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authorHye-Shik Chang <perky@FreeBSD.org>2002-08-13 11:53:43 +0000
committerHye-Shik Chang <perky@FreeBSD.org>2002-08-13 11:53:43 +0000
commitdc8e3f8160546d987bb175d8d1d7a5bb214e4e11 (patch)
tree1a5a6df87dd684f75ae929df14a66a5232f43732 /biology
parentupgrade to 0.8.3 (diff)
Add pymol 0.82, Free and Open-Source molecular modeling system.
PR: 40694 Submitted by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
Notes
Notes: svn path=/head/; revision=64463
Diffstat (limited to 'biology')
-rw-r--r--biology/Makefile1
-rw-r--r--biology/pymol/Makefile43
-rw-r--r--biology/pymol/distinfo1
-rw-r--r--biology/pymol/files/patch-aa91
-rw-r--r--biology/pymol/files/patch-ab18
-rw-r--r--biology/pymol/pkg-comment1
-rw-r--r--biology/pymol/pkg-descr9
-rw-r--r--biology/pymol/pkg-plist551
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
+share/pymol/modules/chempy/fragments/ace.pkl
+share/pymol/modules/chempy/fragments/acetylene.pkl
+share/pymol/modules/chempy/fragments/ala.pkl
+share/pymol/modules/chempy/fragments/arg.pkl
+share/pymol/modules/chempy/fragments/asn.pkl
+share/pymol/modules/chempy/fragments/asp.pkl
+share/pymol/modules/chempy/fragments/benzene.pkl
+share/pymol/modules/chempy/fragments/butane.pkl
+share/pymol/modules/chempy/fragments/ct_ala.pkl
+share/pymol/modules/chempy/fragments/ct_arg.pkl
+share/pymol/modules/chempy/fragments/ct_asn.pkl
+share/pymol/modules/chempy/fragments/ct_asp.pkl
+share/pymol/modules/chempy/fragments/ct_cys.pkl
+share/pymol/modules/chempy/fragments/ct_gln.pkl
+share/pymol/modules/chempy/fragments/ct_glu.pkl
+share/pymol/modules/chempy/fragments/ct_gly.pkl
+share/pymol/modules/chempy/fragments/ct_hid.pkl
+share/pymol/modules/chempy/fragments/ct_hie.pkl
+share/pymol/modules/chempy/fragments/ct_hip.pkl
+share/pymol/modules/chempy/fragments/ct_his.pkl
+share/pymol/modules/chempy/fragments/ct_ile.pkl
+share/pymol/modules/chempy/fragments/ct_leu.pkl
+share/pymol/modules/chempy/fragments/ct_lys.pkl
+share/pymol/modules/chempy/fragments/ct_met.pkl
+share/pymol/modules/chempy/fragments/ct_phe.pkl
+share/pymol/modules/chempy/fragments/ct_pro.pkl
+share/pymol/modules/chempy/fragments/ct_ser.pkl
+share/pymol/modules/chempy/fragments/ct_thr.pkl
+share/pymol/modules/chempy/fragments/ct_trp.pkl
+share/pymol/modules/chempy/fragments/ct_tyr.pkl
+share/pymol/modules/chempy/fragments/ct_val.pkl
+share/pymol/modules/chempy/fragments/cyclobutane.pkl
+share/pymol/modules/chempy/fragments/cycloheptane.pkl
+share/pymol/modules/chempy/fragments/cyclohexane.pkl
+share/pymol/modules/chempy/fragments/cyclopentadiene.pkl
+share/pymol/modules/chempy/fragments/cyclopentane.pkl
+share/pymol/modules/chempy/fragments/cys.pkl
+share/pymol/modules/chempy/fragments/formaldehyde.pkl
+share/pymol/modules/chempy/fragments/formamide.pkl
+share/pymol/modules/chempy/fragments/gln.pkl
+share/pymol/modules/chempy/fragments/glu.pkl
+share/pymol/modules/chempy/fragments/gly.pkl
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+share/pymol/modules/chempy/fragments/met.pkl
+share/pymol/modules/chempy/fragments/methane.pkl
+share/pymol/modules/chempy/fragments/nme.pkl
+share/pymol/modules/chempy/fragments/nt_ala.pkl
+share/pymol/modules/chempy/fragments/nt_arg.pkl
+share/pymol/modules/chempy/fragments/nt_asn.pkl
+share/pymol/modules/chempy/fragments/nt_asp.pkl
+share/pymol/modules/chempy/fragments/nt_cys.pkl
+share/pymol/modules/chempy/fragments/nt_gln.pkl
+share/pymol/modules/chempy/fragments/nt_glu.pkl
+share/pymol/modules/chempy/fragments/nt_gly.pkl
+share/pymol/modules/chempy/fragments/nt_hid.pkl
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+share/pymol/modules/chempy/fragments/nt_his.pkl
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+share/pymol/modules/chempy/fragments/nt_leu.pkl
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+share/pymol/modules/chempy/fragments/nt_met.pkl
+share/pymol/modules/chempy/fragments/nt_phe.pkl
+share/pymol/modules/chempy/fragments/nt_pro.pkl
+share/pymol/modules/chempy/fragments/nt_ser.pkl
+share/pymol/modules/chempy/fragments/nt_thr.pkl
+share/pymol/modules/chempy/fragments/nt_trp.pkl
+share/pymol/modules/chempy/fragments/nt_tyr.pkl
+share/pymol/modules/chempy/fragments/nt_val.pkl
+share/pymol/modules/chempy/fragments/peptide.pkl
+share/pymol/modules/chempy/fragments/phe.pkl
+share/pymol/modules/chempy/fragments/pro.pkl
+share/pymol/modules/chempy/fragments/realtime.pkl
+share/pymol/modules/chempy/fragments/ser.pkl
+share/pymol/modules/chempy/fragments/sulfone.pkl
+share/pymol/modules/chempy/fragments/thr.pkl
+share/pymol/modules/chempy/fragments/trp.pkl
+share/pymol/modules/chempy/fragments/tyr.pkl
+share/pymol/modules/chempy/fragments/val.pkl
+share/pymol/modules/chempy/gamess1.py
+share/pymol/modules/chempy/gamess1.pyc
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+share/pymol/modules/chempy/gms.py
+share/pymol/modules/chempy/gms.pyc
+share/pymol/modules/chempy/gms.pyo
+share/pymol/modules/chempy/hetatm.py
+share/pymol/modules/chempy/hetatm.pyc
+share/pymol/modules/chempy/hetatm.pyo
+share/pymol/modules/chempy/io.py
+share/pymol/modules/chempy/io.pyc
+share/pymol/modules/chempy/io.pyo
+share/pymol/modules/chempy/lst.py
+share/pymol/modules/chempy/lst.pyc
+share/pymol/modules/chempy/lst.pyo
+share/pymol/modules/chempy/mae.py
+share/pymol/modules/chempy/mae.pyc
+share/pymol/modules/chempy/mae.pyo
+share/pymol/modules/chempy/map.py
+share/pymol/modules/chempy/map.pyc
+share/pymol/modules/chempy/map.pyo
+share/pymol/modules/chempy/mmd.py
+share/pymol/modules/chempy/mmd.pyc
+share/pymol/modules/chempy/mmd.pyo
+share/pymol/modules/chempy/models.py
+share/pymol/modules/chempy/models.pyc
+share/pymol/modules/chempy/models.pyo
+share/pymol/modules/chempy/mol.py
+share/pymol/modules/chempy/mol.pyc
+share/pymol/modules/chempy/mol.pyo
+share/pymol/modules/chempy/neighbor.py
+share/pymol/modules/chempy/neighbor.pyc
+share/pymol/modules/chempy/neighbor.pyo
+share/pymol/modules/chempy/pdb.py
+share/pymol/modules/chempy/pdb.pyc
+share/pymol/modules/chempy/pdb.pyo
+share/pymol/modules/chempy/pkl.py
+share/pymol/modules/chempy/pkl.pyc
+share/pymol/modules/chempy/pkl.pyo
+share/pymol/modules/chempy/place.py
+share/pymol/modules/chempy/place.pyc
+share/pymol/modules/chempy/place.pyo
+share/pymol/modules/chempy/protein.py
+share/pymol/modules/chempy/protein.pyc
+share/pymol/modules/chempy/protein.pyo
+share/pymol/modules/chempy/protein_amber.py
+share/pymol/modules/chempy/protein_amber.pyc
+share/pymol/modules/chempy/protein_amber.pyo
+share/pymol/modules/chempy/protein_amber99.py
+share/pymol/modules/chempy/protein_amber99.pyc
+share/pymol/modules/chempy/protein_amber99.pyo
+share/pymol/modules/chempy/protein_mmff.py
+share/pymol/modules/chempy/protein_mmff.pyc
+share/pymol/modules/chempy/protein_mmff.pyo
+share/pymol/modules/chempy/protein_residues.py
+share/pymol/modules/chempy/protein_residues.pyc
+share/pymol/modules/chempy/protein_residues.pyo
+share/pymol/modules/chempy/sdf.py
+share/pymol/modules/chempy/sdf.pyc
+share/pymol/modules/chempy/sdf.pyo
+share/pymol/modules/chempy/sidechains/generate1.py
+share/pymol/modules/chempy/sidechains/generate1.pyc
+share/pymol/modules/chempy/sidechains/generate1.pyo
+share/pymol/modules/chempy/sidechains/generate2.py
+share/pymol/modules/chempy/sidechains/generate2.pyc
+share/pymol/modules/chempy/sidechains/generate2.pyo
+share/pymol/modules/chempy/sidechains/sc_library.pkl
+share/pymol/modules/chempy/solvate.py
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