4 files changed, 328 insertions, 309 deletions

diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile
index 6af4fd3c6fab..11af04acd5d1 100644
--- a/biology/pymol/Makefile
+++ b/biology/pymol/Makefile
@@ -5,7 +5,7 @@
 # $FreeBSD$
 
 PORTNAME=	pymol
-PORTVERSION=	0.86
+PORTVERSION=	0.90
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	pymol
diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo
index eb546ea16d68..5379be65faf0 100644
--- a/biology/pymol/distinfo
+++ b/biology/pymol/distinfo
@@ -1 +1 @@
-MD5 (pymol-0_86-src.tgz) = 7610bb7689230eff2ec945236fdce0b8
+MD5 (pymol-0_90-src.tgz) = be181d10df622b011725d9541da22070
diff --git a/biology/pymol/files/patch-Rules.make b/biology/pymol/files/patch-Rules.make
index ead488b0a7d9..aa4c69fccdf5 100644
--- a/biology/pymol/files/patch-Rules.make
+++ b/biology/pymol/files/patch-Rules.make
@@ -1,6 +1,6 @@
---- Rules.make.orig	Wed Apr 30 11:42:37 2003
-+++ Rules.make	Wed Apr 30 11:52:50 2003
-@@ -4,42 +4,42 @@
+--- Rules.make.orig	Thu Jul 24 15:21:01 2003
++++ Rules.make	Thu Jul 24 15:27:58 2003
+@@ -4,22 +4,22 @@
  #
  #- Building ----------------------------------------------------------
  #--- Tell "make" how to get to PyMOL 
@@ -19,32 +19,23 @@
 +PYTHON_EXE = $(PYMOL_PATH)/bin/python
  PYTHON_LIB =
  PYTHON_LIB_DIR = 
--PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.1 \
--	-I$(PYMOL_PATH)/ext/include/python2.1/Numeric
+-PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.2 \
+-	-I$(PYMOL_PATH)/ext/include/python2.2/Numeric
 +PYTHON_INC_DIR = -I$(PYMOL_PATH)/include/@PYTHON_VERSION@ \
 +	-I$(PYMOL_PATH)/include/@PYTHON_VERSION@/Numeric
  #--- Other external dependencies
 -EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include
 -EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib
-+EXT_INC_DIR = -I$(PYMOL_PATH)/include -I.
++EXT_INC_DIR = -I$(PYMOL_PATH)/include
 +EXT_LIB_DIR = -L$(PYMOL_PATH)/lib
  #---------------------------------------------------------------------
  #
--#- Build for LINUX as an importable module ---------------------------
-+#- Build for FreeBSD as an importable module ---------------------------
- #--- System libraries
--LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -ldl -lpng -lXmu $(ZLIB) -lm
-+LIBS = $(PYTHON_LIB) -lglut -lGL -lGLU -lpng -lXmu $(ZLIB) -lm
- #--- PyMOL configuration
- DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY 
- #--- How we build shared libraries
- BUILD = -shared 
+ #- Build for LINUX as an importable module ---------------------------
+@@ -32,14 +32,14 @@
  #--- What are we trying to build?
--DEST = -o modules/pymol/_cmd.so
--#--- Gcc Options for Linux
+ DEST = -o modules/pymol/_cmd.so
+ #--- Gcc Options for Linux
 -CCOPT1 = -march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
-+DEST = -o modules/_cmd.so
-+#--- Gcc Options for FreeBSD
 +CCOPT1 = #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
  #--- libraries for PyOpenGL 
  PYOGL_LIB =  -lglut -lGL -lGLU -lXmu -lXi
@@ -57,15 +48,6 @@
  #--- GCC Profiling
  #CCOPT2 = -pg -O3 -funroll-loops
  #--- Debugging
-@@ -47,7 +47,7 @@
- #---------------------------------------------------------------------
- #
- #- Choose One --------------------------------------------------------
--#--- Workaround for XFree86/DRI linux dll problem for module build
-+#--- Workaround for XFree86/DRI FreeBSD dll problem for module build
- BUGS = -D_DRI_WORKAROUND
- #---
- #BUGS =
 @@ -69,18 +69,19 @@
  # No changes normally required below here
  #---------------------------------------------------------------------
diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist
index 843bbcdc555a..79ce103ff778 100644
--- a/biology/pymol/pkg-plist
+++ b/biology/pymol/pkg-plist
@@ -1,385 +1,371 @@
 bin/pymol
-%%PORTDOCS%%share/examples/pymol/chempy/generate_amber.py
-%%PORTDOCS%%share/examples/pymol/chempy/generate_mmff.py
-%%PORTDOCS%%share/examples/pymol/cookbook/contact.pml
-%%PORTDOCS%%share/examples/pymol/cookbook/README
-%%PORTDOCS%%share/examples/pymol/cookbook/density.pml
-%%PORTDOCS%%share/examples/pymol/cookbook/groel_es.pml
-%%PORTDOCS%%share/examples/pymol/cookbook/packing.pml
-%%PORTDOCS%%share/examples/pymol/cookbook/packsurf.pml
-%%PORTDOCS%%share/examples/pymol/cookbook/ribosome.pml
-%%PORTDOCS%%share/examples/pymol/devel/brick01.py
-%%PORTDOCS%%share/examples/pymol/devel/cgo01.py
-%%PORTDOCS%%share/examples/pymol/devel/cgo02.py
-%%PORTDOCS%%share/examples/pymol/devel/cgo03.py
-%%PORTDOCS%%share/examples/pymol/devel/cgo_3Dtext01.py
-%%PORTDOCS%%share/examples/pymol/devel/cgo_label_hack.py
-%%PORTDOCS%%share/examples/pymol/devel/chempy_model01.py
-%%PORTDOCS%%share/examples/pymol/devel/chempy_model02.py
-%%PORTDOCS%%share/examples/pymol/devel/chempy_model03.py
-%%PORTDOCS%%share/examples/pymol/devel/gl01.py
-%%PORTDOCS%%share/examples/pymol/devel/gl02.py
-%%PORTDOCS%%share/examples/pymol/devel/gl03.py
-%%PORTDOCS%%share/examples/pymol/devel/povray01.py
-%%PORTDOCS%%share/examples/pymol/devel/sele_wiz.py
-%%PORTDOCS%%share/examples/pymol/devel/start_pymol.py
-%%PORTDOCS%%share/examples/pymol/devel/xmlrpc01.py
+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
+share/pymol/modules/chempy/bond_mmff.pyc
+share/pymol/modules/chempy/bond_mmff.pyo
 share/pymol/modules/chempy/bonds.py
+share/pymol/modules/chempy/bonds.pyc
+share/pymol/modules/chempy/bonds.pyo
 share/pymol/modules/chempy/brick.py
+share/pymol/modules/chempy/brick.pyc
+share/pymol/modules/chempy/brick.pyo
 share/pymol/modules/chempy/cc1.py
+share/pymol/modules/chempy/cc1.pyc
+share/pymol/modules/chempy/cc1.pyo
 share/pymol/modules/chempy/cex.py
+share/pymol/modules/chempy/cex.pyc
+share/pymol/modules/chempy/cex.pyo
+share/pymol/modules/chempy/champ/__init__.py
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+share/pymol/modules/chempy/champ/__init__.pyo
 share/pymol/modules/chempy/charge.py
+share/pymol/modules/chempy/charge.pyc
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+share/pymol/modules/chempy/cpv.pyc
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+share/pymol/modules/chempy/mmd.pyc
+share/pymol/modules/chempy/mmd.pyo
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+share/pymol/modules/chempy/models.pyc
+share/pymol/modules/chempy/models.pyo
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+share/pymol/modules/chempy/mol.pyc
+share/pymol/modules/chempy/mol.pyo
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+share/pymol/modules/chempy/neighbor.pyc
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 share/pymol/modules/chempy/pdb.py
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+share/pymol/modules/chempy/place.pyc
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+share/pymol/modules/chempy/protein.pyc
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 share/pymol/modules/chempy/protein_amber.py
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 share/pymol/modules/chempy/protein_amber99.py
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-share/pymol/modules/chempy/fragments/__init__.pyo
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 share/pymol/modules/chempy/tinker/__init__.py
-share/pymol/modules/chempy/tinker/amber.py
-share/pymol/modules/chempy/tinker/keyword.py
-share/pymol/modules/chempy/tinker/realtime.py
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 share/pymol/modules/chempy/tinker/__init__.pyc
-share/pymol/modules/chempy/tinker/amber.pyc
-share/pymol/modules/chempy/tinker/keyword.pyc
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-share/pymol/modules/chempy/tinker/state.pyc
 share/pymol/modules/chempy/tinker/__init__.pyo
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+share/pymol/modules/chempy/tinker/amber.pyc
 share/pymol/modules/chempy/tinker/amber.pyo
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-share/pymol/modules/chempy/bond_mmff.pyc
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-share/pymol/modules/chempy/cex.pyc
-share/pymol/modules/chempy/charge.pyc
-share/pymol/modules/chempy/cpv.pyc
-share/pymol/modules/chempy/dictdb.pyc
-share/pymol/modules/chempy/gamess1.pyc
-share/pymol/modules/chempy/gms.pyc
-share/pymol/modules/chempy/hetatm.pyc
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-share/pymol/modules/chempy/lst.pyc
-share/pymol/modules/chempy/mae.pyc
-share/pymol/modules/chempy/map.pyc
-share/pymol/modules/chempy/mass.pyc
-share/pymol/modules/chempy/mmd.pyc
-share/pymol/modules/chempy/models.pyc
-share/pymol/modules/chempy/mol.pyc
-share/pymol/modules/chempy/neighbor.pyc
-share/pymol/modules/chempy/pdb.pyc
-share/pymol/modules/chempy/pkl.pyc
-share/pymol/modules/chempy/place.pyc
-share/pymol/modules/chempy/protein.pyc
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-share/pymol/modules/chempy/protein_amber99.pyc
-share/pymol/modules/chempy/protein_mmff.pyc
-share/pymol/modules/chempy/protein_residues.pyc
-share/pymol/modules/chempy/sdf.pyc
-share/pymol/modules/chempy/solvate.pyc
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 share/pymol/modules/chempy/water_amber.pyc
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-share/pymol/modules/chempy/xyz.pyc
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 share/pymol/modules/pmg_wx/__init__.py
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+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
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-share/pymol/test/inp/C0020pdb.pml
 share/pymol/test/inp/B01.py
 share/pymol/test/inp/B02.py
+share/pymol/test/inp/B03.py
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 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
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 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
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 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
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 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
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 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%%