diff options
-rw-r--r-- | biology/pymol/DESCR | 5 | ||||
-rw-r--r-- | biology/pymol/Makefile | 40 | ||||
-rw-r--r-- | biology/pymol/PLIST | 779 | ||||
-rw-r--r-- | biology/pymol/distinfo | 5 |
4 files changed, 829 insertions, 0 deletions
diff --git a/biology/pymol/DESCR b/biology/pymol/DESCR new file mode 100644 index 00000000000..dc8397207b7 --- /dev/null +++ b/biology/pymol/DESCR @@ -0,0 +1,5 @@ +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/pymol/Makefile b/biology/pymol/Makefile new file mode 100644 index 00000000000..fdd81b01854 --- /dev/null +++ b/biology/pymol/Makefile @@ -0,0 +1,40 @@ +# $NetBSD: Makefile,v 1.1 2005/10/07 19:41:07 perry Exp $ + +DISTNAME= pymol-0_98-src +PKGNAME= pymol-0.98 +WRKSRC= ${WRKDIR}/${PKGNAME} +CATEGORIES= biology +MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=pymol/} +EXTRACT_SUFX= .tgz + +MAINTAINER= perry@NetBSD.org +HOMEPAGE= http://pymol.sourceforge.net/ +COMMENT= Molecular Visualization System + +PYTHON_VERSIONS_ACCEPTED= 23 24 + +PYDISTUTILSPKG= yes +PYBINMODULE= yes +PYSETUP= setup.py + +post-install: + (cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${PYTHONBIN} setup2.py) + ${INSTALL_SCRIPT} ${WRKSRC}/pymol.com ${PREFIX}/bin/pymol + +.include "../../devel/zlib/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/extension.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/pymol/PLIST b/biology/pymol/PLIST new file mode 100644 index 00000000000..4f2e57e1ce2 --- /dev/null +++ b/biology/pymol/PLIST @@ -0,0 +1,779 @@ +@comment $NetBSD: PLIST,v 1.1 2005/10/07 19:41:07 perry 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 +${PYSITELIB}/chempy/charge.pyo +${PYSITELIB}/chempy/cpv.py +${PYSITELIB}/chempy/cpv.pyc +${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 +${PYSITELIB}/chempy/gms.pyo +${PYSITELIB}/chempy/hetatm.py +${PYSITELIB}/chempy/hetatm.pyc +${PYSITELIB}/chempy/hetatm.pyo +${PYSITELIB}/chempy/io.py +${PYSITELIB}/chempy/io.pyc +${PYSITELIB}/chempy/io.pyo +${PYSITELIB}/chempy/lst.py +${PYSITELIB}/chempy/lst.pyc +${PYSITELIB}/chempy/lst.pyo +${PYSITELIB}/chempy/mae.py +${PYSITELIB}/chempy/mae.pyc +${PYSITELIB}/chempy/mae.pyo +${PYSITELIB}/chempy/map.py +${PYSITELIB}/chempy/map.pyc +${PYSITELIB}/chempy/map.pyo +${PYSITELIB}/chempy/mass.py +${PYSITELIB}/chempy/mass.pyc +${PYSITELIB}/chempy/mass.pyo +${PYSITELIB}/chempy/mmd.py +${PYSITELIB}/chempy/mmd.pyc +${PYSITELIB}/chempy/mmd.pyo +${PYSITELIB}/chempy/models.py +${PYSITELIB}/chempy/models.pyc +${PYSITELIB}/chempy/models.pyo +${PYSITELIB}/chempy/mol.py +${PYSITELIB}/chempy/mol.pyc +${PYSITELIB}/chempy/mol.pyo +${PYSITELIB}/chempy/neighbor.py +${PYSITELIB}/chempy/neighbor.pyc +${PYSITELIB}/chempy/neighbor.pyo +${PYSITELIB}/chempy/pdb.py +${PYSITELIB}/chempy/pdb.pyc +${PYSITELIB}/chempy/pdb.pyo +${PYSITELIB}/chempy/pkl.py +${PYSITELIB}/chempy/pkl.pyc +${PYSITELIB}/chempy/pkl.pyo +${PYSITELIB}/chempy/place.py +${PYSITELIB}/chempy/place.pyc +${PYSITELIB}/chempy/place.pyo +${PYSITELIB}/chempy/protein.py +${PYSITELIB}/chempy/protein.pyc +${PYSITELIB}/chempy/protein.pyo +${PYSITELIB}/chempy/protein_amber.py +${PYSITELIB}/chempy/protein_amber.pyc +${PYSITELIB}/chempy/protein_amber.pyo +${PYSITELIB}/chempy/protein_amber99.py +${PYSITELIB}/chempy/protein_amber99.pyc +${PYSITELIB}/chempy/protein_amber99.pyo +${PYSITELIB}/chempy/protein_mmff.py +${PYSITELIB}/chempy/protein_mmff.pyc +${PYSITELIB}/chempy/protein_mmff.pyo +${PYSITELIB}/chempy/protein_residues.py +${PYSITELIB}/chempy/protein_residues.pyc +${PYSITELIB}/chempy/protein_residues.pyo +${PYSITELIB}/chempy/sdf.py +${PYSITELIB}/chempy/sdf.pyc +${PYSITELIB}/chempy/sdf.pyo +${PYSITELIB}/chempy/solvate.py +${PYSITELIB}/chempy/solvate.pyc +${PYSITELIB}/chempy/solvate.pyo +${PYSITELIB}/chempy/tinker/__init__.py +${PYSITELIB}/chempy/tinker/__init__.pyc +${PYSITELIB}/chempy/tinker/__init__.pyo +${PYSITELIB}/chempy/tinker/amber.py +${PYSITELIB}/chempy/tinker/amber.pyc +${PYSITELIB}/chempy/tinker/amber.pyo +${PYSITELIB}/chempy/tinker/keyword.py +${PYSITELIB}/chempy/tinker/keyword.pyc +${PYSITELIB}/chempy/tinker/keyword.pyo +${PYSITELIB}/chempy/tinker/realtime.py +${PYSITELIB}/chempy/tinker/realtime.pyc +${PYSITELIB}/chempy/tinker/realtime.pyo +${PYSITELIB}/chempy/tinker/state.py +${PYSITELIB}/chempy/tinker/state.pyc +${PYSITELIB}/chempy/tinker/state.pyo +${PYSITELIB}/chempy/water_amber.py +${PYSITELIB}/chempy/water_amber.pyc +${PYSITELIB}/chempy/water_amber.pyo +${PYSITELIB}/chempy/water_residues.py +${PYSITELIB}/chempy/water_residues.pyc +${PYSITELIB}/chempy/water_residues.pyo +${PYSITELIB}/chempy/xyz.py +${PYSITELIB}/chempy/xyz.pyc +${PYSITELIB}/chempy/xyz.pyo +${PYSITELIB}/pmg_tk/ColorEditor.py +${PYSITELIB}/pmg_tk/ColorEditor.pyc +${PYSITELIB}/pmg_tk/ColorEditor.pyo +${PYSITELIB}/pmg_tk/Demo.py +${PYSITELIB}/pmg_tk/Demo.pyc +${PYSITELIB}/pmg_tk/Demo.pyo +${PYSITELIB}/pmg_tk/PMGApp.py +${PYSITELIB}/pmg_tk/PMGApp.pyc +${PYSITELIB}/pmg_tk/PMGApp.pyo +${PYSITELIB}/pmg_tk/SetEditor.py +${PYSITELIB}/pmg_tk/SetEditor.pyc +${PYSITELIB}/pmg_tk/SetEditor.pyo +${PYSITELIB}/pmg_tk/Setting.py +${PYSITELIB}/pmg_tk/Setting.pyc +${PYSITELIB}/pmg_tk/Setting.pyo +${PYSITELIB}/pmg_tk/__init__.py +${PYSITELIB}/pmg_tk/__init__.pyc +${PYSITELIB}/pmg_tk/__init__.pyo +${PYSITELIB}/pmg_tk/skins/__init__.py +${PYSITELIB}/pmg_tk/skins/__init__.pyc +${PYSITELIB}/pmg_tk/skins/__init__.pyo +${PYSITELIB}/pmg_tk/skins/normal/__init__.py +${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 +${PYSITELIB}/pmg_tk/startup/__init__.py +${PYSITELIB}/pmg_tk/startup/__init__.pyc +${PYSITELIB}/pmg_tk/startup/__init__.pyo +${PYSITELIB}/pmg_tk/startup/apbs_tools.py +${PYSITELIB}/pmg_tk/startup/apbs_tools.pyc +${PYSITELIB}/pmg_tk/startup/apbs_tools.pyo + +${PYSITELIB}/pmg_tk/startup/remote_pdb_load.py +${PYSITELIB}/pmg_tk/startup/remote_pdb_load.pyc +${PYSITELIB}/pmg_tk/startup/remote_pdb_load.pyo +${PYSITELIB}/pmg_wx/__init__.py +${PYSITELIB}/pmg_wx/__init__.pyc +${PYSITELIB}/pmg_wx/__init__.pyo +${PYSITELIB}/pymol/ExtensionClass.so +${PYSITELIB}/pymol/__init__.py +${PYSITELIB}/pymol/__init__.pyc +${PYSITELIB}/pymol/__init__.pyo +${PYSITELIB}/pymol/_cmd.so +${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/cmd.py +${PYSITELIB}/pymol/cmd.pyc +${PYSITELIB}/pymol/cmd.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 +${PYSITELIB}/pymol/controlling.py +${PYSITELIB}/pymol/controlling.pyc +${PYSITELIB}/pymol/controlling.pyo +${PYSITELIB}/pymol/creating.py +${PYSITELIB}/pymol/creating.pyc +${PYSITELIB}/pymol/creating.pyo +${PYSITELIB}/pymol/editing.py +${PYSITELIB}/pymol/editing.pyc +${PYSITELIB}/pymol/editing.pyo +${PYSITELIB}/pymol/editor.py +${PYSITELIB}/pymol/editor.pyc +${PYSITELIB}/pymol/editor.pyo +${PYSITELIB}/pymol/experimenting.py +${PYSITELIB}/pymol/experimenting.pyc +${PYSITELIB}/pymol/experimenting.pyo +${PYSITELIB}/pymol/exporting.py +${PYSITELIB}/pymol/exporting.pyc +${PYSITELIB}/pymol/exporting.pyo +${PYSITELIB}/pymol/externing.py +${PYSITELIB}/pymol/externing.pyc +${PYSITELIB}/pymol/externing.pyo +${PYSITELIB}/pymol/fitting.py +${PYSITELIB}/pymol/fitting.pyc +${PYSITELIB}/pymol/fitting.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 +${PYSITELIB}/pymol/invocation.py +${PYSITELIB}/pymol/invocation.pyc +${PYSITELIB}/pymol/invocation.pyo +${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/movie.py +${PYSITELIB}/pymol/movie.pyc +${PYSITELIB}/pymol/movie.pyo +${PYSITELIB}/pymol/moving.py +${PYSITELIB}/pymol/moving.pyc +${PYSITELIB}/pymol/moving.pyo +${PYSITELIB}/pymol/opengl/__init__.py +${PYSITELIB}/pymol/opengl/__init__.pyc +${PYSITELIB}/pymol/opengl/__init__.pyo +${PYSITELIB}/pymol/opengl/gl/__init__.py +${PYSITELIB}/pymol/opengl/gl/__init__.pyc +${PYSITELIB}/pymol/opengl/gl/__init__.pyo +${PYSITELIB}/pymol/opengl/gl/_opengl.so +${PYSITELIB}/pymol/opengl/gl/_opengl_num.so +${PYSITELIB}/pymol/opengl/gl/glconst.py +${PYSITELIB}/pymol/opengl/gl/glconst.pyc +${PYSITELIB}/pymol/opengl/gl/glconst.pyo +${PYSITELIB}/pymol/opengl/gl/openglutil.so +${PYSITELIB}/pymol/opengl/gl/openglutil_num.so +${PYSITELIB}/pymol/opengl/glu/__init__.py +${PYSITELIB}/pymol/opengl/glu/__init__.pyc +${PYSITELIB}/pymol/opengl/glu/__init__.pyo +${PYSITELIB}/pymol/opengl/glu/_glu.so +${PYSITELIB}/pymol/opengl/glu/_glu_num.so +${PYSITELIB}/pymol/opengl/glu/gluconst.py +${PYSITELIB}/pymol/opengl/glu/gluconst.pyc +${PYSITELIB}/pymol/opengl/glu/gluconst.pyo +${PYSITELIB}/pymol/opengl/glut/__init__.py +${PYSITELIB}/pymol/opengl/glut/__init__.pyc +${PYSITELIB}/pymol/opengl/glut/__init__.pyo +${PYSITELIB}/pymol/opengl/glut/_glut.so +${PYSITELIB}/pymol/opengl/glut/glutconst.py +${PYSITELIB}/pymol/opengl/glut/glutconst.pyc +${PYSITELIB}/pymol/opengl/glut/glutconst.pyo +${PYSITELIB}/pymol/parser.py +${PYSITELIB}/pymol/parser.pyc +${PYSITELIB}/pymol/parser.pyo +${PYSITELIB}/pymol/parsing.py +${PYSITELIB}/pymol/parsing.pyc +${PYSITELIB}/pymol/parsing.pyo +${PYSITELIB}/pymol/povray.py +${PYSITELIB}/pymol/povray.pyc +${PYSITELIB}/pymol/povray.pyo +${PYSITELIB}/pymol/preset.py +${PYSITELIB}/pymol/preset.pyc +${PYSITELIB}/pymol/preset.pyo +${PYSITELIB}/pymol/pymol_path/LICENSE +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ace.pkl +${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 +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/asn.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/asp.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/benzene.pkl +${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 +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_asn.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_asp.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_gly.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_hid.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_hie.pkl +${PYSITELIB}/pymol/pymol_path/data/chempy/fragments/ct_hip.pkl +${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 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+@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 ${PYSITELIB}/chempy diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo new file mode 100644 index 00000000000..b23867bcecc --- /dev/null +++ b/biology/pymol/distinfo @@ -0,0 +1,5 @@ +$NetBSD: distinfo,v 1.1 2005/10/07 19:41:07 perry Exp $ + +SHA1 (pymol-0_98-src.tgz) = 7140eb0478d41705ee2affb6527f7cacd0ff9ace +RMD160 (pymol-0_98-src.tgz) = 0aa31ffc1fb85e1c03320fb806a76b315a847bbd +Size (pymol-0_98-src.tgz) = 3033733 bytes |