Reimport biology/pymol as py-mol, and change its PKGNAME to follow the

python-in-pkgsrc standards.

Add conflict with old pkgname.

Keep PKGREVISION even though the package has a new name to confuse the
users less.

4 files changed, 834 insertions, 0 deletions

diff --git a/biology/py-mol/DESCR b/biology/py-mol/DESCR
new file mode 100644
index 00000000000..4db4e9dc525
--- /dev/null
+++ b/biology/py-mol/DESCR
@@ -0,0 +1,4 @@
+PyMOL is a molecular visualization program. It excels at 3D
+visualization of proteins, small molecules, density, surfaces, and
+trajectories. It also includes molecular editing, ray tracing, and
+movies.
diff --git a/biology/py-mol/Makefile b/biology/py-mol/Makefile
new file mode 100644
index 00000000000..d5573caaf72
--- /dev/null
+++ b/biology/py-mol/Makefile
@@ -0,0 +1,47 @@
+# $NetBSD: Makefile,v 1.1.1.1 2007/08/12 03:19:18 wiz Exp $
+
+DISTNAME=	pymol-0_98-src
+PKGNAME=	${PYPKGPREFIX}-mol-0.98
+PKGREVISION=	4
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_SOURCEFORGE:=pymol/}
+EXTRACT_SUFX=	.tgz
+
+MAINTAINER=	pkgsrc-users@NetBSD.org
+HOMEPAGE=	http://pymol.sourceforge.net/
+COMMENT=	Molecular Visualization System
+
+PYTHON_VERSIONS_ACCEPTED=	24 23
+
+WRKSRC=		${WRKDIR}/pymol-0.98
+PYDISTUTILSPKG=	yes
+PYBINMODULE=	yes
+PYSETUP=	setup.py
+
+CONFLICTS=	pymol-[0-9]*
+
+REPLACE_PYTHON=	test/cyg test/run test/show test/win.py
+
+post-install:
+	cd ${WRKSRC} && env ${MAKE_ENV} ${PYTHONBIN} setup2.py
+	${INSTALL_SCRIPT} ${WRKSRC}/pymol.com ${PREFIX}/bin/pymol
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../graphics/glu/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 "../../mk/bsd.pkg.mk"
diff --git a/biology/py-mol/PLIST b/biology/py-mol/PLIST
new file mode 100644
index 00000000000..d22ada57e85
--- /dev/null
+++ b/biology/py-mol/PLIST
@@ -0,0 +1,778 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2007/08/12 03:19:19 wiz Exp $
+bin/pymol
+${PYSITELIB}/chempy/__init__.py
+${PYSITELIB}/chempy/__init__.pyc
+${PYSITELIB}/chempy/__init__.pyo
+${PYSITELIB}/chempy/arc.py
+${PYSITELIB}/chempy/arc.pyc
+${PYSITELIB}/chempy/arc.pyo
+${PYSITELIB}/chempy/bmin/__init__.py
+${PYSITELIB}/chempy/bmin/__init__.pyc
+${PYSITELIB}/chempy/bmin/__init__.pyo
+${PYSITELIB}/chempy/bmin/commands.py
+${PYSITELIB}/chempy/bmin/commands.pyc
+${PYSITELIB}/chempy/bmin/commands.pyo
+${PYSITELIB}/chempy/bmin/realtime.py
+${PYSITELIB}/chempy/bmin/realtime.pyc
+${PYSITELIB}/chempy/bmin/realtime.pyo
+${PYSITELIB}/chempy/bmin/state.py
+${PYSITELIB}/chempy/bmin/state.pyc
+${PYSITELIB}/chempy/bmin/state.pyo
+${PYSITELIB}/chempy/bmin/util.py
+${PYSITELIB}/chempy/bmin/util.pyc
+${PYSITELIB}/chempy/bmin/util.pyo
+${PYSITELIB}/chempy/bond_amber.py
+${PYSITELIB}/chempy/bond_amber.pyc
+${PYSITELIB}/chempy/bond_amber.pyo
+${PYSITELIB}/chempy/bond_mmff.py
+${PYSITELIB}/chempy/bond_mmff.pyc
+${PYSITELIB}/chempy/bond_mmff.pyo
+${PYSITELIB}/chempy/bonds.py
+${PYSITELIB}/chempy/bonds.pyc
+${PYSITELIB}/chempy/bonds.pyo
+${PYSITELIB}/chempy/brick.py
+${PYSITELIB}/chempy/brick.pyc
+${PYSITELIB}/chempy/brick.pyo
+${PYSITELIB}/chempy/cc1.py
+${PYSITELIB}/chempy/cc1.pyc
+${PYSITELIB}/chempy/cc1.pyo
+${PYSITELIB}/chempy/cex.py
+${PYSITELIB}/chempy/cex.pyc
+${PYSITELIB}/chempy/cex.pyo
+${PYSITELIB}/chempy/champ/__init__.py
+${PYSITELIB}/chempy/champ/__init__.pyc
+${PYSITELIB}/chempy/champ/__init__.pyo
+${PYSITELIB}/chempy/champ/_champ.so
+${PYSITELIB}/chempy/champ/amber99.py
+${PYSITELIB}/chempy/champ/amber99.pyc
+${PYSITELIB}/chempy/champ/amber99.pyo
+${PYSITELIB}/chempy/champ/assign.py
+${PYSITELIB}/chempy/champ/assign.pyc
+${PYSITELIB}/chempy/champ/assign.pyo
+${PYSITELIB}/chempy/champ/formal_charges.py
+${PYSITELIB}/chempy/champ/formal_charges.pyc
+${PYSITELIB}/chempy/champ/formal_charges.pyo
+${PYSITELIB}/chempy/charge.py
+${PYSITELIB}/chempy/charge.pyc
+${PYSITELIB}/chempy/charge.pyo
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+${PYSITELIB}/chempy/cpv.pyc
+${PYSITELIB}/chempy/cpv.pyo
+${PYSITELIB}/chempy/dictdb.py
+${PYSITELIB}/chempy/dictdb.pyc
+${PYSITELIB}/chempy/dictdb.pyo
+${PYSITELIB}/chempy/fast/__init__.py
+${PYSITELIB}/chempy/fast/__init__.pyc
+${PYSITELIB}/chempy/fast/__init__.pyo
+${PYSITELIB}/chempy/fragments/__init__.py
+${PYSITELIB}/chempy/fragments/__init__.pyc
+${PYSITELIB}/chempy/fragments/__init__.pyo
+${PYSITELIB}/chempy/gamess1.py
+${PYSITELIB}/chempy/gamess1.pyc
+${PYSITELIB}/chempy/gamess1.pyo
+${PYSITELIB}/chempy/gms.py
+${PYSITELIB}/chempy/gms.pyc
+${PYSITELIB}/chempy/gms.pyo
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+${PYSITELIB}/chempy/hetatm.pyc
+${PYSITELIB}/chempy/hetatm.pyo
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+${PYSITELIB}/chempy/io.pyc
+${PYSITELIB}/chempy/io.pyo
+${PYSITELIB}/chempy/lst.py
+${PYSITELIB}/chempy/lst.pyc
+${PYSITELIB}/chempy/lst.pyo
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+${PYSITELIB}/chempy/mass.py
+${PYSITELIB}/chempy/mass.pyc
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+${PYSITELIB}/chempy/mmd.pyo
+${PYSITELIB}/chempy/models.py
+${PYSITELIB}/chempy/models.pyc
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+${PYSITELIB}/chempy/mol.py
+${PYSITELIB}/chempy/mol.pyc
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+${PYSITELIB}/chempy/place.py
+${PYSITELIB}/chempy/place.pyc
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+${PYSITELIB}/chempy/protein.py
+${PYSITELIB}/chempy/protein.pyc
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+${PYSITELIB}/chempy/tinker/__init__.pyc
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+${PYSITELIB}/pmg_tk/PMGApp.pyc
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+${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_gly.pkl
+${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl
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+${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl
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+${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_phe.pkl
+${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_pro.pkl
+${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_ser.pkl
+${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_thr.pkl
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+${PYSITELIB}/pymol/pymol_path/test/ref/C0080create.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0100select.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0105names.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0106order.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0140iterate.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0150alter.1.pdb
+${PYSITELIB}/pymol/pymol_path/test/ref/C0150alter.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0160get.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0170scene.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0180embed.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0181embed.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0200feedback.log
+${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/C0600util.log
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+${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.2.pdb
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+${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.5.pdb
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+${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.7.pdb
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+${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.9.pdb
+${PYSITELIB}/pymol/pymol_path/test/ref/C0700odd.A.pdb
+${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.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C0800matrices.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C1000viewing.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C1010helping.log
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+${PYSITELIB}/pymol/pymol_path/test/ref/C1070exporting.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C1080isomore.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C1090coulomb.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C1095slice.log
+${PYSITELIB}/pymol/pymol_path/test/ref/C1100do.log
+${PYSITELIB}/pymol/pymol_path/test/ref/L0010ccp4read.log
+${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
+${PYSITELIB}/pymol/pymol_path/test/ref/T01.log
+${PYSITELIB}/pymol/pymol_path/test/ref/U01.log
+${PYSITELIB}/pymol/pymol_path/test/run
+${PYSITELIB}/pymol/pymol_path/test/show
+${PYSITELIB}/pymol/pymol_path/test/trim.py
+${PYSITELIB}/pymol/pymol_path/test/vdiff
+${PYSITELIB}/pymol/pymol_path/test/win.py
+${PYSITELIB}/pymol/querying.py
+${PYSITELIB}/pymol/querying.pyc
+${PYSITELIB}/pymol/querying.pyo
+${PYSITELIB}/pymol/rpc.py
+${PYSITELIB}/pymol/rpc.pyc
+${PYSITELIB}/pymol/rpc.pyo
+${PYSITELIB}/pymol/selecting.py
+${PYSITELIB}/pymol/selecting.pyc
+${PYSITELIB}/pymol/selecting.pyo
+${PYSITELIB}/pymol/selector.py
+${PYSITELIB}/pymol/selector.pyc
+${PYSITELIB}/pymol/selector.pyo
+${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
+${PYSITELIB}/pymol/util.py
+${PYSITELIB}/pymol/util.pyc
+${PYSITELIB}/pymol/util.pyo
+${PYSITELIB}/pymol/vfont.py
+${PYSITELIB}/pymol/vfont.pyc
+${PYSITELIB}/pymol/vfont.pyo
+${PYSITELIB}/pymol/viewing.py
+${PYSITELIB}/pymol/viewing.pyc
+${PYSITELIB}/pymol/viewing.pyo
+${PYSITELIB}/pymol/wizard/__init__.py
+${PYSITELIB}/pymol/wizard/__init__.pyc
+${PYSITELIB}/pymol/wizard/__init__.pyo
+${PYSITELIB}/pymol/wizard/annotation.py
+${PYSITELIB}/pymol/wizard/annotation.pyc
+${PYSITELIB}/pymol/wizard/annotation.pyo
+${PYSITELIB}/pymol/wizard/appearance.py
+${PYSITELIB}/pymol/wizard/appearance.pyc
+${PYSITELIB}/pymol/wizard/appearance.pyo
+${PYSITELIB}/pymol/wizard/benchmark.py
+${PYSITELIB}/pymol/wizard/benchmark.pyc
+${PYSITELIB}/pymol/wizard/benchmark.pyo
+${PYSITELIB}/pymol/wizard/charge.py
+${PYSITELIB}/pymol/wizard/charge.pyc
+${PYSITELIB}/pymol/wizard/charge.pyo
+${PYSITELIB}/pymol/wizard/cleanup.py
+${PYSITELIB}/pymol/wizard/cleanup.pyc
+${PYSITELIB}/pymol/wizard/cleanup.pyo
+${PYSITELIB}/pymol/wizard/demo.py
+${PYSITELIB}/pymol/wizard/demo.pyc
+${PYSITELIB}/pymol/wizard/demo.pyo
+${PYSITELIB}/pymol/wizard/density.py
+${PYSITELIB}/pymol/wizard/density.pyc
+${PYSITELIB}/pymol/wizard/density.pyo
+${PYSITELIB}/pymol/wizard/distance.py
+${PYSITELIB}/pymol/wizard/distance.pyc
+${PYSITELIB}/pymol/wizard/distance.pyo
+${PYSITELIB}/pymol/wizard/fedora.py
+${PYSITELIB}/pymol/wizard/fedora.pyc
+${PYSITELIB}/pymol/wizard/fedora.pyo
+${PYSITELIB}/pymol/wizard/filter.py
+${PYSITELIB}/pymol/wizard/filter.pyc
+${PYSITELIB}/pymol/wizard/filter.pyo
+${PYSITELIB}/pymol/wizard/label.py
+${PYSITELIB}/pymol/wizard/label.pyc
+${PYSITELIB}/pymol/wizard/label.pyo
+${PYSITELIB}/pymol/wizard/measurement.py
+${PYSITELIB}/pymol/wizard/measurement.pyc
+${PYSITELIB}/pymol/wizard/measurement.pyo
+${PYSITELIB}/pymol/wizard/message.py
+${PYSITELIB}/pymol/wizard/message.pyc
+${PYSITELIB}/pymol/wizard/message.pyo
+${PYSITELIB}/pymol/wizard/mutagenesis.py
+${PYSITELIB}/pymol/wizard/mutagenesis.pyc
+${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/renaming.py
+${PYSITELIB}/pymol/wizard/renaming.pyc
+${PYSITELIB}/pymol/wizard/renaming.pyo
+${PYSITELIB}/pymol/wizard/sculpting.py
+${PYSITELIB}/pymol/wizard/sculpting.pyc
+${PYSITELIB}/pymol/wizard/sculpting.pyo
+${PYSITELIB}/pymol/wizard/security.py
+${PYSITELIB}/pymol/wizard/security.pyc
+${PYSITELIB}/pymol/wizard/security.pyo
+${PYSITELIB}/pymol/wizarding.py
+${PYSITELIB}/pymol/wizarding.pyc
+${PYSITELIB}/pymol/wizarding.pyo
+${PYSITELIB}/pymol/xray.py
+${PYSITELIB}/pymol/xray.pyc
+${PYSITELIB}/pymol/xray.pyo
+${PYSITELIB}/pymol/xwin.py
+${PYSITELIB}/pymol/xwin.pyc
+${PYSITELIB}/pymol/xwin.pyo
+@dirrm ${PYSITELIB}/pymol/wizard
+@dirrm ${PYSITELIB}/pymol/pymol_path/test/ref
+@dirrm ${PYSITELIB}/pymol/pymol_path/test/inp
+@dirrm ${PYSITELIB}/pymol/pymol_path/test/dat
+@dirrm ${PYSITELIB}/pymol/pymol_path/test
+@dirrm ${PYSITELIB}/pymol/pymol_path/scripts/metaphorics
+@dirrm ${PYSITELIB}/pymol/pymol_path/scripts
+@dirrm ${PYSITELIB}/pymol/pymol_path/examples/package/redhat
+@dirrm ${PYSITELIB}/pymol/pymol_path/examples/package
+@dirrm ${PYSITELIB}/pymol/pymol_path/examples/launching
+@dirrm ${PYSITELIB}/pymol/pymol_path/examples/devel
+@dirrm ${PYSITELIB}/pymol/pymol_path/examples/cookbook
+@dirrm ${PYSITELIB}/pymol/pymol_path/examples/chempy
+@dirrm ${PYSITELIB}/pymol/pymol_path/examples
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/tut
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/pymol/matrices
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/pymol
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps/builder
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/pmg_tk/bitmaps
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/pmg_tk
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/demo
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/chempy/tinker
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/chempy/sidechains
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/chempy/fragments
+@dirrm ${PYSITELIB}/pymol/pymol_path/data/chempy
+@dirrm ${PYSITELIB}/pymol/pymol_path/data
+@dirrm ${PYSITELIB}/pymol/pymol_path
+@dirrm ${PYSITELIB}/pymol/opengl/glut
+@dirrm ${PYSITELIB}/pymol/opengl/glu
+@dirrm ${PYSITELIB}/pymol/opengl/gl
+@dirrm ${PYSITELIB}/pymol/opengl
+@dirrm ${PYSITELIB}/pymol
+@dirrm ${PYSITELIB}/pmg_wx
+@dirrm ${PYSITELIB}/pmg_tk/startup
+@dirrm ${PYSITELIB}/pmg_tk/skins/normal
+@dirrm ${PYSITELIB}/pmg_tk/skins
+@dirrm ${PYSITELIB}/pmg_tk
+@dirrm ${PYSITELIB}/chempy/tinker
+@dirrm ${PYSITELIB}/chempy/fragments
+@dirrm ${PYSITELIB}/chempy/fast
+@dirrm ${PYSITELIB}/chempy/champ
+@dirrm ${PYSITELIB}/chempy/bmin
+@dirrm ${PYSITELIB}/chempy
diff --git a/biology/py-mol/distinfo b/biology/py-mol/distinfo
new file mode 100644
index 00000000000..6734a6c262a
--- /dev/null
+++ b/biology/py-mol/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1.1.1 2007/08/12 03:19:18 wiz Exp $
+
+SHA1 (pymol-0_98-src.tgz) = 7140eb0478d41705ee2affb6527f7cacd0ff9ace
+RMD160 (pymol-0_98-src.tgz) = 0aa31ffc1fb85e1c03320fb806a76b315a847bbd
+Size (pymol-0_98-src.tgz) = 3033733 bytes