Update py-mol to 1.4.1.

many improvements and bug fixes.

3 files changed, 238 insertions, 39 deletions

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