update to 0.97

1 files changed, 348 insertions, 302 deletions

diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist
index d90d2476eda2..9df559b09878 100644
--- a/biology/pymol/pkg-plist
+++ b/biology/pymol/pkg-plist
@@ -1,397 +1,434 @@
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 share/pymol/modules/pymol/xwin.pyo
-share/pymol/test/README
-share/pymol/test/cyg
-share/pymol/test/dat/odd01.pdb
+share/pymol/modules/compile_pymol.pyc
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+share/pymol/modules/launch_pymol.pyo
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 share/pymol/test/dat/3al1.pdb
 share/pymol/test/dat/3al1.r3d
 share/pymol/test/dat/helix_amber.pdb
 share/pymol/test/dat/il2.pdb
 share/pymol/test/dat/names.pdb
+share/pymol/test/dat/odd01.pdb
 share/pymol/test/dat/pept.pdb
 share/pymol/test/dat/pept.pkl
 share/pymol/test/dat/pept.r3d
 share/pymol/test/dat/small01.mol
+share/pymol/test/dat/small02.pdb
 share/pymol/test/dat/tiny.pdb
 share/pymol/test/dat/water.pdb
-share/pymol/test/inp/B04.py
-share/pymol/test/inp/B05.py
-share/pymol/test/inp/C0700odd.pml
-share/pymol/test/inp/C1100do.py
+share/pymol/test/README
+share/pymol/test/cyg
+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/B04.py
+share/pymol/test/inp/B05.py
+share/pymol/test/inp/B06.py
+share/pymol/test/inp/B07.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
@@ -410,6 +447,7 @@ 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/C0700odd.pml
 share/pymol/test/inp/C1000viewing.pml
 share/pymol/test/inp/C1010helping.pml
 share/pymol/test/inp/C1020querying.pml
@@ -420,6 +458,7 @@ 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/C1100do.py
 share/pymol/test/inp/L0010ccp4read.pml
 share/pymol/test/inp/L0020xplorread.pml
 share/pymol/test/inp/L0030isomesh.pml
@@ -431,15 +470,6 @@ 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/C0700odd.1.pdb
-share/pymol/test/ref/C0700odd.2.pdb
-share/pymol/test/ref/C0700odd.3.pdb
-share/pymol/test/ref/C0700odd.4.pdb
-share/pymol/test/ref/C0700odd.5.pdb
-share/pymol/test/ref/C0700odd.6.pdb
-share/pymol/test/ref/C0700odd.7.pdb
-share/pymol/test/ref/C0700odd.log
-share/pymol/test/ref/C1100do.log
 share/pymol/test/ref/C0001quit.log
 share/pymol/test/ref/C0010hello.log
 share/pymol/test/ref/C0020pdb.log
@@ -459,6 +489,7 @@ 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/T01.log
 share/pymol/test/ref/C0170scene.log
 share/pymol/test/ref/C0200feedback.log
 share/pymol/test/ref/C0201extend.log
@@ -466,6 +497,22 @@ share/pymol/test/ref/C0202help_python.log
 share/pymol/test/ref/C0300session.log
 share/pymol/test/ref/C0500misc.log
 share/pymol/test/ref/C0600util.log
+share/pymol/test/ref/C0700odd.1.pdb
+share/pymol/test/ref/C0700odd.2.pdb
+share/pymol/test/ref/C0700odd.3.pdb
+share/pymol/test/ref/C0700odd.4.pdb
+share/pymol/test/ref/C0700odd.5.pdb
+share/pymol/test/ref/C0700odd.6.pdb
+share/pymol/test/ref/C0700odd.7.pdb
+share/pymol/test/ref/C0700odd.8.pdb
+share/pymol/test/ref/C0700odd.9.pdb
+share/pymol/test/ref/C0700odd.A.pdb
+share/pymol/test/ref/C0700odd.B.pdb
+share/pymol/test/ref/C0700odd.C.pdb
+share/pymol/test/ref/C0700odd.D.pdb
+share/pymol/test/ref/U01.log
+share/pymol/test/ref/C0700odd.E.pdb
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 share/pymol/test/ref/C1000viewing.log
 share/pymol/test/ref/C1010helping.log
 share/pymol/test/ref/C1020querying.log
@@ -476,47 +523,17 @@ 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/C1100do.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
-@dirrm share/pymol/test
-@dirrm share/pymol/modules/pymol/wizard
-@dirrm share/pymol/modules/pymol/opengl/glut
-@dirrm share/pymol/modules/pymol/opengl/glu
-@dirrm share/pymol/modules/pymol/opengl/gl
-@dirrm share/pymol/modules/pymol/opengl
-@dirrm share/pymol/modules/pymol/embed/wxpymol
-@dirrm share/pymol/modules/pymol/embed/epymol
-@dirrm share/pymol/modules/pymol/embed
-@dirrm share/pymol/modules/pymol
-@dirrm share/pymol/modules/pmg_wx
-@dirrm share/pymol/modules/pmg_tk/startup
-@dirrm share/pymol/modules/pmg_tk
-@dirrm share/pymol/modules/chempy/tinker
-@dirrm share/pymol/modules/chempy/fragments
-@dirrm share/pymol/modules/chempy/fast
-@dirrm share/pymol/modules/chempy/champ
-@dirrm share/pymol/modules/chempy/bmin
-@dirrm share/pymol/modules/chempy
-@dirrm share/pymol/modules
-@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/README
 %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/density.pml
 %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/groel_es.pml
 %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/packing.pml
@@ -528,19 +545,24 @@ share/pymol/test/win.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo03.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_3Dtext01.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_label_hack.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_plane.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/mutate01.pml
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/mutate02.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/pick_wiz.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/povray01.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/sd_annotate.pml
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/sele_wiz.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/start_pymol.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/xmlrpc01.py
-%%PORTDOCS%%%%EXAMPLESDIR%%/devel/pick_wiz.py
-%%PORTDOCS%%%%EXAMPLESDIR%%/launching/README
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/xmlrpc02.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/launching/README
 %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_demo.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_no_tk.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch_viewer1.py
@@ -550,3 +572,27 @@ share/pymol/test/win.py
 %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/cookbook
 %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/chempy
 %%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
+@dirrm share/pymol/test/ref
+@dirrm share/pymol/test/inp
+@dirrm share/pymol/test/dat
+@dirrm share/pymol/test
+@dirrm share/pymol/modules/pymol/wizard
+@dirrm share/pymol/modules/pymol/opengl/glut
+@dirrm share/pymol/modules/pymol/opengl/glu
+@dirrm share/pymol/modules/pymol/opengl/gl
+@dirrm share/pymol/modules/pymol/opengl
+@dirrm share/pymol/modules/pymol/embed/wxpymol
+@dirrm share/pymol/modules/pymol/embed/epymol
+@dirrm share/pymol/modules/pymol/embed
+@dirrm share/pymol/modules/pymol
+@dirrm share/pymol/modules/pmg_wx
+@dirrm share/pymol/modules/pmg_tk/startup
+@dirrm share/pymol/modules/pmg_tk
+@dirrm share/pymol/modules/chempy/tinker
+@dirrm share/pymol/modules/chempy/fragments
+@dirrm share/pymol/modules/chempy/fast
+@dirrm share/pymol/modules/chempy/champ
+@dirrm share/pymol/modules/chempy/bmin
+@dirrm share/pymol/modules/chempy
+@dirrm share/pymol/modules
+@dirrm share/pymol