirrm share/pymol/modules/chempy/fragments -@dirrm share/pymol/modules/chempy/fast -@dirrm share/pymol/modules/chempy/champ -@dirrm share/pymol/modules/chempy/bmin -@dirrm share/pymol/modules/chempy -@dirrm share/pymol/modules -@dirrm share/pymol %%PORTDOCS%%%%EXAMPLESDIR%%/chempy/generate_amber.py %%PORTDOCS%%%%EXAMPLESDIR%%/chempy/generate_mmff.py -%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/README %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/contact.pml +%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/README %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/density.pml %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/groel_es.pml %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/packing.pml @@ -528,19 +545,24 @@ share/pymol/test/win.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo03.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_3Dtext01.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_label_hack.py +%%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_plane.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/chempy_model01.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/chempy_model02.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/chempy_model03.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/gl01.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/gl02.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/gl03.py +%%PORTDOCS%%%%EXAMPLESDIR%%/devel/mutate01.pml +%%PORTDOCS%%%%EXAMPLESDIR%%/devel/mutate02.py +%%PORTDOCS%%%%EXAMPLESDIR%%/devel/pick_wiz.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/povray01.py +%%PORTDOCS%%%%EXAMPLESDIR%%/devel/sd_annotate.pml %%PORTDOCS%%%%EXAMPLESDIR%%/devel/sele_wiz.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/start_pymol.py %%PORTDOCS%%%%EXAMPLESDIR%%/devel/xmlrpc01.py -%%PORTDOCS%%%%EXAMPLESDIR%%/devel/pick_wiz.py -%%PORTDOCS%%%%EXAMPLESDIR%%/launching/README +%%PORTDOCS%%%%EXAMPLESDIR%%/devel/xmlrpc02.py %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch.py +%%PORTDOCS%%%%EXAMPLESDIR%%/launching/README %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_demo.py %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_no_tk.py %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_viewer1.py @@ -550,3 +572,27 @@ share/pymol/test/win.py %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/cookbook %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/chempy %%PORTDOCS%%@dirrm %%EXAMPLESDIR%% +@dirrm share/pymol/test/ref +@dirrm share/pymol/test/inp +@dirrm share/pymol/test/dat +@dirrm share/pymol/test +@dirrm share/pymol/modules/pymol/wizard +@dirrm share/pymol/modules/pymol/opengl/glut +@dirrm share/pymol/modules/pymol/opengl/glu +@dirrm share/pymol/modules/pymol/opengl/gl +@dirrm share/pymol/modules/pymol/opengl +@dirrm share/pymol/modules/pymol/embed/wxpymol +@dirrm share/pymol/modules/pymol/embed/epymol +@dirrm share/pymol/modules/pymol/embed +@dirrm share/pymol/modules/pymol +@dirrm share/pymol/modules/pmg_wx +@dirrm share/pymol/modules/pmg_tk/startup +@dirrm share/pymol/modules/pmg_tk +@dirrm share/pymol/modules/chempy/tinker +@dirrm share/pymol/modules/chempy/fragments +@dirrm share/pymol/modules/chempy/fast +@dirrm share/pymol/modules/chempy/champ +@dirrm share/pymol/modules/chempy/bmin +@dirrm share/pymol/modules/chempy +@dirrm share/pymol/modules +@dirrm share/pymol |