3 files changed, 363 insertions, 318 deletions

diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile
index 39aa9aeb7c72..efb1bc020af8 100644
--- a/biology/pymol/Makefile
+++ b/biology/pymol/Makefile
@@ -5,7 +5,7 @@
 # $FreeBSD$
 
 PORTNAME=	pymol
-PORTVERSION=	0.97
+PORTVERSION=	0.98
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	pymol
diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo
index 8b31ff1b9c8e..19d350203399 100644
--- a/biology/pymol/distinfo
+++ b/biology/pymol/distinfo
@@ -1,2 +1,2 @@
-MD5 (pymol-0_97-src.tgz) = e1220898cea37483ddd6f410a6fc02d2
-SIZE (pymol-0_97-src.tgz) = 2753262
+MD5 (pymol-0_98-src.tgz) = 096cc1d06fa36eb1c8ad30560d06b81e
+SIZE (pymol-0_98-src.tgz) = 3033733
diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist
index 9df559b09878..9ed068d748bb 100644
--- a/biology/pymol/pkg-plist
+++ b/biology/pymol/pkg-plist
@@ -1,408 +1,432 @@
 bin/pymol
+share/pymol/modules/chempy/__init__.py
+share/pymol/modules/chempy/__init__.pyc
+share/pymol/modules/chempy/__init__.pyo
+share/pymol/modules/chempy/arc.py
+share/pymol/modules/chempy/arc.pyc
+share/pymol/modules/chempy/arc.pyo
 share/pymol/modules/chempy/bmin/__init__.py
-share/pymol/modules/chempy/bmin/commands.py
-share/pymol/modules/chempy/bmin/realtime.py
-share/pymol/modules/chempy/bmin/state.py
-share/pymol/modules/chempy/bmin/util.py
 share/pymol/modules/chempy/bmin/__init__.pyc
-share/pymol/modules/chempy/bmin/commands.pyc
-share/pymol/modules/chempy/bmin/realtime.pyc
-share/pymol/modules/chempy/bmin/state.pyc
-share/pymol/modules/chempy/bmin/util.pyc
 share/pymol/modules/chempy/bmin/__init__.pyo
+share/pymol/modules/chempy/bmin/commands.py
+share/pymol/modules/chempy/bmin/commands.pyc
 share/pymol/modules/chempy/bmin/commands.pyo
+share/pymol/modules/chempy/bmin/realtime.py
+share/pymol/modules/chempy/bmin/realtime.pyc
 share/pymol/modules/chempy/bmin/realtime.pyo
+share/pymol/modules/chempy/bmin/state.py
+share/pymol/modules/chempy/bmin/state.pyc
 share/pymol/modules/chempy/bmin/state.pyo
+share/pymol/modules/chempy/bmin/util.py
+share/pymol/modules/chempy/bmin/util.pyc
 share/pymol/modules/chempy/bmin/util.pyo
-share/pymol/modules/chempy/fast/__init__.py
-share/pymol/modules/chempy/fast/__init__.pyc
-share/pymol/modules/chempy/fast/__init__.pyo
-share/pymol/modules/chempy/__init__.py
-share/pymol/modules/chempy/arc.py
 share/pymol/modules/chempy/bond_amber.py
+share/pymol/modules/chempy/bond_amber.pyc
+share/pymol/modules/chempy/bond_amber.pyo
 share/pymol/modules/chempy/bond_mmff.py
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 share/pymol/modules/chempy/bonds.py
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 share/pymol/modules/chempy/brick.py
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 share/pymol/modules/chempy/cc1.py
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 share/pymol/modules/chempy/cex.py
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 share/pymol/modules/chempy/charge.py
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 share/pymol/modules/chempy/dictdb.py
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 share/pymol/modules/chempy/tinker/__init__.py
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 share/pymol/modules/chempy/tinker/realtime.pyo
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@@ -410,16 +434,9 @@ share/pymol/test/dat/pept.pkl
 share/pymol/test/dat/pept.r3d
 share/pymol/test/dat/small01.mol
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+share/pymol/test/dat/small03.mol2
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 share/pymol/test/inp/B01.py
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@@ -429,7 +446,11 @@ share/pymol/test/inp/B06.py
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@@ -437,10 +458,13 @@ share/pymol/test/inp/C0070rep.pml
 share/pymol/test/inp/C0080create.pml
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@@ -448,16 +472,19 @@ share/pymol/test/inp/C0300session.pml
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+share/pymol/test/inp/C1035wildcards.pml
 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/C1095slice.pml
 share/pymol/test/inp/C1100do.py
 share/pymol/test/inp/L0010ccp4read.pml
 share/pymol/test/inp/L0020xplorread.pml
@@ -474,7 +501,10 @@ share/pymol/test/ref/C0001quit.log
 share/pymol/test/ref/C0010hello.log
 share/pymol/test/ref/C0020pdb.log
 share/pymol/test/ref/C0020pdb.pdb
+share/pymol/test/ref/C0021pdbstr.log
 share/pymol/test/ref/C0025mol.log
+share/pymol/test/ref/C0026sdf.log
+share/pymol/test/ref/C0027mol2.log
 share/pymol/test/ref/C0030pkl.log
 share/pymol/test/ref/C0030pkl.pdb
 share/pymol/test/ref/C0050multi.log
@@ -485,12 +515,14 @@ share/pymol/test/ref/C0080create.2.pdb
 share/pymol/test/ref/C0080create.log
 share/pymol/test/ref/C0100select.log
 share/pymol/test/ref/C0105names.log
+share/pymol/test/ref/C0106order.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/T01.log
 share/pymol/test/ref/C0170scene.log
+share/pymol/test/ref/C0180embed.log
+share/pymol/test/ref/C0181embed.log
 share/pymol/test/ref/C0200feedback.log
 share/pymol/test/ref/C0201extend.log
 share/pymol/test/ref/C0202help_python.log
@@ -510,19 +542,21 @@ 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
 share/pymol/test/ref/C0700odd.log
+share/pymol/test/ref/C0800matrices.log
 share/pymol/test/ref/C1000viewing.log
 share/pymol/test/ref/C1010helping.log
 share/pymol/test/ref/C1020querying.log
 share/pymol/test/ref/C1030selecting.log
+share/pymol/test/ref/C1035wildcards.log
 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/C1095slice.log
 share/pymol/test/ref/C1100do.log
 share/pymol/test/ref/L0010ccp4read.log
 share/pymol/test/ref/L0020xplorread.log
@@ -530,10 +564,44 @@ 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/skins/normal
+@dirrm share/pymol/modules/pmg_tk/skins
+@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/contact.pml
 %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/README
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/build_peptide.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/contact.pml
 %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/density.pml
 %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/groel_es.pml
 %%PORTDOCS%%%%EXAMPLESDIR%%/cookbook/packing.pml
@@ -543,6 +611,7 @@ share/pymol/test/ref/L0200electro.log
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo01.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo02.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo03.py
+%%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo04.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_3Dtext01.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_label_hack.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/cgo_plane.py
@@ -561,8 +630,8 @@ share/pymol/test/ref/L0200electro.log
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/start_pymol.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/xmlrpc01.py
 %%PORTDOCS%%%%EXAMPLESDIR%%/devel/xmlrpc02.py
-%%PORTDOCS%%%%EXAMPLESDIR%%/launching/launch.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
@@ -572,27 +641,3 @@ share/pymol/test/ref/L0200electro.log
 %%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