diff options
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/pymol/Makefile | 43 | ||||
| -rw-r--r-- | biology/pymol/distinfo | 1 | ||||
| -rw-r--r-- | biology/pymol/files/patch-aa | 91 | ||||
| -rw-r--r-- | biology/pymol/files/patch-ab | 18 | ||||
| -rw-r--r-- | biology/pymol/pkg-comment | 1 | ||||
| -rw-r--r-- | biology/pymol/pkg-descr | 9 | ||||
| -rw-r--r-- | biology/pymol/pkg-plist | 551 |
8 files changed, 715 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 88c38ca..87633a9 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -41,6 +41,7 @@ SUBDIR += povchem SUBDIR += psi88 SUBDIR += py-biopython + SUBDIR += pymol SUBDIR += rasmol SUBDIR += recombine SUBDIR += ruby-bio diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile new file mode 100644 index 0000000..2c41629 --- /dev/null +++ b/biology/pymol/Makefile @@ -0,0 +1,43 @@ +# New ports collection makefile for: pymol +# Date created: July 18, 2002 +# Whom: Nakata Maho <chat95@mbox.kyoto-inet.or.jp> +# +# $FreeBSD$ + +PORTNAME= pymol +PORTVERSION= 0.82 +CATEGORIES= biology python +MASTER_SITES= ${MASTER_SITE_SOURCEFORGE} +MASTER_SITE_SUBDIR= pymol +DISTNAME= pymol-${PORTVERSION:S/./_/}-src +EXTRACT_SUFX= .tgz + +MAINTAINER= chat95@mbox.kyoto-inet.or.jp + +BUILD_DEPENDS= ${PYNUMERIC} +RUN_DEPENDS= ${PYNUMERIC} \ + ${PYTHON_SITELIBDIR}/_tkinter.so:${PORTSDIR}/x11-toolkits/py-tkinter +LIB_DEPENDS= glut.3:${PORTSDIR}/graphics/Mesa3 + +WRKSRC= ${WRKDIR}/${PKGNAME} +USE_GMAKE= yes +USE_REINPLACE= yes +USE_PYTHON= yes + +pre-patch: + @${INSTALL_DATA} ${WRKSRC}/setup/Rules.linux ${WRKSRC}/Rules.make + +post-patch: + @${INSTALL_DATA} ${WRKSRC}/setup/pymol.com.linux-rh7x ${WRKSRC}/setup/pymol.com + @${REINPLACE_CMD} 's,@PREFIX@,${PREFIX},g' ${WRKSRC}/setup/pymol.com + @${REINPLACE_CMD} 's,@PYTHON_VERSION@,${PYTHON_VERSION},g' ${WRKSRC}/Rules.make + +do-install: + @${INSTALL_SCRIPT} ${WRKSRC}/setup/pymol.com ${PREFIX}/bin/pymol + @${MKDIR} ${PREFIX}/share/pymol + @${TAR} -C ${WRKSRC} -chf - modules test | \ + ${TAR} -xf - -C ${PREFIX}/share/pymol + @${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py ${PREFIX}/share/pymol/modules + @${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py ${PREFIX}/share/pymol/modules + +.include <bsd.port.mk> diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo new file mode 100644 index 0000000..fd43630 --- /dev/null +++ b/biology/pymol/distinfo @@ -0,0 +1 @@ +MD5 (pymol-0_82-src.tgz) = d01bf39dbaa3ada27809a0ba013a162a diff --git a/biology/pymol/files/patch-aa b/biology/pymol/files/patch-aa new file mode 100644 index 0000000..cd49db0 --- /dev/null +++ b/biology/pymol/files/patch-aa @@ -0,0 +1,91 @@ +--- Rules.make.orig Thu Jul 11 08:11:51 2002 ++++ Rules.make Thu Jul 11 08:23:03 2002 +@@ -4,42 +4,42 @@ + # + #- Building ---------------------------------------------------------- + #--- Tell "make" how to get to PyMOL +-PYMOL_PATH = /users/warren/pymol ++PYMOL_PATH = ${PREFIX} + #--------------------------------------------------------------------- + # + #- Dependencies ------------------------------------------------------ + #--- X-windows +-XLIB_DIR = -L/usr/X11R6/lib +-XINC_DIR = -I/usr/X11R6/include ++XLIB_DIR = -L${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/python2.1 \ +- -I$(PYMOL_PATH)/ext/include/python2.1/Numeric ++PYTHON_INC_DIR = -I$(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 -I. ++EXT_LIB_DIR = -L$(PYMOL_PATH)/lib + #--------------------------------------------------------------------- + # +-#- Build for LINUX as an importable module --------------------------- ++#- Build for FreeBSD 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 + #--- How we build shared libraries + BUILD = -shared + #--- What are we trying to build? + DEST = -o modules/_cmd.so +-#--- Gcc Options for Linux +-CCOPT1 = -m486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes ++#--- Gcc Options for FreeBSD ++CCOPT1 = #-m486 -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 + #--- GCC Profiling + #CCOPT2 = -pg -O3 -funroll-loops + #--- Debugging +@@ -47,7 +47,7 @@ + #--------------------------------------------------------------------- + # + #- Choose One -------------------------------------------------------- +-#--- Workaround for XFree86/DRI linux dll problem for module build ++#--- Workaround for XFree86/DRI FreeBSD dll problem for module build + BUGS = -D_DRI_WORKAROUND + #--- + #BUGS = +@@ -69,18 +69,19 @@ + # No changes normally required below here + #--------------------------------------------------------------------- + +-CC = cc ++override 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) ++ ++override CFLAGS := $(C_FLAGS) ${CFLAGS} + +-CFLAGS = $(C_FLAGS) + + + diff --git a/biology/pymol/files/patch-ab b/biology/pymol/files/patch-ab new file mode 100644 index 0000000..07ae40a --- /dev/null +++ b/biology/pymol/files/patch-ab @@ -0,0 +1,18 @@ +--- setup/pymol.com.linux-rh7x.orig Thu Jul 11 08:33:42 2002 ++++ setup/pymol.com.linux-rh7x Thu Jul 11 08:34:37 2002 +@@ -5,7 +5,7 @@ + # ============================================================== + # Set PYMOL_PATH to point at the correct location on your system + # +-setenv PYMOL_PATH /usr/local/pymol ++setenv PYMOL_PATH @PREFIX@/share/pymol + # + # ============================================================== + # (no changes usually required below here) +@@ -21,5 +21,5 @@ + # + #dbx /usr/bin/python + #gdb /usr/bin/python +-/usr/bin/python $PYMOL_PATH/modules/launch_pymol.py $* ++@PREFIX@/bin/python $PYMOL_PATH/modules/launch_pymol.py $* + diff --git a/biology/pymol/pkg-comment b/biology/pymol/pkg-comment new file mode 100644 index 0000000..6c056b0 --- /dev/null +++ b/biology/pymol/pkg-comment @@ -0,0 +1 @@ +Free and Open-Source molecular modeling system diff --git a/biology/pymol/pkg-descr b/biology/pymol/pkg-descr new file mode 100644 index 0000000..dfd8cdf --- /dev/null +++ b/biology/pymol/pkg-descr @@ -0,0 +1,9 @@ +PyMOL is a molecular graphics system with an embedded Python interpreter +designed for real-time visualization and rapid generation of +high-quality molecular graphics images and animations. It is fully extensible +and available free to everyone via the "Python" license. +PyMOL can be used to create images and animations with unprecedented ease. +It can also perform many other valuable tasks (such as editing PDB files) +to assist you in your research. + +WWW: http://pymol.sourceforge.net/ diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist new file mode 100644 index 0000000..7bf636d --- /dev/null +++ b/biology/pymol/pkg-plist @@ -0,0 +1,551 @@ +bin/pymol +share/pymol/modules/ExtensionClass.so +share/pymol/modules/_cmd.so +share/pymol/modules/_glu_nummodule.so +share/pymol/modules/_glumodule.so +share/pymol/modules/_glutmodule.so +share/pymol/modules/_opengl_nummodule.so +share/pymol/modules/_openglmodule.so +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/champ/__init__.py +share/pymol/modules/chempy/champ/__init__.pyc +share/pymol/modules/chempy/champ/__init__.pyo +share/pymol/modules/chempy/charge.py +share/pymol/modules/chempy/charge.pyc +share/pymol/modules/chempy/charge.pyo +share/pymol/modules/chempy/cpv.py +share/pymol/modules/chempy/cpv.pyc +share/pymol/modules/chempy/cpv.pyo +share/pymol/modules/chempy/dictdb.py +share/pymol/modules/chempy/dictdb.pyc +share/pymol/modules/chempy/dictdb.pyo +share/pymol/modules/chempy/fast/__init__.py +share/pymol/modules/chempy/fast/__init__.pyc +share/pymol/modules/chempy/fast/__init__.pyo +share/pymol/modules/chempy/fragments/__init__.py +share/pymol/modules/chempy/fragments/__init__.pyc 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