--- pymol-0.98+0.99rc6.orig/modules/pymol/wizard/demo.py +++ pymol-0.98+0.99rc6/modules/pymol/wizard/demo.py @@ -228,7 +228,7 @@ try: cmd.set("suspend_updates",1,quiet=1) cmd.disable() - cmd.load("$TUT/1hpv.pdb") + cmd.load("$PYMOL_DATA/demo/1hpv.pdb") util.chainbow("1hpv") cmd.hide("everything","1hpv") cmd.show("cartoon","1hpv") --- pymol-0.98+0.99rc6.orig/modules/pymol/wizard/mutagenesis.py +++ pymol-0.98+0.99rc6/modules/pymol/wizard/mutagenesis.py @@ -35,8 +35,8 @@ self.dep = default_dep - self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ - "/data/chempy/sidechains/sc_bb_ind.pkl") + self.library = io.pkl.fromFile(os.environ['CHEMPY_DATA']+ + "/sidechains/sc_library.pkl") self.load_library() self.status = 0 # 0 no selection, 1 mutagenizing self.bump_check = 1 --- pymol-0.98+0.99rc6.orig/debian/patches/01_data_path.dpatch +++ pymol-0.98+0.99rc6/debian/patches/01_data_path.dpatch @@ -0,0 +1,205 @@ +#! /bin/sh -e +## 01_data_path.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: Patch to put all data files under /usr/share/pymol and not +## DP: into $PYMOL_PATH. + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +--- pymol-0.88.orig/modules/chempy/__init__.py ++++ pymol-0.88/modules/chempy/__init__.py +@@ -205,7 +205,7 @@ + elif os.environ.has_key('FREEMOL_MODULES'): + path = os.environ['FREEMOL_MODULES'] + '/chempy/' + else: +- path = '' ++ path = '$CHEMPY_DATA_PATH/' + + # double check these values... + #hvd values obtained from http://www.webelements.com/ and recorded to their +--- pymol-0.88.orig/modules/chempy/fragments/__init__.py ++++ pymol-0.88/modules/chempy/fragments/__init__.py +@@ -2,7 +2,7 @@ + import chempy + from chempy import io + +-path = chempy.path + 'fragments/' ++path = '$CHEMPY_DATA_PATH/fragments/' + + def get(name): + return io.pkl.fromFile(path+name+'.pkl') +--- pymol-0.88.orig/modules/chempy/tinker/__init__.py ++++ pymol-0.88/modules/chempy/tinker/__init__.py +@@ -151,3 +151,4 @@ + if os.path.exists(test_path): + params_path = test_path + ++params_path = '$CHEMPY_DATA_PATH/tinker' +--- pymol-0.88.orig/modules/pymol/commanding.py ++++ pymol-0.88/modules/pymol/commanding.py +@@ -111,7 +111,7 @@ + r = None + mode = int(mode) + if mode == 1: # just show PNG +- png_path = os.path.expandvars("$PYMOL_PATH/data/pymol/splash.png") ++ png_path = os.path.expandvars("$PYMOL_DATA_PATH/splash.png") + if os.path.exists(png_path): + cmd.do("_ cmd.load_png('%s',0,quiet=1)"%png_path) + r = 1 +--- pymol-0.88.orig/modules/pymol/fitting.py ++++ pymol-0.88/modules/pymol/fitting.py +@@ -59,7 +59,7 @@ + r = None + source = selector.process(source) + target = selector.process(target) +- mfile = os.path.expandvars("$PYMOL_PATH/data/pymol/matrices/"+matrix) ++ mfile = os.path.expandvars("$PYMOL_DATA_PATH/matrices/"+matrix) + if object==None: object='' + try: + lock() +--- pymol-0.88.orig/modules/pymol/wizard/demo.py ++++ pymol-0.88/modules/pymol/wizard/demo.py +@@ -80,10 +80,10 @@ + try: + cmd.set("suspend_updates",1,quiet=1) + cmd.disable() +- cmd.do("cd $PYMOL_PATH") ++ cmd.do("cd $PYMOL_DATA_PATH") + cmd.delete("pept") + cmd.delete("pept_dist") +- cmd.load("test/dat/pept.pdb") ++ cmd.load("demo/pept.pdb") + cmd.show("sticks","(pept and not i;5:7)") + cmd.show("surface","(pept and i;5,6)") + cmd.show("mesh","(pept and i;1,11,12,13)") +@@ -103,7 +103,7 @@ + if not cleanup: + cmd.disable() + cmd.set("suspend_updates",1,quiet=1) +- cmd.load("$PYMOL_PATH/test/dat/pept.pdb","rep1") ++ cmd.load("$PYMOL_DATA_PATH/demo/pept.pdb","rep1") + cmd.alter("rep1///1-5+8-13/","ss='S'") + cmd.cartoon("auto") + cmd.hide("everything","rep1") +@@ -181,7 +181,7 @@ + -0.000086844, 0.000019042, -133.217041016,\ + 11.377667427, 21.768899918, 9.270449638,\ + 105.029335022, 169.626159668, 0.000000000 )) +- cmd.load("$TUT/1hpv.r3d","cgo1") ++ cmd.load("$PYMOL_DATA_PATH/demo/1hpv.r3d","cgo1") + # cmd.delete("cgo1") + # cmd.delete("cgo2") + # cmd.load("test/dat/pept.r3d","cgo") +@@ -195,10 +195,10 @@ + def cgo(self,cleanup=0): + if not cleanup: + cmd.disable() +- cmd.do("cd $PYMOL_PATH") ++ cmd.do("cd $PYMOL_DATA_PATH") + try: + cmd.set("suspend_updates",1,quiet=1) +- cmd.do("run examples/devel/cgo03.py") ++ cmd.do("run demo/cgo03.py") + finally: + cmd.set("suspend_updates",0,quiet=1) + else: +@@ -236,7 +236,7 @@ + try: + cmd.set("suspend_updates",1,quiet=1) + cmd.disable() +- cmd.load("$TUT/1hpv.pdb") ++ cmd.load("$PYMOL_DATA_PATH/demo/1hpv.pdb") + util.chainbow("1hpv") + cmd.hide("everything","1hpv") + cmd.show("cartoon","1hpv") +@@ -282,7 +282,7 @@ + + def roving(self,cleanup=0): + if not cleanup: +- cmd.load("$PYMOL_PATH/test/dat/il2.pdb") ++ cmd.load("$PYMOL_DATA_PATH/demo/il2.pdb") + cmd.remove("hydro") + cmd.disable() + cmd.enable("il2") +@@ -308,7 +308,7 @@ + def roving_density(self,cleanup=0): + if not cleanup: + try: +- cmd.load("$PYMOL_PATH/test/dat/il2.pdb") ++ cmd.load("$PYMOL_DATA_PATH/demo/il2.pdb") + cmd.set("suspend_updates",1,quiet=1) + cmd.remove("hydro") + cmd.disable() +@@ -354,7 +354,7 @@ + cmd.set("suspend_updates",1,quiet=1) + cmd.disable() + cmd.delete("1tii") +- cmd.load("$PYMOL_PATH/test/dat/1tii.pdb") ++ cmd.load("$PYMOL_DATA_PATH/demo/1tii.pdb") + cmd.hide("(1tii)") + cmd.show("cartoon","1tii") + cmd.zoom("1tii") +@@ -373,7 +373,7 @@ + cmd.delete("pept") + cmd.delete("e_pot") + cmd.delete("e_lvl") +- cmd.load("$PYMOL_PATH/test/dat/pept.pkl") ++ cmd.load("$PYMOL_DATA_PATH/demo/pept.pkl") + cmd.hide("(pept)") + cmd.show("surface","pept") + cmd.set("coulomb_dielectric",80.0) +@@ -392,7 +392,7 @@ + cmd.set("suspend_updates",1,quiet=1) + cmd.disable() + cmd.delete("trans") +- cmd.load("$PYMOL_PATH/test/dat/pept.pdb","trans") ++ cmd.load("$PYMOL_DATA_PATH/demo/pept.pdb","trans") + cmd.hide("(trans)") + cmd.show("surface","trans") + cmd.show("sticks","trans") +@@ -410,7 +410,7 @@ + cmd.set("suspend_updates",1,quiet=1) + cmd.disable() + cmd.delete("ray") +- cmd.load("$PYMOL_PATH/test/dat/il2.pdb","ray") ++ cmd.load("$PYMOL_DATA_PATH/demo/il2.pdb","ray") + cmd.remove("(ray and hydro)") + cmd.hide("lines","ray") + cmd.show("spheres","ray") +@@ -433,7 +433,7 @@ + cmd.set("suspend_updates",1,quiet=1) + cmd.disable() + cmd.delete("sculpt") +- cmd.load("$PYMOL_PATH/test/dat/pept.pdb","sculpt") ++ cmd.load("$PYMOL_DATA_PATH/demo/pept.pdb","sculpt") + cmd.hide("lines","sculpt") + cmd.show("sticks","sculpt") + cmd.show("spheres","sculpt") +--- pymol-0.88.orig/modules/pymol/wizard/mutagenesis.py ++++ pymol-0.88/modules/pymol/wizard/mutagenesis.py +@@ -27,8 +27,7 @@ + + Wizard.__init__(self) + +- self.library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ +- "/data/chempy/sidechains/sc_library.pkl") ++ self.library = io.pkl.fromFile("$CHEMPY_DATA_PATH/sidechains/sc_library.pkl") + + self.status = 0 # 0 no selection, 1 mutagenizing + self.error = None --- pymol-0.98+0.99rc6.orig/debian/patches/03_povray.dpatch +++ pymol-0.98+0.99rc6/debian/patches/03_povray.dpatch @@ -0,0 +1,34 @@ +#! /bin/sh -e +## 03_povray.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: Adjust povray options + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +--- pymol-0.98+0.99rc6/modules/pymol/povray.py.orig 2006-06-30 01:02:06.000000000 +0200 ++++ pymol-0.98+0.99rc6/modules/pymol/povray.py 2006-06-30 01:03:42.000000000 +0200 +@@ -17,7 +17,7 @@ + import os + import traceback + +- povray_exe = "povray" ++ povray_exe = "povray +FN" + + def render_from_string(header,pov_inp,prefix,width,height,antialias): + r = None --- pymol-0.98+0.99rc6.orig/debian/patches/07_setup.py._opengl-libs.dpatch +++ pymol-0.98+0.99rc6/debian/patches/07_setup.py._opengl-libs.dpatch @@ -0,0 +1,34 @@ +#! /bin/sh -e +## 07_setup.py._opengl-libs.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: add OpenGL libraries to pyopengl_libs + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +--- pymol-0.90.orig/setup.py ++++ pymol-0.90/setup.py +@@ -32,7 +32,7 @@ + else: + inc_dirs=["layer0","layer1","layer2","layer3","layer4","layer5"] + libs=["GL","GLU","glut","png"] +- pyogl_libs = [] ++ pyogl_libs = ["GL","GLU","glut","png"] + lib_dirs=["/usr/X11R6/lib"] + def_macros=[("_PYMOL_MODULE",None), + # ("_PYMOL_NUMPY",None), --- pymol-0.98+0.99rc6.orig/debian/patches/09_chempy_data_path.dpatch +++ pymol-0.98+0.99rc6/debian/patches/09_chempy_data_path.dpatch @@ -0,0 +1,43 @@ +#! /bin/sh -e +## 09_chempy_data_path.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: Patch replacing CHEMPY_DATA_PATH by PYMOL_PATH + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +--- pymol-0.98+0.99rc6/modules/pymol/wizard/mutagenesis.py 2006-06-30 01:11:35.000000000 +0200 ++++ pymol-0.98+0.99rc6/modules/pymol/wizard/mutagenesis.py.orig 2006-06-30 01:11:09.000000000 +0200 +@@ -35,8 +35,8 @@ + + self.dep = default_dep + +- self.library = io.pkl.fromFile(os.environ['CHEMPY_DATA']+ +- "/sidechains/sc_library.pkl") ++ self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ ++ "/data/chempy/sidechains/sc_bb_ind.pkl") + self.load_library() + self.status = 0 # 0 no selection, 1 mutagenizing + self.bump_check = 1 +--- pymol-0.88.orig/modules/chempy/tinker/__init__.py ++++ pymol-0.88/modules/chempy/tinker/__init__.py +@@ -151,3 +151,4 @@ + if os.path.exists(test_path): + params_path = test_path + ++params_path = os.environ['CHEMPY_DATA'] + '/tinker' --- pymol-0.98+0.99rc6.orig/debian/patches/00list +++ pymol-0.98+0.99rc6/debian/patches/00list @@ -0,0 +1,7 @@ +02_test-suite.dpatch +03_povray.dpatch +04_Rules.make.dpatch +05_examples_data_path.dpatch +06_remove_shebang.dpatch +09_chempy_data_path.dpatch +11_fix__cmd_import.dpatch --- pymol-0.98+0.99rc6.orig/debian/patches/08_setup.py_missing_file.dpatch +++ pymol-0.98+0.99rc6/debian/patches/08_setup.py_missing_file.dpatch @@ -0,0 +1,34 @@ +#! /bin/sh -e +## 08_setup.py_missing_file.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: add one missing source file to layer0 sources + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +--- pymol-0.90.orig/setup.py ++++ pymol-0.90/setup.py +@@ -72,6 +72,7 @@ + "layer0/Match.c", + "layer0/Matrix.c", + "layer0/MemoryDebug.c", ++ "layer0/MemoryCache.c", + "layer0/MyPNG.c", + "layer0/Parse.c", + "layer0/Queue.c", + --- pymol-0.98+0.99rc6.orig/debian/patches/02_test-suite.dpatch +++ pymol-0.98+0.99rc6/debian/patches/02_test-suite.dpatch @@ -0,0 +1,89 @@ +#! /bin/sh -e +## 02_test-suite.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: Patch to make the test-suite work during debian build-time. + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +--- pymol-0.98+0.99rc6/test/run.orig 2006-06-30 00:59:34.000000000 +0200 ++++ pymol-0.98+0.99rc6/test/run 2006-06-30 01:00:09.000000000 +0200 +@@ -36,7 +36,7 @@ + # --- + + pymol = "pymol" +-cmd = "../pymol" ++cmd = "./pymol-test" + if not os.path.exists(cmd): + cmd = "../../Contents/MacOS/MacPyMOL" + cmp = "cmp" +@@ -94,7 +94,8 @@ + diffs = df.readlines() + df.close() + print " run_tests: "+ \ +- postfx+" DIFFERS over about %d lines." % int(len(diffs)/2) ++ postfx+" DIFFERS over about %d lines:" % int(len(diffs)/2) ++ print diffs + else: + print " run_tests: "+postfx+" is missing." + +--- pymol-0.88.orig/test/pymol-test ++++ pymol-0.88/test/pymol-test +@@ -0,0 +1,42 @@ ++#!/usr/bin/env python ++# NOTE: This file is now obsolete. However it has been left functional ++# and intact in order to promote backwards compatibility with existing ++# PyMOL installs. ++# ++# Future installations should launch pymol by running: ++# "python $PYMOL_PATH/modules/pymol/__init__.py" instead. ++# or ++# by importing "pymol" from within a standalone Python script ++# followed immediately by a call to pymol.finish_launching() ++ ++import thread ++import threading ++import os ++import sys ++import time ++import __main__ ++ ++# let pymol/__init__.py known that we're launching using the old way ++ ++__main__.pymol_launch = 0 ++ ++if hasattr(__main__,"pymol_argv"): ++ pymol_argv = __main__.pymol_argv ++else: ++ pymol_argv = sys.argv ++ ++modules_path = '../debian/pymol/usr/lib/python' + sys.version[0:3] + '/site-packages' ++ ++if modules_path not in sys.path: ++ sys.path.append(modules_path) ++ ++import pymol ++ ++pymol.invocation.parse_args(pymol_argv) ++ ++pymol.start_pymol() ++ ++ ++ ++ ++ --- pymol-0.98+0.99rc6.orig/debian/patches/05_examples_data_path.dpatch +++ pymol-0.98+0.99rc6/debian/patches/05_examples_data_path.dpatch @@ -0,0 +1,80 @@ +#! /bin/sh -e +## 05_examples_data_path.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: Patch to put let the examples find their data. + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +diff -urNad /home/mbanck/debian/mine/pymol-0.93/examples/chempy/generate_amber.py pymol-0.93/examples/chempy/generate_amber.py +--- /home/mbanck/debian/mine/pymol-0.93/examples/chempy/generate_amber.py 2004-01-03 23:06:05.000000000 +0100 ++++ pymol-0.93/examples/chempy/generate_amber.py 2004-01-03 23:07:06.000000000 +0100 +@@ -3,8 +3,9 @@ + from chempy import io + from chempy import protein + from chempy import protein_amber99 ++import os + +-model= io.pdb.fromFile("../../test/dat/pept.pdb") ++model= io.pdb.fromFile("/usr/share/pymol/demo/pept.pdb") + + model= protein.generate(model,forcefield=protein_amber99) + +diff -urNad /home/mbanck/debian/mine/pymol-0.93/examples/chempy/generate_mmff.py pymol-0.93/examples/chempy/generate_mmff.py +--- /home/mbanck/debian/mine/pymol-0.93/examples/chempy/generate_mmff.py 2004-01-03 23:06:05.000000000 +0100 ++++ pymol-0.93/examples/chempy/generate_mmff.py 2004-01-03 23:07:06.000000000 +0100 +@@ -4,6 +4,7 @@ + from chempy import protein + from chempy import protein_mmff + from chempy import bond_mmff ++import os + + # + #print 'normal' +@@ -13,7 +14,7 @@ + #print 'c_terminal' + #protein_mmff.check_sum(protein_mmff.c_terminal) + +-model= io.pdb.fromFile("../../test/dat/pept.pdb") ++model= io.pdb.fromFile("/usr/share/pymol/demo/pept.pdb") + + model= protein.generate(model,forcefield=protein_mmff,bondfield=bond_mmff) + +diff -urNad /home/mbanck/debian/mine/pymol-0.93/examples/devel/povray01.py pymol-0.93/examples/devel/povray01.py +--- /home/mbanck/debian/mine/pymol-0.93/examples/devel/povray01.py 2004-01-03 23:06:05.000000000 +0100 ++++ pymol-0.93/examples/devel/povray01.py 2004-01-03 23:07:06.000000000 +0100 +@@ -4,7 +4,7 @@ + if not ('pept' in cmd.get_names()): + cmd.delete('all') + util.ray_shadows('heavy') +- cmd.do('load $PYMOL_PATH/test/dat/pept.pdb') ++ cmd.do('load $PYMOL_DATA_PATH/pept.pdb') + cmd.do('set surface_quality=1') + cmd.do('show surface;hide lines;') + cmd.zoom('all',10) +--- pymol-0.98+0.99rc6/modules/pymol/wizard/demo.py 2006-06-30 01:07:27.000000000 +0200 ++++ pymol-0.98+0.99rc6/modules/pymol/wizard/demo.py.orig 2006-06-30 01:07:14.000000000 +0200 +@@ -228,7 +228,7 @@ + try: + cmd.set("suspend_updates",1,quiet=1) + cmd.disable() +- cmd.load("$PYMOL_DATA/demo/1hpv.pdb") ++ cmd.load("$TUT/1hpv.pdb") + util.chainbow("1hpv") + cmd.hide("everything","1hpv") + cmd.show("cartoon","1hpv") --- pymol-0.98+0.99rc6.orig/debian/patches/06_remove_shebang.dpatch +++ pymol-0.98+0.99rc6/debian/patches/06_remove_shebang.dpatch @@ -0,0 +1,31 @@ +#! /bin/sh -e +## 06_remove_shebang.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: Removes the "#! /usr/bin/env pathon" from module files + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +diff -urNad /home/mbanck/debian/mine/pymol-0.90/modules/chempy/cex.py pymol-0.90/modules/chempy/cex.py +--- /home/mbanck/debian/mine/pymol-0.90/modules/chempy/cex.py 2002-12-18 18:01:45.000000000 +0100 ++++ pymol-0.90/modules/chempy/cex.py 2003-08-29 22:29:30.000000000 +0200 +@@ -1,4 +1,3 @@ +-#! /usr/bin/env python + #A* ------------------------------------------------------------------- + #B* This file contains source code for the PyMOL computer program + #C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific. --- pymol-0.98+0.99rc6.orig/debian/patches/04_Rules.make.dpatch +++ pymol-0.98+0.99rc6/debian/patches/04_Rules.make.dpatch @@ -0,0 +1,110 @@ +#! /bin/sh -e +## 04_Rules.make.dpatch by Michael Banck +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: The global Makefile + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +--- pymol-0.88.orig/Rules.make ++++ pymol-0.88/Rules.make +@@ -0,0 +1,84 @@ ++#--------------------------------------------------------------------- ++# PyMOL Makefile Rules ++#--------------------------------------------------------------------- ++# ++# This version is for RedHat 7.x, Python 2.1, with Numeric Python ++# ++#- Building ---------------------------------------------------------- ++#--- Tell "make" how to get to PyMOL during build ++PYMOL_PATH = #/var/tmp/pymol-root/usr/lib/python2.1/site-packages/pymol ++#--------------------------------------------------------------------- ++# ++#- Dependencies ------------------------------------------------------ ++#--- X-windows ++XLIB_DIR = -L/usr/X11R6/lib ++XINC_DIR = -I/usr/X11R6/include ++#--- Python ++PYTHON_EXE = /usr/bin/python2.2 ++PYTHON_LIB = -lpython2.2 ++PYTHON_LIB_DIR = -L/usr/lib/python2.2/config ++PYTHON_INC_DIR = -I/usr/include/python2.2 -I/usr/include/python2.2/Numeric ++#--- Other external dependencies ++EXT_INC_DIR = ++EXT_LIB_DIR = ++#--------------------------------------------------------------------- ++# ++#- Build for LINUX as an importable module --------------------------- ++#--- System libraries ++LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -ldl -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 = -fPIC -ffast-math -Wall -ansi -Wmissing-prototypes ++#--- libraries for PyOpenGL ++PYOGL_LIB = -lglut -lGL -lGLU -lXmu -lXi ++#--------------------------------------------------------------------- ++# ++#- Choose One -------------------------------------------------------- ++#--- GCC Optimized ++CCOPT2 = -O2 ++#--- GCC Profiling ++#CCOPT2 = -pg -O3 -funroll-loops ++#--- Debugging ++#CCOPT2 = -g ++#--------------------------------------------------------------------- ++# ++#- Choose One -------------------------------------------------------- ++#--- Workaround for XFree86/DRI linux dll problem for module build ++BUGS = -D_DRI_WORKAROUND ++#--- ++#BUGS = ++#--------------------------------------------------------------------- ++# ++#- Choose One Pair --------------------------------------------------- ++#--- Libpng2 available and contains zlib ++PNG = -D_HAVE_LIBPNG ++ZLIB = ++#--- Libpng2 available but needs zlib ++#PNG = -D_HAVE_LIBPNG ++#ZLIB = -lz ++#--- Libpng2 not available ++#PNG = ++#ZLIB = ++#--------------------------------------------------------------------- ++# ++#--------------------------------------------------------------------- ++# No changes normally required below here ++#--------------------------------------------------------------------- ++ ++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 ++ ++C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \ ++ $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) ++ ++CFLAGS = $(C_FLAGS) --- pymol-0.98+0.99rc6.orig/debian/patches/10_png_includes.dpatch +++ pymol-0.98+0.99rc6/debian/patches/10_png_includes.dpatch @@ -0,0 +1,40 @@ +#! /bin/sh -e +## 10_png_includes by Warren DeLano +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: Reorder includes in MyPng.c + +[ -f debian/patches/00patch-opts ] && . debian/patches/00patch-opts +patch_opts="${patch_opts:--f --no-backup-if-mismatch}" + +if [ $# -ne 1 ]; then + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1 +fi +case "$1" in + -patch) patch $patch_opts -p1 < $0;; + -unpatch) patch $patch_opts -p1 -R < $0;; + *) + echo >&2 "`basename $0`: script expects -patch|-unpatch as argument" + exit 1;; +esac + +exit 0 +@DPATCH@ +--- pymol-0.96/layer0/MyPNG.c 2004-07-13 02:18:12.000000000 +0200 ++++ pymol-0.95/layer0/MyPNG.c 2004-07-13 02:46:20.000000000 +0200 +@@ -14,14 +14,6 @@ + Z* ------------------------------------------------------------------- + */ + +-#include"os_predef.h" +-#include"os_std.h" +- +-#include"Base.h" +-#include "MyPNG.h" +-#include"MemoryDebug.h" +-#include "Setting.h" +- + #ifdef _HAVE_LIBPNG + #include + --- pymol-0.98+0.99rc6.orig/debian/patches/11_fix__cmd_import.dpatch +++ pymol-0.98+0.99rc6/debian/patches/11_fix__cmd_import.dpatch @@ -0,0 +1,19 @@ +#! /bin/sh /usr/share/dpatch/dpatch-run +## 11_fix__cmd_import.dpatch by Pierre Habouzit +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: No description. + +@DPATCH@ +diff -urNad pymol-0.98+0.99rc6~/modules/pymol/__init__.py pymol-0.98+0.99rc6/modules/pymol/__init__.py +--- pymol-0.98+0.99rc6~/modules/pymol/__init__.py 2006-08-30 11:44:52.000000000 +0200 ++++ pymol-0.98+0.99rc6/modules/pymol/__init__.py 2006-08-30 11:48:51.000000000 +0200 +@@ -350,7 +350,7 @@ + _cmd.runpymol(block_input_hook) # only returns if we are running pretend GLUT + # from pymol.embed import wxpymol # never returns + +- import _cmd ++ from pymol import _cmd + import cmd + + def thread_launch(pa): --- pymol-0.98+0.99rc6.orig/debian/pymol.mime +++ pymol-0.98+0.99rc6/debian/pymol.mime @@ -0,0 +1 @@ +chemical/x-pdb; viewer=/usr/bin/pymol; test=test "$DISPLAY" != ""; description=Protein DataBank Format; nametemplate=%s.pdb; priority=6 --- pymol-0.98+0.99rc6.orig/debian/control +++ pymol-0.98+0.99rc6/debian/control @@ -0,0 +1,20 @@ +Source: pymol +Section: science +Priority: optional +Maintainer: Michael Banck +Build-Depends: debhelper (>= 4.0.0), dpatch, python-dev, python-numeric, glutg3-dev, libpng12-0-dev, tk8.4-dev, libfreetype6-dev, python-support (>= 0.4) +Standards-Version: 3.7.2 + +Package: pymol +Architecture: any +Depends: ${python:Depends}, ${shlibs:Depends}, python-tk, python-pmw +Recommends: apbs +Description: An OpenGL Molecular Graphics System written in Python + 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. Although a newcomer + to the field, PyMOL can already be used to generate stunning 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. + --- pymol-0.98+0.99rc6.orig/debian/examples +++ pymol-0.98+0.99rc6/debian/examples @@ -0,0 +1,4 @@ +test/dat/*.pdb +examples/chempy/generate_amber.py +examples/chempy/generate_mmff.py +examples/devel/povray01.py --- pymol-0.98+0.99rc6.orig/debian/dirs +++ pymol-0.98+0.99rc6/debian/dirs @@ -0,0 +1 @@ +/usr/share/pymol --- pymol-0.98+0.99rc6.orig/debian/pymol.applications +++ pymol-0.98+0.99rc6/debian/pymol.applications @@ -0,0 +1,6 @@ +pymol + requires_terminal=false + command=pymol + can_open_multiple_files=false + name=pymol + mime_types=chemical/x-pdb --- pymol-0.98+0.99rc6.orig/debian/changelog +++ pymol-0.98+0.99rc6/debian/changelog @@ -0,0 +1,305 @@ +pymol (0.98+0.99rc6-2build1) feisty; urgency=low + + * Rebuild for python2.5 as the default python version. + + -- Matthias Klose Fri, 12 Jan 2007 13:20:53 +0000 + +pymol (0.98+0.99rc6-2) unstable; urgency=low + + * debian/control (Recommends): Added apbs. + * Sync with Ubuntu; closes: #379508, #378825. + * Acknowledge NMU; closes: #380910. + + -- Michael Banck Tue, 26 Sep 2006 00:08:41 +0200 + +pymol (0.98+0.99rc6-1.1) unstable; urgency=low + + * Non-maintainer upload. + * Update packate to the last python policy (Closes: 380910): + + use dh_pysupport. + + add 11_fix__cmd_import.dpatch to fix an import that does not behaves + well. + + adapt the wrapper to the new path's. + * Bump Standards-Version to 3.7.2. + * Bump DH_COMPAT to 4. + * Fix more files that have wrong executable bits set. + + -- Pierre Habouzit Wed, 30 Aug 2006 11:09:00 +0200 + +pymol (0.98+0.99rc6-1ubuntu1) edgy; urgency=low + + * Re-merge with Debian + + -- Barry deFreese Sun, 23 Jul 2006 17:39:15 -0400 + +pymol (0.98+0.99rc6-1) unstable; urgency=low + + * New upstream release candidate. + * debian/patches/02_test-suite.dpatch: Resync. + * debian/patches/03_povray.dpatch: Likewise. + * debian/patches/05_examples_data_path.dpatch: Likewise. + * debian/patches/09_chempy_data_path.dpatch: Likewise. + * debian/control (Build-Depends): Added libfreetype6-dev. + + -- Michael Banck Fri, 30 Jun 2006 02:05:00 +0200 + +pymol (0.98-1ubuntu2) dapper; urgency=low + + * Merged existing desktop files and updated to current freedestkop + standards. Closes Ubuntu #36435 + + -- Zygmunt Krynicki Sat, 25 Mar 2006 01:22:38 ++0100 + +pymol (0.98-1ubuntu1) breezy; urgency=low + + * Resynchronise with Debian. + * Sponsored for Barry DeFreese (Closes: Ubuntu #12487) + + -- Stephan Hermann Sun, 24 Jul 2005 11:43:59 +0200 + +pymol (0.98-1ubuntu2) dapper; urgency=low + + * Merged existing desktop files and updated to current freedestkop + standards. Closes Ubuntu #36435 + + -- Zygmunt Krynicki Sat, 25 Mar 2006 01:22:38 ++0100 + +pymol (0.98-1ubuntu1) breezy; urgency=low + + * Resynchronise with Debian. + * Sponsored for Barry DeFreese (Closes: Ubuntu #12487) + + -- Stephan Hermann Sun, 24 Jul 2005 11:43:59 +0200 + +pymol (0.98-1) unstable; urgency=low + + * The 'Fixing Ubunt^W^WPreparing for Python Transition' Release. + * New upstream release. + * debian/patches/03_povray.dpatch: Updated. + * debian/rules (install): Create application-registry directory. + * debian/patches/02_test-suite.dpatch (pymol-test): Do not + hardcode python version. + * debian/pymol.launch: Renamed to ... + * debian/pymol.launch.in: ... this, and generalize occurances of + python versions to @PYTHON_VERSION@. + * debian/rules (debian/pymol.launch): New rule, processing + debian/pymol.launch.in. + * debian/rules (build-stamp): Depend on debian/pymol.launch. + + -- Michael Banck Sun, 3 Jul 2005 12:56:15 +0200 + +pymol (0.97-3) unstable; urgency=low + + * debian/control (Depends): Use ${python:Depends} instead of + exlicitely specifying the current default python version. + * (Build-Depends): Use python-dev and python-numeric rather than + specific versions. + * debian/pymol.dirs: Removed. + * debian/rules (install): Grouped creation of directories together + and create missing directories under $(BUILD_DIR)/usr/share as + well as $(BUILD_DIR)/usr/bin. + + -- Michael Banck Tue, 5 Apr 2005 13:14:24 +0200 + +pymol (0.97-2) unstable; urgency=low + + * debian/patches/09_chempy_data_path.dpatch: Include relevant chempy + changes from the old 01_data_path.dpatch and adopt it slightly to + use CHEMPY_PATH. Reported by Christoph Scheurer. + * debian/pymol.launch: Use $CHEMPY_PATH instead of $CHEMPY_DATA_PATH. + + -- Michael Banck Sat, 8 Jan 2005 15:50:45 +0100 + +pymol (0.97-1) unstable; urgency=low + + * New upstream release. + * debian/patches/10_png_includes: Dropped, included upstream. + * debian/patches/00list (10_png_includes.dpatch): Removed. + * debian/control (Build-Depends): Added python; closes: #261040. + * debian/pymol.launch (PYMOL_PATH): New environment variable to work + around upstream breakage for the time being. + + -- Michael Banck Fri, 6 Aug 2004 03:02:32 +0200 + +pymol (0.95-1) unstable; urgency=low + + * New upstream release. + * (layer0/MyPNG.c): Reorder #includes in MyPNG.c. + (10_png_includes.dpatch) + * debian/patches/00list (10_png_includes.dpatch): Added. + * debian/control (Build-Depends): Drop gcc-2.95 again, #229080 does + not show up anymore with th current gcc. + * debian/rules (CC): Removed. + + -- Michael Banck Wed, 7 Apr 2004 21:34:02 +0200 + +pymol (0.93-5) unstable; urgency=low + + * debian/control (Build-Depends): Really only depend on gcc-2.95 on + ia64 and hppa; closes: #235709. + * debian/rules (PYMOL_PATH): New variable, to make sure the test- + suite is able to find its data files. + + -- Michael Banck Tue, 2 Mar 2004 15:20:32 +0100 + +pymol (0.93-4) unstable; urgency=low + + * debian/rules: Only set CC=2.95 if not building for ia64 or hppa. + * debian/control: Do not Build-Depend on gcc-2.95 on ia64 and hppa; + closes: #235658. + + -- Michael Banck Mon, 1 Mar 2004 23:04:21 +0100 + +pymol (0.93-3) unstable; urgency=low + + * debian/control (Build-Depends): Revert to gcc-2.95 to evade segmen- + tation faults when rendering lines with binaries built with gcc-3.x. + * debian/rules: Export CC=gcc-2.95; closes: #229080. + + -- Michael Banck Sun, 22 Feb 2004 11:12:13 +0100 + +pymol (0.93-2) unstable; urgency=low + + * Fix environment-variable handling in modules/pymol/wizards/ + mutagenesis.py; closes: #225590. + (09_chempy_data_path.dpatch) + * 05_examples_data_path.dpatch: Updated to find 1hpv.pdb for the + 'Scripted Animation' demo. + + -- Michael Banck Sat, 3 Jan 2004 23:08:13 +0100 + +pymol (0.93-1) unstable; urgency=low + + * New upstream release. + * debian/patches/00list (01_data_path.dpatch): Dropped, fixed + upstream. + (07_setup.py._opengl-libs.dpatch): Likewise. + (08_setup.py_missing_file.dpatch): Likewise. + * debian/pymol.launch: Changed $PYMOL_DATA_PATH to $PYMOL_DATA, in + order to follow upstream. + + -- Michael Banck Sun, 2 Nov 2003 12:06:10 +0100 + +pymol (0.90-2) unstable; urgency=low + + * 01_data_path.dpatch: + - Factor out examples/-directory into 05_examples_data_path.dpatch. + - Factor out patch for modules/chempy/cex.py into + 06_remove_shebang.dpatch. + * debian/pymol.launch: Pass command-line arguments to pymol through + the wrapper script, thanks to Gabor Tusnady for reporting this. + * setup.py (pyogl_libs): Added "GL","GLU","glut" and "png"; + closes: #214026. (07_setup.py._opengl-libs.dpatch) + * (setup Extension): Added layer0/MemoryCache.c. + (08_setup.py_missing_file.dpatch) + + -- Michael Banck Sat, 4 Oct 2003 21:54:58 +0200 + +pymol (0.90-1) unstable; urgency=low + + * 02_test-suite.dpatch: Updated for python2.3, thanks to Matt Kraai; + closes: #207706, #207711 + * 04_Rules.make.dpatch: Activated + * debian/rules: Remove Rules.make linking/removing, handled by + dpatch now + + -- Michael Banck Mon, 1 Sep 2003 19:16:02 +0200 + +pymol (0.90-0.1) unstable; urgency=low + + * NMU + * New upstream release. + * Update for python2.3 (closes: #206302). + + -- Matthias Klose Thu, 28 Aug 2003 21:04:16 +0200 + +pymol (0.88-1) unstable; urgency=low + + * New upstream release; closes: #196159 + * debian/pymol.menu: Moved menu entry from Math to Science section + * modules/pymol/povray.py: Fixed command-line again + * debian/control, debian/rules: Switch to dpatch + + -- Michael Banck Mon, 16 Jun 2003 18:16:41 +0200 + +pymol (0.86-3) unstable; urgency=low + + * renamed said hacked pymol script to test/pymol-test + * debian/rules: make test/pymol-test executable + * modules/chempy/cex.py: Removed !# from top, this is no script + as far as pymol is concerned + + -- Michael Banck Mon, 13 Jan 2003 17:36:24 +0100 + +pymol (0.86-2) unstable; urgency=low + + * test/run: Fixed test-suite to import the pymol modules under + debian/pymol by providing a hacked pymol script in test/ + + -- Michael Banck Mon, 13 Jan 2003 14:36:48 +0100 + +pymol (0.86-1) unstable; urgency=low + + * New upstream release; closes: #175881 + - Patch for pmw got applied upstream; closes: #160584 + - Hacked around $PYMOL_PATH once more in various places + - Followed Upstream's layout of the data a bit by using + /usr/share/pymol and /usr/share/chempy along with their + subdirectories respectively + * test/run: display the diff in case the test failed + * debian/rules: Use setup.py in build: and clean: target now + * debian/control: Build with libpng12-0-dev now + + -- Michael Banck Mon, 13 Jan 2003 01:16:35 +0100 + +pymol (0.82-2) unstable; urgency=low + + * Switched to python-2.2; closes: #158931 + * modules/pymol/povray.py: Changed PovRay-command + from x-povray to povray; closes: #151190 + * debian/control: Bumped Standards-Version to 3.5.6.1 + + -- Michael Banck Mon, 16 Sep 2002 01:11:57 +0200 + +pymol (0.82-1) unstable; urgency=low + + * New upstream release + * Included pymol.xpm icon for menu-system, + fixing the menu entry; closes: #148400 + * debian/control: Removed the Suggestion of pymol-doc for now as + the manual is out of date, documented its website in README.Debian + instead. Still no manpage, sorry + * Included splash.png in /usr/share/pymol and changed + modules/pymol/invocation.py accordingly + * debian/rules: Triggered the test-run + * modules/pmg_tk/Demo.py: Changed all cmd.load to look for the + .pdb-files in /usr/share/pymol/demo and installed those files + there; closes: #148153, #150070 + * debian/control: Trimmed Build-Depends: + + -- Michael Banck Fri, 21 Jun 2002 00:45:18 +0200 + +pymol (0.80-3) unstable; urgency=low + + * Actually compile shared libraries with -fPIC this time + + -- Michael Banck Sat, 25 May 2002 13:08:19 +0200 + +pymol (0.80-2) unstable; urgency=low + + * Suggests: pymol-doc now + * Build shared libraries with -fPIC; closes: #148118 + + -- Michael Banck Sat, 25 May 2002 09:35:51 +0200 + +pymol (0.80-1) unstable; urgency=low + + * Initial Release; closes: #146024 + * Moved data files to /usr/share/pymol + * Removed need for environment variables during execution, hardcoding + the paths for the moment + * Added a link to undocumented.1 for pymol.1 for the moment + + -- Michael Banck Sun, 19 May 2002 15:56:00 +0200 --- pymol-0.98+0.99rc6.orig/debian/gnome-pymol.mime +++ pymol-0.98+0.99rc6/debian/gnome-pymol.mime @@ -0,0 +1,3 @@ +chemical/x-pdb + ext: pdb + --- pymol-0.98+0.99rc6.orig/debian/rules +++ pymol-0.98+0.99rc6/debian/rules @@ -0,0 +1,95 @@ +#!/usr/bin/make -f +# -*- Makefile -*- + +export DH_COMPAT=4 + +DEB_BUILD_ARCH=$(shell dpkg-architecture -qDEB_BUILD_ARCH) + +export PYMOL_PATH=$(CURDIR) +PYTHON_VERSION := $(shell pyversions -dv) + +include /usr/share/dpatch/dpatch.make + +BUILD_DIR=$(CURDIR)/debian/pymol + +build: build-stamp +build-stamp: patch-stamp debian/pymol.launch + dh_testdir + python setup.py build + touch build-stamp + +clean: unpatch + dh_testdir + dh_testroot + -$(MAKE) distclean + rm -rf test/tmp test/cmp + python setup.py clean + rm -f build-stamp install-stamp + rm -f debian/pymol.launch + dh_clean + +install: build-stamp + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + # Fix some permissions: + chmod -x data/chempy/tinker/parm94.dat + chmod -x data/pymol/splash.png + python setup.py install --prefix $(BUILD_DIR)/usr + -find $(BUILD_DIR)/usr -name '*.py[co]' | xargs rm -f + install -d $(BUILD_DIR)/usr/bin + install -d $(BUILD_DIR)/usr/share/pymol + install -d $(BUILD_DIR)/usr/share/pymol/demo + install -d $(BUILD_DIR)/usr/share/chempy + install -d $(BUILD_DIR)/usr/share/pixmaps + install -d $(BUILD_DIR)/usr/share/mime-info + install -d $(BUILD_DIR)/usr/share/gnome/apps/Graphics + install -d $(BUILD_DIR)/usr/share/applnk/Graphics + install -d $(BUILD_DIR)/usr/share/application-registry + install -d $(BUILD_DIR)/usr/share/applications + install -m 755 debian/pymol.launch $(BUILD_DIR)/usr/bin/pymol + cp -ra data/chempy $(BUILD_DIR)/usr/share + cp -ra data/pymol $(BUILD_DIR)/usr/share + install -m 644 data/demo/* $(BUILD_DIR)/usr/share/pymol/demo + #install -m 644 examples/devel/cgo03.py $(BUILD_DIR)/usr/share/pymol/demo + install -m 644 data/tut/* $(BUILD_DIR)/usr/share/pymol/demo + cp debian/pymol.xpm $(BUILD_DIR)/usr/share/pixmaps/pymol.xpm + cp debian/pymol.desktop $(BUILD_DIR)/usr/share/applications + cp debian/gnome-pymol.keys $(BUILD_DIR)/usr/share/mime-info/pymol.keys + cp debian/gnome-pymol.mime $(BUILD_DIR)/usr/share/mime-info/pymol.mime + cp debian/pymol.applications $(BUILD_DIR)/usr/share/application-registry + +test-run: + chmod +x test/pymol-test + (cd test && ./run) + +debian/pymol.launch: + sed -e s/@PYTHON_VERSION@/$(PYTHON_VERSION)/g < debian/pymol.launch.in > debian/pymol.launch + +binary-indep: build install + +binary-arch: build install test-run + dh_testdir + dh_testroot + dh_installmenu + dh_installmime + dh_installexamples + chmod -x $(BUILD_DIR)/usr/share/doc/pymol/examples/*.pdb + chmod -x $(BUILD_DIR)/usr/share/pymol/cmyk.png + dh_installdocs -A DEVELOPERS README + dh_installchangelogs CHANGES +# dh_undocumented pymol.1 + dh_link + dh_pysupport + dh_strip + dh_compress -Xpdb + dh_fixperms + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch +.PHONY: binary clean --- pymol-0.98+0.99rc6.orig/debian/gnome-pymol.keys +++ pymol-0.98+0.99rc6/debian/gnome-pymol.keys @@ -0,0 +1,10 @@ +chemical/x-pdb + description=Protein DataBank Format + default_action_type=application + short_list_application_ids_for_novice_user_level=pymol + short_list_application_ids_for_intermediate_user_level=pymol + short_list_application_ids_for_advanced_user_level=pymol + category=Graphics + icon-filename=/usr/share/pixmaps/pymol.png + use_category_default=yes + --- pymol-0.98+0.99rc6.orig/debian/pymol.xpm +++ pymol-0.98+0.99rc6/debian/pymol.xpm @@ -0,0 +1,192 @@ +/* XPM */ +static char *pymol[] = { +/* columns rows colors chars-per-pixel */ +"48 48 138 2", +" c #000000", +". c #0c0c0c", +"X c #131313", +"o c #1b1a1b", +"O c #232323", +"+ c #2b2b2b", +"@ c #333332", +"# c #383737", +"$ c #3b3b3b", +"% c #3e403e", +"& c #40403f", +"* c #434343", +"= c #474748", +"- c #484747", +"; c #484748", +": c #4b4b4b", +"> c #4f4f50", +", c #4c524c", +"< c #4f5050", +"1 c #514e4e", +"2 c #504f50", +"3 c #50504f", +"4 c #535353", +"5 c #555458", +"6 c #555955", +"7 c #585957", +"8 c #5b5b5b", +"9 c #504f61", +"0 c #5e5e60", +"q c #545577", +"w c #5c645d", +"e c #5a6a5a", +"r c #537652", +"t c #59735a", +"y c #5a7b5a", +"u c #5f6e60", +"i c #5e6278", +"p c #615254", +"a c #785f5c", +"s c #60615e", +"d c #616c5f", +"f c #6d655d", +"g c #636363", +"h c #66666f", +"j c #616b61", +"k c #676868", +"l c #6b6b6b", +"z c #6f6f77", +"x c #677367", +"c c #657c65", +"v c #6d736d", +"b c #6a7d69", +"n c #726c6c", +"m c #7b6c65", +"M c #72706e", +"N c #707e6f", +"B c #7b756d", +"V c #727372", +"C c #717279", +"Z c #747b74", +"A c #777878", +"S c #787575", +"D c #797876", +"F c #7a7b7a", +"G c #696989", +"H c #77788e", +"J c #5a8659", +"K c #5d8d5d", +"L c #628763", +"P c #658f65", +"I c #6d836b", +"U c #6c8c6c", +"Y c #6b916d", +"T c #6e9e6e", +"R c #758375", +"E c #738d73", +"W c #798577", +"Q c #7c827c", +"! c #788877", +"~ c #7b8a7c", +"^ c #769477", +"/ c #739c72", +"( c #7a917b", +") c #7a9a7a", +"_ c #75ae74", +"` c #7aa17a", +"' c #7eb47d", +"] c #7f9580", +"[ c #7fa380", +"{ c #8e6c6d", +"} c #817271", +"| c #857f77", +" . c #837978", +".. c #818c7d", +"X. c #8d847c", +"o. c #8b8e7b", +"O. c #83987f", +"+. c #938d7b", +"@. c #80a47f", +"#. c #a38f75", +"$. c #a48f78", +"%. c #a1917b", +"&. c #828382", +"*. c #838b84", +"=. c #878988", +"-. c #8a8788", +";. c #888f87", +":. c #8a8a8a", +">. c #839283", +",. c #849b84", +"<. c #879e89", +"1. c #8c938d", +"2. c #8b9c8b", +"3. c #889e90", +"4. c #928b80", +"5. c #908f90", +"6. c #91928d", +"7. c #92988c", +"8. c #929393", +"9. c #929d92", +"0. c #9a9b99", +"q. c #83a282", +"w. c #8ba28b", +"e. c #90a291", +"r. c #94ab94", +"t. c #97aa98", +"y. c #98a497", +"u. c #9da59d", +"i. c #9bad9a", +"p. c #93b093", +"a. c #96b098", +"s. c #9bb39b", +"d. c #a09f9f", +"f. c #a0a49f", +"g. c #a4a4a5", +"h. c #a4aba4", +"j. c #a9aba9", +"k. c #b1b1b1", +/* pixels */ +" ", +" ", +" ", +" ", +" ", +" ", +" . ", +" X O + o . ", +" o * 5 7 1 + ", +" . ; g V A A k * @ X ", +" X 8 V -.0.F V k 4 $ X ", +" O 7 k &.j.&.F &.M 5 @ . ", +" . @ 7 l H i.2.*.f.=.g ; O . ", +" . - V &.5.p.r.9.e.F l : @ ", +" O g :.0.f.r.s.i.e.F z 1 $ . ", +" . . . . . * .0.g.h.s.y.u.a.F k 1 * X ", +" . @ = - + X . . 1 &.0.j.j.s.0.0.r.R 8 8 : + ", +" O < p 5 * # @ X X : A 5.0.u.p.1.5.w.N 8 l 4 $ ", +" $ 7 k V 7 g V l 1 O . @ 0 F &.] ' ( F ! c u 5 < * . ", +" . # , V :.A =.:.&.V : X O - 8 0 u _ Y l ! v 4 ; * # ", +" X $ g l >.2.5.8.5.&.g + . . # : 5 0 ) [ W ] u : ; $ O ", +" o : k A ;.2.9.y.8.=.k $ o . @ 7 n A <.[ ^ U w > ; - o ", +" o 1 l &.1.2.2.<.>.A 8 - O + 7 V &.h.;.c T e ; 5 - O ", +" o : k A 1.9.1.,.) V 8 7 * X o g A :.k.5.Z Y e & 5 : $ . ", +" X $ 8 V *.9.8.~ ) R A n 2 @ . . ; l F :.&.A i q 5 0 8 * X ", +" . + : g V *.;.Q <.<.-.F 0 * . + 7 l V V g 9 G z u : ; o ", +" o ; 8 p V >.>.>.2.5.-.F 8 X . O $ ; : : < h H V 0 2 & X ", +" + - , 0 R >.*.3.d.8.&.g X X + @ @ @ @ : k Q 3.*.F z 2 O ", +" X # $ 8 Z ..>.2.8.5.] 0 O # * ; 4 # & 8 V *.w.;.&.A k + ", +" . @ @ : k S ..2.5.:.z : * ; : g V * * k A =.6.6.-.&.V # . ", +" X + $ 5 k A ..X.k : 4 8 5 5 e e $ $ g D *.7.7.-.&.V @ ", +" X + : g V .} : 2 w l g u L r , & 7 V &.w.7.:.F g O ", +" . $ 8 g n { a s s v ! U J K y 4 = u ! q.w.=.l : o ", +" o & 1 7 p m Y U ) O.d , e P U c t I U ^ k 8 8 O ", +" X @ : : : 8 x E ,.&.l 7 7 t / E j 4 7 *.5.A l + ", +" X * * ; g M R ] &.A n l N ) Z l 2 0 ] 8.F k # ", +" . O ; k V Z q.~ F | A +.o.V C 5 g M l k 7 O ", +" X & s z R ` ) ,.+.X.$.X.V l 5 : 7 7 1 * . ", +" o : 8 A 9.I b ..%.$.$.M l g - O O @ O X ", +" O 7 V 5.A 6 g Z D B f 8 8 4 & X ", +" o ; k l 7 1 w z v g 7 7 7 1 @ . ", +" . @ 1 g 4 = 6 p 0 7 5 5 1 : O ", +" . o + o o o @ * : : ; * + ", +" . o + @ O X . ", +" . ", +" ", +" ", +" " +}; --- pymol-0.98+0.99rc6.orig/debian/pymol.menu +++ pymol-0.98+0.99rc6/debian/pymol.menu @@ -0,0 +1,7 @@ +?package(pymol):\ + needs="x11" \ + section="Apps/Science" \ + command="/usr/bin/pymol" \ + icon="/usr/share/pixmaps/pymol.xpm" \ + title="PyMOL" \ + longtitle="PyMOL Molecular Graphics System" --- pymol-0.98+0.99rc6.orig/debian/copyright +++ pymol-0.98+0.99rc6/debian/copyright @@ -0,0 +1,60 @@ +This package was debianized by Michael Banck on +Tue, 7 May 2002 23:17:42 +0200. + +It was downloaded from http://pymol.sourceforge.net + +Upstream Author: Warren L. DeLano + +Copyright: + +The PyMOL source code is copyrighted, but you can freely use and copy +it as long as you don't change or remove any of the copyright notices. + +---------------------------------------------------------------------- +PyMOL is Copyright 1998-2002 by Warren L. DeLano of +DeLano Scientific, San Carlos, CA, USA (www.delanoscientific.com). + + All Rights Reserved + +Permission to use, copy, modify, distribute, and distribute modified +versions of this software and its documentation for any purpose and +without fee is hereby granted, provided that the above copyright +notice appear in all copies and that both the copyright notice and +this permission notice appear in supporting documentation, and that +the names of Warren L. DeLano or DeLano Scientific not be used in +advertising or publicity pertaining to distribution of the software +without specific, written prior permission. + +WARREN LYFORD DELANO AND DELANO SCIENTIFIC DISCLAIM ALL WARRANTIES +WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL WARREN LYFORD DELANO +OR DELANO SCIENTIFIC BE LIABLE FOR ANY SPECIAL, INDIRECT OR +CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE +USE OR PERFORMANCE OF THIS SOFTWARE. +---------------------------------------------------------------------- + +Where indicated, portions of the PyMOL system are instead protected +under the copyrights of the respective authors. However, all code in +the PyMOL system is released as non-restrictive open-source software +under the above license or an equivalent license. + +PyMOL Trademark Notice +====================== + +PyMOL(TM) is a trademark of DeLano Scientific. Derivate software +which contains PyMOL source code must be plainly distinguished from +the PyMOL package distributed by DeLano Scientific in all publicity, +advertising, and documentation. + +The slogans, "Includes PyMOL(TM).", "Based on PyMOL(TM) technology.", +"Contains PyMOL(TM) source code.", and "Built using PyMOL(TM).", may +be used in advertising, publicity, and documentation of derivate +software provided that the notice, "PyMOL is a trademark of DeLano +Scientific.", is included in a footnote or at the end of the document. + +All other endorsements employing the PyMOL trademark require specific, +written prior permission. + +--Warren L. DeLano (warren@delanoscientific.com) --- pymol-0.98+0.99rc6.orig/debian/pymol.launch.in +++ pymol-0.98+0.99rc6/debian/pymol.launch.in @@ -0,0 +1,8 @@ +#!/bin/sh +# debian wrapper script for pymol + +export PYMOL_DATA=/usr/share/pymol +export PYMOL_PATH=/var/lib/python-support/python@PYTHON_VERSION@/pymol/ +export CHEMPY_DATA=/usr/share/chempy + +python@PYTHON_VERSION@ ${PYMOL_PATH}/__init__.py "$*" --- pymol-0.98+0.99rc6.orig/debian/README.Debian +++ pymol-0.98+0.99rc6/debian/README.Debian @@ -0,0 +1,15 @@ +pymol for Debian +---------------- + +There is an extensive (but outdated) manual for pymol in html and +pdf-format available at http://pymol.sourceforge.net/html/toc.html +I'll package the html version as soon as it gets current. + + -- Michael Banck , Thu, 20 Jun 2002 22:53:55 +0200 + +As I moved all data files to /usr/share/pymol, I might have missed +some changes in the code. *Please* file bugs if something seems +wrong during operation, I was not yet able to test every bit of the +package. + + -- Michael Banck , Sun, 19 May 2002 18:02:20 +0000 --- pymol-0.98+0.99rc6.orig/debian/pymol.desktop +++ pymol-0.98+0.99rc6/debian/pymol.desktop @@ -0,0 +1,14 @@ +[Desktop Entry] +Version=1.0 +Encoding=UTF-8 +Name=PyMOL Molecular Graphics System +Name[pl]=PyMOL, graficzny modeler cząsteczek +GenericName=Molecular Modeller +GenericName[pl]=Modeler cząsteczek +Comment=Model molecular structures and produce high-quality images of them +Comment[pl]=Program do tworzenia i wizualizowania modeli cząsteczek +Type=Application +Exec=pymol +Icon=pymol +MimeType=chemical/x-pdb +Categories=Application;Education;Science;Chemistry;