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wip/py-mol: import py-mol-2.5.0
Module Name: pkgsrc-wip
Committed By: Thomas Klausner <tk%giga.or.at@localhost>
Pushed By: wiz
Date: Thu Feb 17 10:34:20 2022 +0100
Changeset: 846733226a379ee418882f1df9d2220af0e542e3
Added Files:
py-mol/DESCR
py-mol/Makefile
py-mol/PLIST
py-mol/TODO
py-mol/distinfo
Log Message:
wip/py-mol: import py-mol-2.5.0
This package does not build yet. If you're interested in this, please
finish it.
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.
TODO:
Fix compilation problem:
c++ -O2 -g -fPIC -D_FORTIFY_SOURCE=2 -fstack-check -I/usr/pkg/include -I/usr/include -I/usr/X11R7/include/freetype2 -I/usr/X11R7/include -I/usr/X11R7/include/libdrm -I/usr/pkg/include/python3.10 -g -I/usr/pkg/include/netlib -I/usr/pkg/include -I/usr/include -I/usr/X11R7/include/freetype2 -I/usr/X11R7/include -I/usr/X11R7/include/libdrm -I/usr/pkg/include/python3.10 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilaye
r1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/include -I/usr/pkg/include/python3.10 -c -MMD layer1/COLLADA.cpp -o build/temp.netbsd-9.99.93-amd64-3.10/layer1/COLLADA.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/COLLADA.cpp:16:10: fatal error: libxml/xmlwriter.h: No such file or directory 16 | #include <libxml/xmlwriter.h> | ^~~~~~~~~~~~~~~~~~~~ compilation terminated.
...
Fix python problem:
error: command '/scratch/biology/py-mol/work/.cwrapper/bin/gcc' failed with exit code 1
Exception ignored in: <function Pool.__del__ at 0x7532caff7fd0>
Traceback (most recent call last):
File "/usr/pkg/lib/python3.10/multiprocessing/pool.py", line 268, in __del__
File "/usr/pkg/lib/python3.10/multiprocessing/queues.py", line 378, in put
File "/usr/pkg/lib/python3.10/multiprocessing/connection.py", line 205, in send_bytes
File "/usr/pkg/lib/python3.10/multiprocessing/connection.py", line 405, in _send_bytes
AttributeError: 'NoneType' object has no attribute 'pack'
*** Error code 1
Convert to py-qt* instead of py-Pmw.
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=846733226a379ee418882f1df9d2220af0e542e3
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
py-mol/DESCR | 4 +
py-mol/Makefile | 42 +++
py-mol/PLIST | 967 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
py-mol/TODO | 20 ++
py-mol/distinfo | 5 +
5 files changed, 1038 insertions(+)
diffs:
diff --git a/py-mol/DESCR b/py-mol/DESCR
new file mode 100644
index 0000000000..4db4e9dc52
--- /dev/null
+++ b/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/py-mol/Makefile b/py-mol/Makefile
new file mode 100644
index 0000000000..2cd60d4a2e
--- /dev/null
+++ b/py-mol/Makefile
@@ -0,0 +1,42 @@
+# $NetBSD: Makefile,v 1.39 2022/01/10 18:46:54 wiz Exp $
+
+DISTNAME= pymol-2.5.0
+PKGNAME= ${PYPKGPREFIX}-${DISTNAME:S/pymol-/mol-/}
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_GITHUB:=schrodinger/}
+GITHUB_PROJECT= pymol-open-source
+GITHUB_TAG= v${PKGVERSION_NOREV}
+
+MAINTAINER= pkgsrc-users%NetBSD.org@localhost
+HOMEPAGE= http://www.pymol.org/
+COMMENT= Molecular Visualization System
+LICENSE= modified-bsd
+
+DEPENDS+= ${PYPKGPREFIX}-Pmw-[0-9]*:../../x11/py-Pmw
+
+CONFLICTS= pymol-[0-9]*
+
+USE_LANGUAGES= c c++11
+USE_TOOLS+= pkg-config
+
+#INSTALLATION_DIRS= bin
+
+# Gross hack
+#PYSETUPBUILDTARGET= install ${_PYSETUPINSTALLARGS}
+
+#post-install:
+# cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} PYTHONPATH=${DESTDIR}${PREFIX}/${PYSITELIB} ${PYTHONBIN} setup2.py install ${_PYSETUPINSTALLARGS}
+# ${INSTALL_SCRIPT} ${WRKSRC}/pymol ${DESTDIR}${PREFIX}/bin/pymol${PYVERSSUFFIX}
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../graphics/freetype2/buildlink3.mk"
+.include "../../graphics/glew/buildlink3.mk"
+.include "../../graphics/freeglut/buildlink3.mk"
+.include "../../graphics/png/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../lang/python/versioned_dependencies.mk"
+.include "../../lang/python/egg.mk"
+.include "../../wip/glm/buildlink3.mk"
+.include "../../textproc/libxml2/buildlink3.mk"
+.include "../../math/py-numpy/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-mol/PLIST b/py-mol/PLIST
new file mode 100644
index 0000000000..4dd385e168
--- /dev/null
+++ b/py-mol/PLIST
@@ -0,0 +1,967 @@
+@comment $NetBSD: PLIST,v 1.7 2022/01/10 18:46:54 wiz Exp $
+bin/pymol${PYVERSSUFFIX}
+${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
+${PYSITELIB}/chempy/cif.py
+${PYSITELIB}/chempy/cif.pyc
+${PYSITELIB}/chempy/cif.pyo
+${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
+${PYSITELIB}/chempy/mol2.py
+${PYSITELIB}/chempy/mol2.pyc
+${PYSITELIB}/chempy/mol2.pyo
+${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/PyMOLMapLoad.py
+${PYSITELIB}/pmg_tk/PyMOLMapLoad.pyc
+${PYSITELIB}/pmg_tk/PyMOLMapLoad.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
+${PYSITELIB}/pmg_tk/skins/normal/ColorMap.py
+${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
+${PYSITELIB}/pmg_tk/startup/__init__.pyo
+${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
+${PYSITELIB}/pymol/__init__.py
+${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/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
+${PYSITELIB}/pymol/constants_palette.py
+${PYSITELIB}/pymol/constants_palette.pyc
+${PYSITELIB}/pymol/constants_palette.pyo
+${PYSITELIB}/pymol/contrib/__init__.py
+${PYSITELIB}/pymol/contrib/__init__.pyc
+${PYSITELIB}/pymol/contrib/__init__.pyo
+${PYSITELIB}/pymol/controlling.py
+${PYSITELIB}/pymol/controlling.pyc
+${PYSITELIB}/pymol/controlling.pyo
+${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/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
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+${PYSITELIB}/pymol/pymol_path/test/ref/M0020multi.log
+${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
+${PYSITELIB}/pymol/pymol_path/test/run
+${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
+${PYSITELIB}/pymol/shortcut.py
+${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
+${PYSITELIB}/pymol/wizard/box.py
+${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
+${PYSITELIB}/pymol/wizard/cleanup.py
+${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
+${PYSITELIB}/pymol/wizard/dragging.py
+${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
+${PYSITELIB}/pymol/wizard/filter.py
+${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
+${PYSITELIB}/pymol/wizard/pseudoatom.py
+${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
+${PYSITELIB}/pymol/wizard/sculpting.py
+${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
+${PYSITELIB}/pymol/wizard/stereodemo.py
+${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
+${PYSITELIB}/pymol/wizarding.pyo
+${PYSITELIB}/pymol/xray.py
+${PYSITELIB}/pymol/xray.pyc
+${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/py-mol/TODO b/py-mol/TODO
new file mode 100644
index 0000000000..2bd23c3036
--- /dev/null
+++ b/py-mol/TODO
@@ -0,0 +1,20 @@
+Fix compilation problem:
+
+c++ -O2 -g -fPIC -D_FORTIFY_SOURCE=2 -fstack-check -I/usr/pkg/include -I/usr/include -I/usr/X11R7/include/freetype2 -I/usr/X11R7/include -I/usr/X11R7/include/libdrm -I/usr/pkg/include/python3.10 -g -I/usr/pkg/include/netlib -I/usr/pkg/include -I/usr/include -I/usr/X11R7/include/freetype2 -I/usr/X11R7/include -I/usr/X11R7/include/libdrm -I/usr/pkg/include/python3.10 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilaye
+r1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/pkg/lib/python3.10/site-packages/numpy/core/include -I/usr/include -I/usr/pkg/include/python3.10 -c -MMD layer1/COLLADA.cpp -o build/temp.netbsd-9.99.93-amd64-3.10/layer1/COLLADA.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -fopenmp layer1/COLLADA.cpp:16:10: fatal error: libxml/xmlwriter.h: No such file or directory 16 | #include <libxml/xmlwriter.h> | ^~~~~~~~~~~~~~~~~~~~ compilation terminated.
+...
+
+
+Fix python problem:
+
+error: command '/scratch/biology/py-mol/work/.cwrapper/bin/gcc' failed with exit code 1
+Exception ignored in: <function Pool.__del__ at 0x7532caff7fd0>
+Traceback (most recent call last):
+ File "/usr/pkg/lib/python3.10/multiprocessing/pool.py", line 268, in __del__
+ File "/usr/pkg/lib/python3.10/multiprocessing/queues.py", line 378, in put
+ File "/usr/pkg/lib/python3.10/multiprocessing/connection.py", line 205, in send_bytes
+ File "/usr/pkg/lib/python3.10/multiprocessing/connection.py", line 405, in _send_bytes
+AttributeError: 'NoneType' object has no attribute 'pack'
+*** Error code 1
+
+Convert to py-qt* instead of py-Pmw.
diff --git a/py-mol/distinfo b/py-mol/distinfo
new file mode 100644
index 0000000000..ed56af4eb9
--- /dev/null
+++ b/py-mol/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.6 2021/10/26 10:03:43 nia Exp $
+
+BLAKE2s (pymol-2.5.0.tar.gz) = ccc7cd9621283d980a5580f61ca1be9abaa8832a43e273e0916a91ba54e15409
+SHA512 (pymol-2.5.0.tar.gz) = 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91
+Size (pymol-2.5.0.tar.gz) = 10470268 bytes
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