Update to 0.90

1 files changed, 316 insertions, 279 deletions

diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist
index 843bbcd..79ce103 100644
--- a/biology/pymol/pkg-plist
+++ b/biology/pymol/pkg-plist
@@ -1,385 +1,371 @@
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-share/pymol/modules/pymol/parser.py
-share/pymol/modules/pymol/rpc.py
-share/pymol/modules/pymol/parsing.py
-share/pymol/modules/pymol/povray.py
-share/pymol/modules/pymol/querying.py
-share/pymol/modules/pymol/selecting.py
-share/pymol/modules/pymol/selector.py
-share/pymol/modules/pymol/setting.py
-share/pymol/modules/pymol/shortcut.py
-share/pymol/modules/pymol/util.py
-share/pymol/modules/pymol/vfont.py
-share/pymol/modules/pymol/viewing.py
-share/pymol/modules/pymol/wizarding.py
-share/pymol/modules/pymol/xray.py
-share/pymol/modules/pymol/xwin.py
+share/pymol/modules/pymol/moving.pyc
+share/pymol/modules/pymol/moving.pyo
+share/pymol/modules/pymol/opengl/__init__.py
+share/pymol/modules/pymol/opengl/__init__.pyc
+share/pymol/modules/pymol/opengl/__init__.pyo
 share/pymol/modules/pymol/opengl/gl/__init__.py
-share/pymol/modules/pymol/opengl/gl/glconst.py
+share/pymol/modules/pymol/opengl/gl/__init__.pyc
+share/pymol/modules/pymol/opengl/gl/__init__.pyo
 share/pymol/modules/pymol/opengl/gl/_opengl_nummodule.so
 share/pymol/modules/pymol/opengl/gl/_openglmodule.so
-share/pymol/modules/pymol/opengl/gl/openglutil.so
-share/pymol/modules/pymol/opengl/gl/openglutil_num.so
-share/pymol/modules/pymol/opengl/gl/__init__.pyc
+share/pymol/modules/pymol/opengl/gl/glconst.py
 share/pymol/modules/pymol/opengl/gl/glconst.pyc
-share/pymol/modules/pymol/opengl/gl/__init__.pyo
 share/pymol/modules/pymol/opengl/gl/glconst.pyo
+share/pymol/modules/pymol/opengl/gl/openglutil.so
+share/pymol/modules/pymol/opengl/gl/openglutil_num.so
 share/pymol/modules/pymol/opengl/glu/__init__.py
-share/pymol/modules/pymol/opengl/glu/gluconst.py
+share/pymol/modules/pymol/opengl/glu/__init__.pyc
+share/pymol/modules/pymol/opengl/glu/__init__.pyo
 share/pymol/modules/pymol/opengl/glu/_glu_nummodule.so
 share/pymol/modules/pymol/opengl/glu/_glumodule.so
-share/pymol/modules/pymol/opengl/glu/__init__.pyc
+share/pymol/modules/pymol/opengl/glu/gluconst.py
 share/pymol/modules/pymol/opengl/glu/gluconst.pyc
-share/pymol/modules/pymol/opengl/glu/__init__.pyo
 share/pymol/modules/pymol/opengl/glu/gluconst.pyo
-share/pymol/modules/pymol/opengl/__init__.py
 share/pymol/modules/pymol/opengl/glut/__init__.py
-share/pymol/modules/pymol/opengl/glut/glutconst.py
-share/pymol/modules/pymol/opengl/glut/_glutmodule.so
 share/pymol/modules/pymol/opengl/glut/__init__.pyc
-share/pymol/modules/pymol/opengl/glut/glutconst.pyc
 share/pymol/modules/pymol/opengl/glut/__init__.pyo
+share/pymol/modules/pymol/opengl/glut/_glutmodule.so
+share/pymol/modules/pymol/opengl/glut/glutconst.py
+share/pymol/modules/pymol/opengl/glut/glutconst.pyc
 share/pymol/modules/pymol/opengl/glut/glutconst.pyo
-share/pymol/modules/pymol/opengl/__init__.pyc
-share/pymol/modules/pymol/opengl/__init__.pyo
-share/pymol/modules/pymol/wizard/__init__.py
-share/pymol/modules/pymol/wizard/charge.py
-share/pymol/modules/pymol/wizard/density.py
-share/pymol/modules/pymol/wizard/distance.py
-share/pymol/modules/pymol/wizard/filter.py
-share/pymol/modules/pymol/wizard/label.py
-share/pymol/modules/pymol/wizard/mutagenesis.py
-share/pymol/modules/pymol/wizard/pair_fit.py
-share/pymol/modules/pymol/wizard/sculpting.py
-share/pymol/modules/pymol/wizard/security.py
-share/pymol/modules/pymol/wizard/__init__.pyc
-share/pymol/modules/pymol/wizard/charge.pyc
-share/pymol/modules/pymol/wizard/density.pyc
-share/pymol/modules/pymol/wizard/distance.pyc
-share/pymol/modules/pymol/wizard/filter.pyc
-share/pymol/modules/pymol/wizard/label.pyc
-share/pymol/modules/pymol/wizard/mutagenesis.pyc
-share/pymol/modules/pymol/wizard/pair_fit.pyc
-share/pymol/modules/pymol/wizard/sculpting.pyc
-share/pymol/modules/pymol/wizard/security.pyc
-share/pymol/modules/pymol/wizard/__init__.pyo
-share/pymol/modules/pymol/wizard/charge.pyo
-share/pymol/modules/pymol/wizard/density.pyo
-share/pymol/modules/pymol/wizard/distance.pyo
-share/pymol/modules/pymol/wizard/filter.pyo
-share/pymol/modules/pymol/wizard/label.pyo
-share/pymol/modules/pymol/wizard/mutagenesis.pyo
-share/pymol/modules/pymol/wizard/pair_fit.pyo
-share/pymol/modules/pymol/wizard/sculpting.pyo
-share/pymol/modules/pymol/wizard/security.pyo
-share/pymol/modules/pymol/ExtensionClass.so
-share/pymol/modules/pymol/sglite.so
-share/pymol/modules/pymol/__init__.pyc
-share/pymol/modules/pymol/callback.pyc
-share/pymol/modules/pymol/cgo.pyc
-share/pymol/modules/pymol/cmd.pyc
-share/pymol/modules/pymol/commanding.pyc
-share/pymol/modules/pymol/contrib.pyc
-share/pymol/modules/pymol/controlling.pyc
-share/pymol/modules/pymol/creating.pyc
-share/pymol/modules/pymol/editing.pyc
-share/pymol/modules/pymol/editor.pyc
-share/pymol/modules/pymol/experimenting.pyc
-share/pymol/modules/pymol/exporting.pyc
-share/pymol/modules/pymol/externing.pyc
-share/pymol/modules/pymol/fitting.pyc
-share/pymol/modules/pymol/helping.pyc
-share/pymol/modules/pymol/importing.pyc
-share/pymol/modules/pymol/invocation.pyc
-share/pymol/modules/pymol/m4x.pyc
-share/pymol/modules/pymol/menu.pyc
-share/pymol/modules/pymol/movie.pyc
-share/pymol/modules/pymol/moving.pyc
+share/pymol/modules/pymol/parser.py
 share/pymol/modules/pymol/parser.pyc
+share/pymol/modules/pymol/parser.pyo
+share/pymol/modules/pymol/parsing.py
 share/pymol/modules/pymol/parsing.pyc
+share/pymol/modules/pymol/parsing.pyo
+share/pymol/modules/pymol/povray.py
 share/pymol/modules/pymol/povray.pyc
+share/pymol/modules/pymol/povray.pyo
+share/pymol/modules/pymol/querying.py
 share/pymol/modules/pymol/querying.pyc
+share/pymol/modules/pymol/querying.pyo
+share/pymol/modules/pymol/rpc.py
 share/pymol/modules/pymol/rpc.pyc
-share/pymol/modules/pymol/selecting.pyc
-share/pymol/modules/pymol/selector.pyc
-share/pymol/modules/pymol/setting.pyc
-share/pymol/modules/pymol/shortcut.pyc
-share/pymol/modules/pymol/util.pyc
-share/pymol/modules/pymol/vfont.pyc
-share/pymol/modules/pymol/viewing.pyc
-share/pymol/modules/pymol/wizarding.pyc
-share/pymol/modules/pymol/xray.pyc
-share/pymol/modules/pymol/xwin.pyc
-share/pymol/modules/pymol/__init__.pyo
-share/pymol/modules/pymol/callback.pyo
-share/pymol/modules/pymol/cgo.pyo
-share/pymol/modules/pymol/cmd.pyo
-share/pymol/modules/pymol/commanding.pyo
-share/pymol/modules/pymol/contrib.pyo
-share/pymol/modules/pymol/controlling.pyo
-share/pymol/modules/pymol/creating.pyo
-share/pymol/modules/pymol/editing.pyo
-share/pymol/modules/pymol/editor.pyo
-share/pymol/modules/pymol/experimenting.pyo
-share/pymol/modules/pymol/exporting.pyo
-share/pymol/modules/pymol/externing.pyo
-share/pymol/modules/pymol/fitting.pyo
-share/pymol/modules/pymol/helping.pyo
-share/pymol/modules/pymol/importing.pyo
-share/pymol/modules/pymol/invocation.pyo
-share/pymol/modules/pymol/m4x.pyo
-share/pymol/modules/pymol/menu.pyo
 share/pymol/modules/pymol/rpc.pyo
-share/pymol/modules/pymol/movie.pyo
-share/pymol/modules/pymol/moving.pyo
-share/pymol/modules/pymol/parser.pyo
-share/pymol/modules/pymol/parsing.pyo
-share/pymol/modules/pymol/povray.pyo
-share/pymol/modules/pymol/querying.pyo
+share/pymol/modules/pymol/selecting.py
+share/pymol/modules/pymol/selecting.pyc
 share/pymol/modules/pymol/selecting.pyo
+share/pymol/modules/pymol/selector.py
+share/pymol/modules/pymol/selector.pyc
 share/pymol/modules/pymol/selector.pyo
+share/pymol/modules/pymol/setting.py
+share/pymol/modules/pymol/setting.pyc
 share/pymol/modules/pymol/setting.pyo
+share/pymol/modules/pymol/sglite.so
+share/pymol/modules/pymol/shortcut.py
+share/pymol/modules/pymol/shortcut.pyc
 share/pymol/modules/pymol/shortcut.pyo
+share/pymol/modules/pymol/util.py
+share/pymol/modules/pymol/util.pyc
 share/pymol/modules/pymol/util.pyo
+share/pymol/modules/pymol/vfont.py
+share/pymol/modules/pymol/vfont.pyc
 share/pymol/modules/pymol/vfont.pyo
+share/pymol/modules/pymol/viewing.py
+share/pymol/modules/pymol/viewing.pyc
 share/pymol/modules/pymol/viewing.pyo
+share/pymol/modules/pymol/wizard/__init__.py
+share/pymol/modules/pymol/wizard/__init__.pyc
+share/pymol/modules/pymol/wizard/__init__.pyo
+share/pymol/modules/pymol/wizard/benchmark.py
+share/pymol/modules/pymol/wizard/benchmark.pyc
+share/pymol/modules/pymol/wizard/benchmark.pyo
+share/pymol/modules/pymol/wizard/charge.py
+share/pymol/modules/pymol/wizard/charge.pyc
+share/pymol/modules/pymol/wizard/charge.pyo
+share/pymol/modules/pymol/wizard/demo.py
+share/pymol/modules/pymol/wizard/demo.pyc
+share/pymol/modules/pymol/wizard/demo.pyo
+share/pymol/modules/pymol/wizard/density.py
+share/pymol/modules/pymol/wizard/density.pyc
+share/pymol/modules/pymol/wizard/density.pyo
+share/pymol/modules/pymol/wizard/distance.py
+share/pymol/modules/pymol/wizard/distance.pyc
+share/pymol/modules/pymol/wizard/distance.pyo
+share/pymol/modules/pymol/wizard/filter.py
+share/pymol/modules/pymol/wizard/filter.pyc
+share/pymol/modules/pymol/wizard/filter.pyo
+share/pymol/modules/pymol/wizard/label.py
+share/pymol/modules/pymol/wizard/label.pyc
+share/pymol/modules/pymol/wizard/label.pyo
+share/pymol/modules/pymol/wizard/message.py
+share/pymol/modules/pymol/wizard/message.pyc
+share/pymol/modules/pymol/wizard/message.pyo
+share/pymol/modules/pymol/wizard/mutagenesis.py
+share/pymol/modules/pymol/wizard/mutagenesis.pyc
+share/pymol/modules/pymol/wizard/mutagenesis.pyo
+share/pymol/modules/pymol/wizard/pair_fit.py
+share/pymol/modules/pymol/wizard/pair_fit.pyc
+share/pymol/modules/pymol/wizard/pair_fit.pyo
+share/pymol/modules/pymol/wizard/sculpting.py
+share/pymol/modules/pymol/wizard/sculpting.pyc
+share/pymol/modules/pymol/wizard/sculpting.pyo
+share/pymol/modules/pymol/wizard/security.py
+share/pymol/modules/pymol/wizard/security.pyc
+share/pymol/modules/pymol/wizard/security.pyo
+share/pymol/modules/pymol/wizarding.py
+share/pymol/modules/pymol/wizarding.pyc
 share/pymol/modules/pymol/wizarding.pyo
+share/pymol/modules/pymol/xray.py
+share/pymol/modules/pymol/xray.pyc
 share/pymol/modules/pymol/xray.pyo
+share/pymol/modules/pymol/xwin.py
+share/pymol/modules/pymol/xwin.pyc
 share/pymol/modules/pymol/xwin.pyo
-share/pymol/modules/_cmd.so
-share/pymol/modules/compile_pymol.pyc
-share/pymol/modules/launch_pymol.pyc
-share/pymol/modules/compile_pymol.pyo
-share/pymol/modules/launch_pymol.pyo
+share/pymol/test/README
+share/pymol/test/cyg
 share/pymol/test/dat/1tii.pdb
 share/pymol/test/dat/3al1.pdb
 share/pymol/test/dat/3al1.r3d
@@ -392,17 +378,12 @@ share/pymol/test/dat/pept.r3d
 share/pymol/test/dat/small01.mol
 share/pymol/test/dat/tiny.pdb
 share/pymol/test/dat/water.pdb
-share/pymol/test/README
-share/pymol/test/run
-share/pymol/test/show
-share/pymol/test/trim.py
-share/pymol/test/vdiff
-share/pymol/test/win.py
-share/pymol/test/inp/C0020pdb.pml
 share/pymol/test/inp/B01.py
 share/pymol/test/inp/B02.py
+share/pymol/test/inp/B03.py
 share/pymol/test/inp/C0001quit.pml
 share/pymol/test/inp/C0010hello.pml
+share/pymol/test/inp/C0020pdb.pml
 share/pymol/test/inp/C0025mol.pml
 share/pymol/test/inp/C0030pkl.pml
 share/pymol/test/inp/C0050multi.pml
@@ -413,6 +394,12 @@ share/pymol/test/inp/C0100select.pml
 share/pymol/test/inp/C0105names.pml
 share/pymol/test/inp/C0140iterate.pml
 share/pymol/test/inp/C0150alter.pml
+share/pymol/test/inp/C0160get.pml
+share/pymol/test/inp/C0170scene.pml
+share/pymol/test/inp/C0200feedback.pml
+share/pymol/test/inp/C0201extend.pml
+share/pymol/test/inp/C0202help_python.pml
+share/pymol/test/inp/C0300session.pml
 share/pymol/test/inp/C0500misc.pml
 share/pymol/test/inp/C0600util.pml
 share/pymol/test/inp/C1000viewing.pml
@@ -423,14 +410,18 @@ share/pymol/test/inp/C1040editing.pml
 share/pymol/test/inp/C1050fitting.py
 share/pymol/test/inp/C1060controlling.py
 share/pymol/test/inp/C1070exporting.pml
+share/pymol/test/inp/C1080isomore.pml
+share/pymol/test/inp/C1090coulomb.pml
 share/pymol/test/inp/L0010ccp4read.pml
 share/pymol/test/inp/L0020xplorread.pml
 share/pymol/test/inp/L0030isomesh.pml
 share/pymol/test/inp/L0040isomesh2.pml
 share/pymol/test/inp/L0100isomisc.pml
+share/pymol/test/inp/L0200electro.pml
 share/pymol/test/inp/T01.py
 share/pymol/test/inp/T02.py
 share/pymol/test/inp/T03.py
+share/pymol/test/inp/T04.py
 share/pymol/test/inp/U01.pml
 share/pymol/test/ref/C0001quit.log
 share/pymol/test/ref/C0010hello.log
@@ -450,8 +441,13 @@ share/pymol/test/ref/C0105names.log
 share/pymol/test/ref/C0140iterate.log
 share/pymol/test/ref/C0150alter.1.pdb
 share/pymol/test/ref/C0150alter.log
+share/pymol/test/ref/C0160get.log
+share/pymol/test/ref/C0170scene.log
+share/pymol/test/ref/C0200feedback.log
+share/pymol/test/ref/C0201extend.log
+share/pymol/test/ref/C0202help_python.log
+share/pymol/test/ref/C0300session.log
 share/pymol/test/ref/C0500misc.log
-share/pymol/test/ref/T01.log
 share/pymol/test/ref/C0600util.log
 share/pymol/test/ref/C1000viewing.log
 share/pymol/test/ref/C1010helping.log
@@ -461,12 +457,21 @@ share/pymol/test/ref/C1040editing.log
 share/pymol/test/ref/C1050fitting.log
 share/pymol/test/ref/C1060controlling.log
 share/pymol/test/ref/C1070exporting.log
+share/pymol/test/ref/C1080isomore.log
+share/pymol/test/ref/C1090coulomb.log
 share/pymol/test/ref/L0010ccp4read.log
 share/pymol/test/ref/L0020xplorread.log
 share/pymol/test/ref/L0030isomesh.log
 share/pymol/test/ref/L0040isomesh2.log
 share/pymol/test/ref/L0100isomisc.log
+share/pymol/test/ref/L0200electro.log
+share/pymol/test/ref/T01.log
 share/pymol/test/ref/U01.log
+share/pymol/test/run
+share/pymol/test/show
+share/pymol/test/trim.py
+share/pymol/test/vdiff
+share/pymol/test/win.py
 @dirrm share/pymol/test/ref
 @dirrm share/pymol/test/inp
 @dirrm share/pymol/test/dat
@@ -489,8 +494,40 @@ share/pymol/test/ref/U01.log
 @dirrm share/pymol/modules/chempy/bmin
 @dirrm share/pymol/modules/chempy
 @dirrm share/pymol/modules
-%%PORTDOCS%%@dirrm share/examples/pymol/devel
-%%PORTDOCS%%@dirrm share/examples/pymol/cookbook
-%%PORTDOCS%%@dirrm share/examples/pymol/chempy
-%%PORTDOCS%%@dirrm share/examples/pymol
 @dirrm share/pymol
+%%PORTDOCS%%%%EXAMPLESDIR%%/chempy/generate_amber.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/chempy/generate_mmff.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/README
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/contact.pml
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/density.pml
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/groel_es.pml
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/packing.pml
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/packsurf.pml
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/ribosome.pml
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/brick01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo02.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo03.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_3Dtext01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_label_hack.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/chempy_model01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/chempy_model02.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/chempy_model03.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/gl01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/gl02.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/gl03.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/povray01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/sele_wiz.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/start_pymol.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/xmlrpc01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/launching/README
+%%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_demo.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_no_tk.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_viewer1.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_viewer2.py
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/launching
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/devel
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/cookbook
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/chempy
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%