From 1904519aae65613822a123646a2f3fc05fbc33ca Mon Sep 17 00:00:00 2001 From: obache Date: Thu, 27 Oct 2011 14:03:17 +0000 Subject: Update py-mol to 1.4.1. many improvements and bug fixes. --- biology/py-mol/Makefile | 45 ++++------ biology/py-mol/PLIST | 224 ++++++++++++++++++++++++++++++++++++++++++++++-- biology/py-mol/distinfo | 8 +- 3 files changed, 238 insertions(+), 39 deletions(-) (limited to 'biology') diff --git a/biology/py-mol/Makefile b/biology/py-mol/Makefile index aedca51f06c..e3883fd8366 100644 --- a/biology/py-mol/Makefile +++ b/biology/py-mol/Makefile @@ -1,50 +1,43 @@ -# $NetBSD: Makefile,v 1.6 2011/01/13 13:37:09 wiz Exp $ +# $NetBSD: Makefile,v 1.7 2011/10/27 14:03:17 obache Exp $ -DISTNAME= pymol-0_98-src -PKGNAME= ${PYPKGPREFIX}-mol-0.98 -PKGREVISION= 6 +DISTNAME= pymol-v1.4.1 +PKGNAME= ${PYPKGPREFIX}-${DISTNAME:S/pymol-v/mol-/} +EGG_NAME= pymol-1.4.0 CATEGORIES= biology MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=pymol/} -EXTRACT_SUFX= .tgz +EXTRACT_SUFX= .tar.bz2 MAINTAINER= pkgsrc-users@NetBSD.org -HOMEPAGE= http://pymol.sourceforge.net/ +HOMEPAGE= http://www.pymol.org/ COMMENT= Molecular Visualization System +DEPENDS+= ${PYPKGPREFIX}-numpy-[0-9]*:../../math/py-numpy +DEPENDS+= ${PYPKGPREFIX}-Pmw-[0-9]*:../../x11/py-Pmw + PKG_DESTDIR_SUPPORT= user-destdir -WRKSRC= ${WRKDIR}/pymol-0.98 -PYDISTUTILSPKG= yes -PYSETUP= setup.py +WRKSRC= ${WRKDIR}/pymol CONFLICTS= pymol-[0-9]* +USE_LANGUAGES= c c++ + REPLACE_PYTHON= test/cyg test/run test/show test/win.py -PYTHON_VERSIONS_ACCEPTED= 25 24 +# not used +CHECK_PORTABILITY_SKIP+= setup/* INSTALLATION_DIRS= bin post-install: - cd ${WRKSRC} && env ${MAKE_ENV} PYTHONPATH=${DESTDIR}${PREFIX}/${PYSITELIB} ${PYTHONBIN} setup2.py - ${INSTALL_SCRIPT} ${WRKSRC}/pymol.com ${DESTDIR}${PREFIX}/bin/pymol + cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} PYTHONPATH=${DESTDIR}${PREFIX}/${PYSITELIB} ${PYTHONBIN} setup2.py install + ${INSTALL_SCRIPT} ${WRKSRC}/pymol ${DESTDIR}${PREFIX}/bin/pymol .include "../../devel/zlib/buildlink3.mk" -.include "../../graphics/glu/buildlink3.mk" +.include "../../graphics/freetype2/buildlink3.mk" +.include "../../graphics/glew/buildlink3.mk" .include "../../graphics/glut/buildlink3.mk" .include "../../graphics/png/buildlink3.mk" -.include "../../math/py-Numeric/buildlink3.mk" -.include "../../lang/tcl/buildlink3.mk" -.include "../../x11/tk/buildlink3.mk" -.include "../../x11/py-Tk/buildlink3.mk" -.include "../../x11/py-Pmw/buildlink3.mk" - -# Note that the website claims this package needs "freeglut", which -# would mean: -# .include "../../graphics/freeglut/buildlink3.mk" -# However, the package seems to link with "glut" and not with "freeglut", -# and no other pkgsrc packages seem to use freeglut. - .include "../../lang/python/application.mk" -.include "../../lang/python/extension.mk" +.include "../../lang/python/distutils.mk" .include "../../mk/bsd.pkg.mk" diff --git a/biology/py-mol/PLIST b/biology/py-mol/PLIST index 98437661aaa..84361f73fc3 100644 --- a/biology/py-mol/PLIST +++ b/biology/py-mol/PLIST @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:34 joerg Exp $ +@comment $NetBSD: PLIST,v 1.3 2011/10/27 14:03:17 obache Exp $ bin/pymol ${PYSITELIB}/chempy/__init__.py ${PYSITELIB}/chempy/__init__.pyc @@ -55,6 +55,9 @@ ${PYSITELIB}/chempy/champ/formal_charges.pyo ${PYSITELIB}/chempy/charge.py ${PYSITELIB}/chempy/charge.pyc ${PYSITELIB}/chempy/charge.pyo +${PYSITELIB}/chempy/cif.py +${PYSITELIB}/chempy/cif.pyc +${PYSITELIB}/chempy/cif.pyo ${PYSITELIB}/chempy/cpv.py ${PYSITELIB}/chempy/cpv.pyc ${PYSITELIB}/chempy/cpv.pyo @@ -100,6 +103,9 @@ ${PYSITELIB}/chempy/models.pyo ${PYSITELIB}/chempy/mol.py ${PYSITELIB}/chempy/mol.pyc ${PYSITELIB}/chempy/mol.pyo +${PYSITELIB}/chempy/mol2.py +${PYSITELIB}/chempy/mol2.pyc +${PYSITELIB}/chempy/mol2.pyo ${PYSITELIB}/chempy/neighbor.py ${PYSITELIB}/chempy/neighbor.pyc ${PYSITELIB}/chempy/neighbor.pyo @@ -178,12 +184,30 @@ ${PYSITELIB}/pmg_tk/__init__.pyo ${PYSITELIB}/pmg_tk/skins/__init__.py ${PYSITELIB}/pmg_tk/skins/__init__.pyc ${PYSITELIB}/pmg_tk/skins/__init__.pyo +${PYSITELIB}/pmg_tk/skins/normal/ColorMap.py +${PYSITELIB}/pmg_tk/skins/normal/ColorMap.pyc +${PYSITELIB}/pmg_tk/skins/normal/ColorMap.pyo +${PYSITELIB}/pmg_tk/skins/normal/ColorRampModel.py +${PYSITELIB}/pmg_tk/skins/normal/ColorRampModel.pyc +${PYSITELIB}/pmg_tk/skins/normal/ColorRampModel.pyo +${PYSITELIB}/pmg_tk/skins/normal/ModalWindow.py +${PYSITELIB}/pmg_tk/skins/normal/ModalWindow.pyc +${PYSITELIB}/pmg_tk/skins/normal/ModalWindow.pyo +${PYSITELIB}/pmg_tk/skins/normal/SimpleColorChooser.py +${PYSITELIB}/pmg_tk/skins/normal/SimpleColorChooser.pyc +${PYSITELIB}/pmg_tk/skins/normal/SimpleColorChooser.pyo ${PYSITELIB}/pmg_tk/skins/normal/__init__.py ${PYSITELIB}/pmg_tk/skins/normal/__init__.pyc ${PYSITELIB}/pmg_tk/skins/normal/__init__.pyo ${PYSITELIB}/pmg_tk/skins/normal/builder.py ${PYSITELIB}/pmg_tk/skins/normal/builder.pyc ${PYSITELIB}/pmg_tk/skins/normal/builder.pyo +${PYSITELIB}/pmg_tk/skins/normal/hist.py +${PYSITELIB}/pmg_tk/skins/normal/hist.pyc +${PYSITELIB}/pmg_tk/skins/normal/hist.pyo +${PYSITELIB}/pmg_tk/skins/normal/volume.py +${PYSITELIB}/pmg_tk/skins/normal/volume.pyc +${PYSITELIB}/pmg_tk/skins/normal/volume.pyo ${PYSITELIB}/pmg_tk/startup/__init__.py ${PYSITELIB}/pmg_tk/startup/__init__.pyc ${PYSITELIB}/pmg_tk/startup/__init__.pyo @@ -196,26 +220,44 @@ ${PYSITELIB}/pmg_tk/startup/remote_pdb_load.pyo ${PYSITELIB}/pmg_wx/__init__.py ${PYSITELIB}/pmg_wx/__init__.pyc ${PYSITELIB}/pmg_wx/__init__.pyo -${PYSITELIB}/pymol/ExtensionClass.so +${PLIST.eggfile}${PYSITELIB}/${EGG_FILE} ${PYSITELIB}/pymol/__init__.py ${PYSITELIB}/pymol/__init__.pyc ${PYSITELIB}/pymol/__init__.pyo ${PYSITELIB}/pymol/_cmd.so +${PYSITELIB}/pymol/api.py +${PYSITELIB}/pymol/api.pyc +${PYSITELIB}/pymol/api.pyo ${PYSITELIB}/pymol/callback.py ${PYSITELIB}/pymol/callback.pyc ${PYSITELIB}/pymol/callback.pyo ${PYSITELIB}/pymol/cgo.py ${PYSITELIB}/pymol/cgo.pyc ${PYSITELIB}/pymol/cgo.pyo +${PYSITELIB}/pymol/checking.py +${PYSITELIB}/pymol/checking.pyc +${PYSITELIB}/pymol/checking.pyo ${PYSITELIB}/pymol/cmd.py ${PYSITELIB}/pymol/cmd.pyc ${PYSITELIB}/pymol/cmd.pyo +${PYSITELIB}/pymol/colorramping.py +${PYSITELIB}/pymol/colorramping.pyc +${PYSITELIB}/pymol/colorramping.pyo ${PYSITELIB}/pymol/commanding.py ${PYSITELIB}/pymol/commanding.pyc ${PYSITELIB}/pymol/commanding.pyo -${PYSITELIB}/pymol/contrib.py -${PYSITELIB}/pymol/contrib.pyc -${PYSITELIB}/pymol/contrib.pyo +${PYSITELIB}/pymol/completing.py +${PYSITELIB}/pymol/completing.pyc +${PYSITELIB}/pymol/completing.pyo +${PYSITELIB}/pymol/computing.py +${PYSITELIB}/pymol/computing.pyc +${PYSITELIB}/pymol/computing.pyo +${PYSITELIB}/pymol/constants.py +${PYSITELIB}/pymol/constants.pyc +${PYSITELIB}/pymol/constants.pyo +${PYSITELIB}/pymol/contrib/__init__.py +${PYSITELIB}/pymol/contrib/__init__.pyc +${PYSITELIB}/pymol/contrib/__init__.pyo ${PYSITELIB}/pymol/controlling.py ${PYSITELIB}/pymol/controlling.pyc ${PYSITELIB}/pymol/controlling.pyo @@ -237,24 +279,48 @@ ${PYSITELIB}/pymol/exporting.pyo ${PYSITELIB}/pymol/externing.py ${PYSITELIB}/pymol/externing.pyc ${PYSITELIB}/pymol/externing.pyo +${PYSITELIB}/pymol/feedingback.py +${PYSITELIB}/pymol/feedingback.pyc +${PYSITELIB}/pymol/feedingback.pyo ${PYSITELIB}/pymol/fitting.py ${PYSITELIB}/pymol/fitting.pyc ${PYSITELIB}/pymol/fitting.pyo +${PYSITELIB}/pymol/gui.py +${PYSITELIB}/pymol/gui.pyc +${PYSITELIB}/pymol/gui.pyo +${PYSITELIB}/pymol/headering.py +${PYSITELIB}/pymol/headering.pyc +${PYSITELIB}/pymol/headering.pyo ${PYSITELIB}/pymol/helping.py ${PYSITELIB}/pymol/helping.pyc ${PYSITELIB}/pymol/helping.pyo ${PYSITELIB}/pymol/importing.py ${PYSITELIB}/pymol/importing.pyc ${PYSITELIB}/pymol/importing.pyo +${PYSITELIB}/pymol/internal.py +${PYSITELIB}/pymol/internal.pyc +${PYSITELIB}/pymol/internal.pyo ${PYSITELIB}/pymol/invocation.py ${PYSITELIB}/pymol/invocation.pyc ${PYSITELIB}/pymol/invocation.pyo +${PYSITELIB}/pymol/keyboard.py +${PYSITELIB}/pymol/keyboard.pyc +${PYSITELIB}/pymol/keyboard.pyo +${PYSITELIB}/pymol/keywords.py +${PYSITELIB}/pymol/keywords.pyc +${PYSITELIB}/pymol/keywords.pyo +${PYSITELIB}/pymol/locking.py +${PYSITELIB}/pymol/locking.pyc +${PYSITELIB}/pymol/locking.pyo ${PYSITELIB}/pymol/m4x.py ${PYSITELIB}/pymol/m4x.pyc ${PYSITELIB}/pymol/m4x.pyo ${PYSITELIB}/pymol/menu.py ${PYSITELIB}/pymol/menu.pyc ${PYSITELIB}/pymol/menu.pyo +${PYSITELIB}/pymol/monitoring.py +${PYSITELIB}/pymol/monitoring.pyc +${PYSITELIB}/pymol/monitoring.pyo ${PYSITELIB}/pymol/movie.py ${PYSITELIB}/pymol/movie.pyc ${PYSITELIB}/pymol/movie.pyo @@ -306,17 +372,23 @@ ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ace.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/acetylene.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ala.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/arg.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/argn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/asn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/asp.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/asph.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/benzene.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/butane.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_ala.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_arg.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_argn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_asp.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_asph.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_cys.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_gln.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_glu.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_gluh.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl @@ -325,6 +397,7 @@ ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_his.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_ile.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_leu.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_lys.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_lysn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_met.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl @@ -333,35 +406,48 @@ ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_val.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/cyanide.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/cyclohexane.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/cyclopentadiene.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/cyclopentane.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/cyclopropane.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/cys.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ethylene.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/formaldehyde.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/formamide.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/formic.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/gln.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/glu.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/gluh.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/gly.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/hid.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/hie.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/hip.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/his.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ile.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/indane.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/leu.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/lys.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/lysn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/met.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/methane.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/methanol.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/napthylene.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nhh.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nitro.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nme.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_ala.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_arg.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_argn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_asn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_asp.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_asph.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_cys.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_gln.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_glu.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_gluh.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_gly.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_hid.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_hie.pkl @@ -370,6 +456,7 @@ ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_his.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_ile.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_leu.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_lys.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_lysn.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_met.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_phe.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_pro.pkl @@ -380,18 +467,24 @@ ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_tyr.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/nt_val.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/peptide.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/phe.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/phosphite.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/pro.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/realtime.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ser.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/sulfone.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/thr.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/trp.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/tyr.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/val.pkl ${PYSITELIB}/pymol/pymol_path/data/chempy/sidechains/generate1.py ${PYSITELIB}/pymol/pymol_path/data/chempy/sidechains/generate2.py +${PYSITELIB}/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/sidechains/sc_bb_dep.py +${PYSITELIB}/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/sidechains/sc_bb_ind.py ${PYSITELIB}/pymol/pymol_path/data/chempy/sidechains/sc_library.pkl -${PYSITELIB}/pymol/pymol_path/data/chempy/tinker/Makefile +${PYSITELIB}/pymol/pymol_path/data/chempy/tinker/Makefile.delsci ${PYSITELIB}/pymol/pymol_path/data/chempy/tinker/chempy.prm ${PYSITELIB}/pymol/pymol_path/data/chempy/tinker/make99_simple.py ${PYSITELIB}/pymol/pymol_path/data/chempy/tinker/make_simple.py @@ -415,6 +508,14 @@ ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.xbm +${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.gif +${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro65.xbm +${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.gif +${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro66.xbm +${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.gif +${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro67.xbm +${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.gif +${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc3.xbm ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.gif ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc4.xbm ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc5.gif @@ -424,40 +525,73 @@ ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc6.xbm ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm ${PYSITELIB}/pymol/pymol_path/data/pymol/cmyk.png +${PYSITELIB}/pymol/pymol_path/data/pymol/hsv.ppm ${PYSITELIB}/pymol/pymol_path/data/pymol/matrices/BLOSUM62 -${PYSITELIB}/pymol/pymol_path/data/pymol/splash.png +${PYSITELIB}/pymol/pymol_path/data/pymol/splash.old.png +${PYSITELIB}/pymol/pymol_path/data/shaders/default.fs +${PYSITELIB}/pymol/pymol_path/data/shaders/default.vs +${PYSITELIB}/pymol/pymol_path/data/shaders/volume.fs +${PYSITELIB}/pymol/pymol_path/data/shaders/volume.vs ${PYSITELIB}/pymol/pymol_path/data/tut/1hpv.pdb ${PYSITELIB}/pymol/pymol_path/examples/chempy/generate_amber.py ${PYSITELIB}/pymol/pymol_path/examples/chempy/generate_mmff.py -${PYSITELIB}/pymol/pymol_path/examples/cookbook/README +${PYSITELIB}/pymol/pymol_path/examples/cookbook/area_diff.pml ${PYSITELIB}/pymol/pymol_path/examples/cookbook/build_peptide.py ${PYSITELIB}/pymol/pymol_path/examples/cookbook/contact.pml +${PYSITELIB}/pymol/pymol_path/examples/cookbook/dali.py ${PYSITELIB}/pymol/pymol_path/examples/cookbook/density.pml ${PYSITELIB}/pymol/pymol_path/examples/cookbook/groel_es.pml +${PYSITELIB}/pymol/pymol_path/examples/cookbook/multiclip_ray.pml ${PYSITELIB}/pymol/pymol_path/examples/cookbook/packing.pml ${PYSITELIB}/pymol/pymol_path/examples/cookbook/packsurf.pml +${PYSITELIB}/pymol/pymol_path/examples/cookbook/ref_frame.pml ${PYSITELIB}/pymol/pymol_path/examples/cookbook/ribosome.pml +${PYSITELIB}/pymol/pymol_path/examples/cookbook/scenes2movie.pml +${PYSITELIB}/pymol/pymol_path/examples/cookbook/seq_match_sele.pml +${PYSITELIB}/pymol/pymol_path/examples/cookbook/ss_xfer.pml +${PYSITELIB}/pymol/pymol_path/examples/cookbook/symsph.py ${PYSITELIB}/pymol/pymol_path/examples/devel/brick01.py +${PYSITELIB}/pymol/pymol_path/examples/devel/cam2crd.pym ${PYSITELIB}/pymol/pymol_path/examples/devel/cgo01.py ${PYSITELIB}/pymol/pymol_path/examples/devel/cgo02.py ${PYSITELIB}/pymol/pymol_path/examples/devel/cgo03.py ${PYSITELIB}/pymol/pymol_path/examples/devel/cgo04.py +${PYSITELIB}/pymol/pymol_path/examples/devel/cgo05.py +${PYSITELIB}/pymol/pymol_path/examples/devel/cgo06.py +${PYSITELIB}/pymol/pymol_path/examples/devel/cgo07.py +${PYSITELIB}/pymol/pymol_path/examples/devel/cgo08.py ${PYSITELIB}/pymol/pymol_path/examples/devel/cgo_3Dtext01.py +${PYSITELIB}/pymol/pymol_path/examples/devel/cgo_axes.py ${PYSITELIB}/pymol/pymol_path/examples/devel/cgo_label_hack.py ${PYSITELIB}/pymol/pymol_path/examples/devel/cgo_plane.py ${PYSITELIB}/pymol/pymol_path/examples/devel/chempy_model01.py ${PYSITELIB}/pymol/pymol_path/examples/devel/chempy_model02.py ${PYSITELIB}/pymol/pymol_path/examples/devel/chempy_model03.py +${PYSITELIB}/pymol/pymol_path/examples/devel/click_ordered_list.py +${PYSITELIB}/pymol/pymol_path/examples/devel/count_molecules.py +${PYSITELIB}/pymol/pymol_path/examples/devel/extend_demo01.py ${PYSITELIB}/pymol/pymol_path/examples/devel/gl01.py ${PYSITELIB}/pymol/pymol_path/examples/devel/gl02.py ${PYSITELIB}/pymol/pymol_path/examples/devel/gl03.py +${PYSITELIB}/pymol/pymol_path/examples/devel/hole_vmd_tri.pym +${PYSITELIB}/pymol/pymol_path/examples/devel/importing.py +${PYSITELIB}/pymol/pymol_path/examples/devel/link_demo.py +${PYSITELIB}/pymol/pymol_path/examples/devel/membrane.py ${PYSITELIB}/pymol/pymol_path/examples/devel/mutate01.pml ${PYSITELIB}/pymol/pymol_path/examples/devel/mutate02.py +${PYSITELIB}/pymol/pymol_path/examples/devel/my_ext_gui.py +${PYSITELIB}/pymol/pymol_path/examples/devel/particle01.py +${PYSITELIB}/pymol/pymol_path/examples/devel/particle02.py ${PYSITELIB}/pymol/pymol_path/examples/devel/pick_wiz.py ${PYSITELIB}/pymol/pymol_path/examples/devel/povray01.py +${PYSITELIB}/pymol/pymol_path/examples/devel/scenes_to_movie01.pml ${PYSITELIB}/pymol/pymol_path/examples/devel/sd_annotate.pml ${PYSITELIB}/pymol/pymol_path/examples/devel/sele_wiz.py ${PYSITELIB}/pymol/pymol_path/examples/devel/start_pymol.py +${PYSITELIB}/pymol/pymol_path/examples/devel/syncmol.py +${PYSITELIB}/pymol/pymol_path/examples/devel/tkwindow.py +${PYSITELIB}/pymol/pymol_path/examples/devel/webgui01.py +${PYSITELIB}/pymol/pymol_path/examples/devel/webgui02.py ${PYSITELIB}/pymol/pymol_path/examples/devel/xmlrpc01.py ${PYSITELIB}/pymol/pymol_path/examples/devel/xmlrpc02.py ${PYSITELIB}/pymol/pymol_path/examples/launching/README @@ -497,6 +631,7 @@ ${PYSITELIB}/pymol/pymol_path/test/dat/il2.pdb ${PYSITELIB}/pymol/pymol_path/test/dat/ligs3d.sdf ${PYSITELIB}/pymol/pymol_path/test/dat/names.pdb ${PYSITELIB}/pymol/pymol_path/test/dat/odd01.pdb +${PYSITELIB}/pymol/pymol_path/test/dat/odd02.pdb ${PYSITELIB}/pymol/pymol_path/test/dat/pept.pdb ${PYSITELIB}/pymol/pymol_path/test/dat/pept.pkl ${PYSITELIB}/pymol/pymol_path/test/dat/pept.r3d @@ -512,6 +647,10 @@ ${PYSITELIB}/pymol/pymol_path/test/inp/B04.py ${PYSITELIB}/pymol/pymol_path/test/inp/B05.py ${PYSITELIB}/pymol/pymol_path/test/inp/B06.py ${PYSITELIB}/pymol/pymol_path/test/inp/B07.py +${PYSITELIB}/pymol/pymol_path/test/inp/B08.py +${PYSITELIB}/pymol/pymol_path/test/inp/B09.py +${PYSITELIB}/pymol/pymol_path/test/inp/B10.py +${PYSITELIB}/pymol/pymol_path/test/inp/B11.py ${PYSITELIB}/pymol/pymol_path/test/inp/C0001quit.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C0010hello.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C0020pdb.pml @@ -538,8 +677,10 @@ ${PYSITELIB}/pymol/pymol_path/test/inp/C0201extend.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C0202help_python.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C0300session.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C0500misc.pml +${PYSITELIB}/pymol/pymol_path/test/inp/C0550pseudo.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C0600util.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C0700odd.pml +${PYSITELIB}/pymol/pymol_path/test/inp/C0740multipdb.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C0800matrices.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C1000viewing.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C1010helping.pml @@ -554,12 +695,29 @@ ${PYSITELIB}/pymol/pymol_path/test/inp/C1080isomore.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C1090coulomb.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C1095slice.pml ${PYSITELIB}/pymol/pymol_path/test/inp/C1100do.py +${PYSITELIB}/pymol/pymol_path/test/inp/C1110matrix_mode.pml +${PYSITELIB}/pymol/pymol_path/test/inp/C1200matrix_maps.pml +${PYSITELIB}/pymol/pymol_path/test/inp/C1300extras.pml +${PYSITELIB}/pymol/pymol_path/test/inp/C2000returns.py ${PYSITELIB}/pymol/pymol_path/test/inp/L0010ccp4read.pml ${PYSITELIB}/pymol/pymol_path/test/inp/L0020xplorread.pml ${PYSITELIB}/pymol/pymol_path/test/inp/L0030isomesh.pml ${PYSITELIB}/pymol/pymol_path/test/inp/L0040isomesh2.pml ${PYSITELIB}/pymol/pymol_path/test/inp/L0100isomisc.pml ${PYSITELIB}/pymol/pymol_path/test/inp/L0200electro.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0001new.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0002start.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0010load.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0020multi.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0021multi.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0025view.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0030scene.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0040do.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0041do.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0050session.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0051session.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0052session.pml +${PYSITELIB}/pymol/pymol_path/test/inp/M0053session.pml ${PYSITELIB}/pymol/pymol_path/test/inp/T01.py ${PYSITELIB}/pymol/pymol_path/test/inp/T02.py ${PYSITELIB}/pymol/pymol_path/test/inp/T03.py @@ -596,7 +754,10 @@ ${PYSITELIB}/pymol/pymol_path/test/ref/C0201extend.log ${PYSITELIB}/pymol/pymol_path/test/ref/C0202help_python.log ${PYSITELIB}/pymol/pymol_path/test/ref/C0300session.log ${PYSITELIB}/pymol/pymol_path/test/ref/C0500misc.log +${PYSITELIB}/pymol/pymol_path/test/ref/C0550pseudo.log ${PYSITELIB}/pymol/pymol_path/test/ref/C0600util.log +${PYSITELIB}/pymol/pymol_path/test/ref/C0700.odd.G.pdb +${PYSITELIB}/pymol/pymol_path/test/ref/C0700.odd.H.pdb ${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.1.pdb ${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.2.pdb ${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.3.pdb @@ -611,7 +772,9 @@ ${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.B.pdb ${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.C.pdb ${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.D.pdb ${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.E.pdb +${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.F.pdb ${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.log +${PYSITELIB}/pymol/pymol_path/test/ref/C0740multipdb.log ${PYSITELIB}/pymol/pymol_path/test/ref/C0800matrices.log ${PYSITELIB}/pymol/pymol_path/test/ref/C1000viewing.log ${PYSITELIB}/pymol/pymol_path/test/ref/C1010helping.log @@ -626,12 +789,29 @@ ${PYSITELIB}/pymol/pymol_path/test/ref/C1080isomore.log ${PYSITELIB}/pymol/pymol_path/test/ref/C1090coulomb.log ${PYSITELIB}/pymol/pymol_path/test/ref/C1095slice.log ${PYSITELIB}/pymol/pymol_path/test/ref/C1100do.log +${PYSITELIB}/pymol/pymol_path/test/ref/C1110matrix_mode.log +${PYSITELIB}/pymol/pymol_path/test/ref/C1200matrix_maps.log +${PYSITELIB}/pymol/pymol_path/test/ref/C1300extras.log +${PYSITELIB}/pymol/pymol_path/test/ref/C2000returns.log ${PYSITELIB}/pymol/pymol_path/test/ref/L0010ccp4read.log ${PYSITELIB}/pymol/pymol_path/test/ref/L0020xplorread.log ${PYSITELIB}/pymol/pymol_path/test/ref/L0030isomesh.log ${PYSITELIB}/pymol/pymol_path/test/ref/L0040isomesh2.log ${PYSITELIB}/pymol/pymol_path/test/ref/L0100isomisc.log ${PYSITELIB}/pymol/pymol_path/test/ref/L0200electro.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0001new.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0002start.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0010load.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0020multi.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0021multi.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0025view.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0030scene.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0040do.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0041do.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0050session.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0051session.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0052session.log +${PYSITELIB}/pymol/pymol_path/test/ref/M0053session.log ${PYSITELIB}/pymol/pymol_path/test/ref/T01.log ${PYSITELIB}/pymol/pymol_path/test/ref/U01.log ${PYSITELIB}/pymol/pymol_path/test/run @@ -654,7 +834,6 @@ ${PYSITELIB}/pymol/selector.pyo ${PYSITELIB}/pymol/setting.py ${PYSITELIB}/pymol/setting.pyc ${PYSITELIB}/pymol/setting.pyo -${PYSITELIB}/pymol/sglite.so ${PYSITELIB}/pymol/shortcut.py ${PYSITELIB}/pymol/shortcut.pyc ${PYSITELIB}/pymol/shortcut.pyo @@ -679,6 +858,9 @@ ${PYSITELIB}/pymol/wizard/appearance.pyo ${PYSITELIB}/pymol/wizard/benchmark.py ${PYSITELIB}/pymol/wizard/benchmark.pyc ${PYSITELIB}/pymol/wizard/benchmark.pyo +${PYSITELIB}/pymol/wizard/box.py +${PYSITELIB}/pymol/wizard/box.pyc +${PYSITELIB}/pymol/wizard/box.pyo ${PYSITELIB}/pymol/wizard/charge.py ${PYSITELIB}/pymol/wizard/charge.pyc ${PYSITELIB}/pymol/wizard/charge.pyo @@ -694,6 +876,9 @@ ${PYSITELIB}/pymol/wizard/density.pyo ${PYSITELIB}/pymol/wizard/distance.py ${PYSITELIB}/pymol/wizard/distance.pyc ${PYSITELIB}/pymol/wizard/distance.pyo +${PYSITELIB}/pymol/wizard/dragging.py +${PYSITELIB}/pymol/wizard/dragging.pyc +${PYSITELIB}/pymol/wizard/dragging.pyo ${PYSITELIB}/pymol/wizard/fedora.py ${PYSITELIB}/pymol/wizard/fedora.pyc ${PYSITELIB}/pymol/wizard/fedora.pyo @@ -715,6 +900,9 @@ ${PYSITELIB}/pymol/wizard/mutagenesis.pyo ${PYSITELIB}/pymol/wizard/pair_fit.py ${PYSITELIB}/pymol/wizard/pair_fit.pyc ${PYSITELIB}/pymol/wizard/pair_fit.pyo +${PYSITELIB}/pymol/wizard/pseudoatom.py +${PYSITELIB}/pymol/wizard/pseudoatom.pyc +${PYSITELIB}/pymol/wizard/pseudoatom.pyo ${PYSITELIB}/pymol/wizard/renaming.py ${PYSITELIB}/pymol/wizard/renaming.pyc ${PYSITELIB}/pymol/wizard/renaming.pyo @@ -724,6 +912,12 @@ ${PYSITELIB}/pymol/wizard/sculpting.pyo ${PYSITELIB}/pymol/wizard/security.py ${PYSITELIB}/pymol/wizard/security.pyc ${PYSITELIB}/pymol/wizard/security.pyo +${PYSITELIB}/pymol/wizard/stereodemo.py +${PYSITELIB}/pymol/wizard/stereodemo.pyc +${PYSITELIB}/pymol/wizard/stereodemo.pyo +${PYSITELIB}/pymol/wizard/toggle.py +${PYSITELIB}/pymol/wizard/toggle.pyc +${PYSITELIB}/pymol/wizard/toggle.pyo ${PYSITELIB}/pymol/wizarding.py ${PYSITELIB}/pymol/wizarding.pyc ${PYSITELIB}/pymol/wizarding.pyo @@ -733,3 +927,15 @@ ${PYSITELIB}/pymol/xray.pyo ${PYSITELIB}/pymol/xwin.py ${PYSITELIB}/pymol/xwin.pyc ${PYSITELIB}/pymol/xwin.pyo +${PYSITELIB}/web/__init__.py +${PYSITELIB}/web/__init__.pyc +${PYSITELIB}/web/__init__.pyo +${PYSITELIB}/web/examples/__init__.py +${PYSITELIB}/web/examples/__init__.pyc +${PYSITELIB}/web/examples/__init__.pyo +${PYSITELIB}/web/examples/justhttpd.py +${PYSITELIB}/web/examples/justhttpd.pyc +${PYSITELIB}/web/examples/justhttpd.pyo +${PYSITELIB}/web/pymolhttpd.py +${PYSITELIB}/web/pymolhttpd.pyc +${PYSITELIB}/web/pymolhttpd.pyo diff --git a/biology/py-mol/distinfo b/biology/py-mol/distinfo index 6734a6c262a..655225bc43a 100644 --- a/biology/py-mol/distinfo +++ b/biology/py-mol/distinfo @@ -1,5 +1,5 @@ -$NetBSD: distinfo,v 1.1.1.1 2007/08/12 03:19:18 wiz Exp $ +$NetBSD: distinfo,v 1.2 2011/10/27 14:03:17 obache Exp $ -SHA1 (pymol-0_98-src.tgz) = 7140eb0478d41705ee2affb6527f7cacd0ff9ace -RMD160 (pymol-0_98-src.tgz) = 0aa31ffc1fb85e1c03320fb806a76b315a847bbd -Size (pymol-0_98-src.tgz) = 3033733 bytes +SHA1 (pymol-v1.4.1.tar.bz2) = 085c83af192c53160060fac14c438ca31c5b6ebf +RMD160 (pymol-v1.4.1.tar.bz2) = 8a9e0c964ff76d6d8e7d837e579953ca8362c626 +Size (pymol-v1.4.1.tar.bz2) = 9105980 bytes -- cgit v1.2.3