Add pymol 0.82, Free and Open-Source molecular modeling system.

PR:		40694
Submitted by:	Nakata Maho <chat95@mbox.kyoto-inet.or.jp>

8 files changed, 715 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 88c38ca56a43..87633a989b20 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 000000000000..2c4162946195
--- /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 000000000000..fd4363004806
--- /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 000000000000..cd49db0abc36
--- /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 000000000000..07ae40a91fc9
--- /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 000000000000..6c056b09dc9c
--- /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 000000000000..dfd8cdfb4d4f
--- /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 000000000000..7bf636d2284f
--- /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
+share/pymol/modules/chempy/fragments/__init__.pyo
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+share/pymol/modules/chempy/fragments/acetylene.pkl
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+share/pymol/modules/chempy/sidechains/generate1.py
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+share/pymol/modules/chempy/tinker/Makefile
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+share/pymol/modules/chempy/tinker/__init__.pyo
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