update to 0.97

4 files changed, 380 insertions, 338 deletions

diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile
index 5606d92..96f12da 100644
--- a/biology/pymol/Makefile
+++ b/biology/pymol/Makefile
@@ -5,7 +5,7 @@
 # $FreeBSD$
 
 PORTNAME=	pymol
-PORTVERSION=	0.93
+PORTVERSION=	0.97
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
 MASTER_SITE_SUBDIR=	pymol
@@ -48,6 +48,10 @@ post-patch:
 		${WRKSRC}/modules/pmg_tk/Demo.py
 	@${RM} -f ${WRKSRC}/modules/pmg_tk/Demo.py.*
 	${REINPLACE_CMD} -e 's,@PYTHON_VERSION@,${PYTHON_VERSION},g' \
+		-e 's,@LOCALBASE@,${LOCALBASE},g' \
+		-e 's,@X11BASE@,${X11BASE},g' \
+		-e 's,@CFLAGS@,${CFLAGS},g' \
+		-e 's,@CC@,${CC},g' \
 		-e 's,@PICFLAG@,${PICFLAG},g' ${WRKSRC}/Rules.make
 
 do-install:
diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo
index 66d4c78..8b31ff1 100644
--- a/biology/pymol/distinfo
+++ b/biology/pymol/distinfo
@@ -1,2 +1,2 @@
-MD5 (pymol-0_93-src.tgz) = f3a4e6d7fb25ad97e07a9f2eead304a5
-SIZE (pymol-0_93-src.tgz) = 2352042
+MD5 (pymol-0_97-src.tgz) = e1220898cea37483ddd6f410a6fc02d2
+SIZE (pymol-0_97-src.tgz) = 2753262
diff --git a/biology/pymol/files/patch-Rules.make b/biology/pymol/files/patch-Rules.make
index 930081b..98559e7 100644
--- a/biology/pymol/files/patch-Rules.make
+++ b/biology/pymol/files/patch-Rules.make
@@ -1,26 +1,26 @@
---- Rules.make.orig	Wed Mar 17 19:40:11 2004
-+++ Rules.make	Wed Mar 17 19:40:33 2004
-@@ -4,22 +4,22 @@
+--- Rules.make~	Mon Feb  7 17:02:46 2005
++++ Rules.make	Mon Feb  7 17:04:11 2005
+@@ -4,27 +4,27 @@
  #
  #- Building ----------------------------------------------------------
  #--- Tell "make" how to get to PyMOL 
--PYMOL_PATH = /users/warren/pymol
-+PYMOL_PATH = ${LOCALBASE}
+-PYMOL_PATH = ${HOME}/pymol
++PYMOL_PATH = @LOCALBASE@
  #---------------------------------------------------------------------
  #
  #- Dependencies ------------------------------------------------------
  #--- X-windows
 -XLIB_DIR = -L/usr/X11R6/lib
 -XINC_DIR = -I/usr/X11R6/include
-+XLIB_DIR = -L${X11BASE}/lib
-+XINC_DIR = -I${X11BASE}/include
++XLIB_DIR = -L@X11BASE@/lib
++XINC_DIR = -I@X11BASE@/include
  #--- Python
 -PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python
 +PYTHON_EXE = $(PYMOL_PATH)/bin/python
  PYTHON_LIB =
  PYTHON_LIB_DIR = 
--PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.2 \
--	-I$(PYMOL_PATH)/ext/include/python2.2/Numeric
+-PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.3 \
+-	-I$(PYMOL_PATH)/ext/include/python2.3/Numeric
 +PYTHON_INC_DIR = -I$(PYMOL_PATH)/include/@PYTHON_VERSION@ \
 +	-I$(PYMOL_PATH)/include/@PYTHON_VERSION@/Numeric
  #--- Other external dependencies
@@ -31,49 +31,41 @@
  #---------------------------------------------------------------------
  #
  #- Build for LINUX as an importable module ---------------------------
-@@ -28,18 +28,18 @@
+ #--- 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 
+ DEFS = -D_PYMOL_MODULE -D_PYMOL_NUMPY -D_PYMOL_INLINE
  #--- How we build shared libraries
--BUILD = -shared 
-+BUILD = -shared
+@@ -32,19 +32,19 @@
  #--- What are we trying to build?
  DEST = -o modules/pymol/_cmd.so
  #--- Gcc Options for Linux
 -CCOPT1 = -march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
-+CCOPT1 = #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
++CCOPT1 = @CFLAGS@ #-march=i486 -D__i686__ -ffast-math -Wall -ansi -Wmissing-prototypes
  #--- libraries for PyOpenGL 
  PYOGL_LIB =  -lglut -lGL -lGLU -lXmu -lXi
  #---------------------------------------------------------------------
  #
  #- Choose One --------------------------------------------------------
  #--- GCC Optimized
--CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer
-+CCOPT2 = #-O3 -funroll-loops -fomit-frame-pointer
+-CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer -finline-limit=10000 
++#CCOPT2 = -O3 -funroll-loops -fomit-frame-pointer -finline-limit=10000 
  #--- GCC Profiling
  #CCOPT2 = -pg -O3 -funroll-loops
  #--- Debugging
-@@ -69,18 +69,19 @@
+ #CCOPT2 = -g -D_MemoryDebug_ON
+-CCOPT2 = -g
++CCOPT2 = #-g
+ #---------------------------------------------------------------------
+ #
+ #- Choose One --------------------------------------------------------
+@@ -70,7 +70,7 @@
  # No changes normally required below here
  #---------------------------------------------------------------------
  
 -CC = cc
-+override CC := ${CC}
++CC = @CC@
  
  LIB_DIRS = $(EXT_LIB_DIR) $(PYTHON_LIB_DIR) $(XLIB_DIR)
  
- # Enable source files to find headers
- PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \
--   -I../layer3 -I../layer4 -I../layer5 
-+   -I../layer3 -I../layer4 -I../layer5 -I../modules/
- 
- C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \
--   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS)
-+   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS) $(PYMOL_INC_DIRS) @PICFLAG@
-+
-+override CFLAGS := $(C_FLAGS) ${CFLAGS}
- 
--CFLAGS = $(C_FLAGS)
- 
- 
- 
diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist
index d90d247..9df559b 100644
--- a/biology/pymol/pkg-plist
+++ b/biology/pymol/pkg-plist
@@ -1,397 +1,434 @@
 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/__init__.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/__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.pyo
+share/pymol/modules/chempy/bmin/realtime.pyo
+share/pymol/modules/chempy/bmin/state.pyo
 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
-share/pymol/modules/chempy/champ/__init__.pyc
-share/pymol/modules/chempy/champ/__init__.pyo
 share/pymol/modules/chempy/charge.py
-share/pymol/modules/chempy/charge.pyc
-share/pymol/modules/chempy/charge.pyo
 share/pymol/modules/chempy/cpv.py
-share/pymol/modules/chempy/cpv.pyc
-share/pymol/modules/chempy/cpv.pyo
 share/pymol/modules/chempy/dictdb.py
-share/pymol/modules/chempy/dictdb.pyc
-share/pymol/modules/chempy/dictdb.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/fragments/__init__.py
-share/pymol/modules/chempy/fragments/__init__.pyc
-share/pymol/modules/chempy/fragments/__init__.pyo
 share/pymol/modules/chempy/gamess1.py
-share/pymol/modules/chempy/gamess1.pyc
-share/pymol/modules/chempy/gamess1.pyo
 share/pymol/modules/chempy/gms.py
-share/pymol/modules/chempy/gms.pyc
-share/pymol/modules/chempy/gms.pyo
 share/pymol/modules/chempy/hetatm.py
-share/pymol/modules/chempy/hetatm.pyc
-share/pymol/modules/chempy/hetatm.pyo
 share/pymol/modules/chempy/io.py
-share/pymol/modules/chempy/io.pyc
-share/pymol/modules/chempy/io.pyo
 share/pymol/modules/chempy/lst.py
-share/pymol/modules/chempy/lst.pyc
-share/pymol/modules/chempy/lst.pyo
 share/pymol/modules/chempy/mae.py
-share/pymol/modules/chempy/mae.pyc
-share/pymol/modules/chempy/mae.pyo
 share/pymol/modules/chempy/map.py
-share/pymol/modules/chempy/map.pyc
-share/pymol/modules/chempy/map.pyo
 share/pymol/modules/chempy/mass.py
-share/pymol/modules/chempy/mass.pyc
-share/pymol/modules/chempy/mass.pyo
 share/pymol/modules/chempy/mmd.py
-share/pymol/modules/chempy/mmd.pyc
-share/pymol/modules/chempy/mmd.pyo
 share/pymol/modules/chempy/models.py
-share/pymol/modules/chempy/models.pyc
-share/pymol/modules/chempy/models.pyo
 share/pymol/modules/chempy/mol.py
-share/pymol/modules/chempy/mol.pyc
-share/pymol/modules/chempy/mol.pyo
 share/pymol/modules/chempy/neighbor.py
-share/pymol/modules/chempy/neighbor.pyc
-share/pymol/modules/chempy/neighbor.pyo
 share/pymol/modules/chempy/pdb.py
-share/pymol/modules/chempy/pdb.pyc
-share/pymol/modules/chempy/pdb.pyo
 share/pymol/modules/chempy/pkl.py
-share/pymol/modules/chempy/pkl.pyc
-share/pymol/modules/chempy/pkl.pyo
 share/pymol/modules/chempy/place.py
-share/pymol/modules/chempy/place.pyc
-share/pymol/modules/chempy/place.pyo
 share/pymol/modules/chempy/protein.py
-share/pymol/modules/chempy/protein.pyc
-share/pymol/modules/chempy/protein.pyo
 share/pymol/modules/chempy/protein_amber.py
-share/pymol/modules/chempy/protein_amber.pyc
-share/pymol/modules/chempy/protein_amber.pyo
 share/pymol/modules/chempy/protein_amber99.py
-share/pymol/modules/chempy/protein_amber99.pyc
-share/pymol/modules/chempy/protein_amber99.pyo
 share/pymol/modules/chempy/protein_mmff.py
-share/pymol/modules/chempy/protein_mmff.pyc
-share/pymol/modules/chempy/protein_mmff.pyo
 share/pymol/modules/chempy/protein_residues.py
-share/pymol/modules/chempy/protein_residues.pyc
-share/pymol/modules/chempy/protein_residues.pyo
 share/pymol/modules/chempy/sdf.py
-share/pymol/modules/chempy/sdf.pyc
-share/pymol/modules/chempy/sdf.pyo
 share/pymol/modules/chempy/solvate.py
-share/pymol/modules/chempy/solvate.pyc
-share/pymol/modules/chempy/solvate.pyo
+share/pymol/modules/chempy/water_amber.py
+share/pymol/modules/chempy/water_residues.py
+share/pymol/modules/chempy/xyz.py
+share/pymol/modules/chempy/champ/__init__.py
+share/pymol/modules/chempy/champ/amber99.py
+share/pymol/modules/chempy/champ/assign.py
+share/pymol/modules/chempy/champ/formal_charges.py
+share/pymol/modules/chempy/champ/_champ.so
+share/pymol/modules/chempy/champ/__init__.pyc
+share/pymol/modules/chempy/champ/amber99.pyc
+share/pymol/modules/chempy/champ/assign.pyc
+share/pymol/modules/chempy/champ/formal_charges.pyc
+share/pymol/modules/chempy/champ/__init__.pyo
+share/pymol/modules/chempy/champ/amber99.pyo
+share/pymol/modules/chempy/champ/assign.pyo
+share/pymol/modules/chempy/champ/formal_charges.pyo
+share/pymol/modules/chempy/fragments/__init__.py
+share/pymol/modules/chempy/fragments/__init__.pyc
+share/pymol/modules/chempy/fragments/__init__.pyo
 share/pymol/modules/chempy/tinker/__init__.py
-share/pymol/modules/chempy/tinker/__init__.pyc
-share/pymol/modules/chempy/tinker/__init__.pyo
 share/pymol/modules/chempy/tinker/amber.py
-share/pymol/modules/chempy/tinker/amber.pyc
-share/pymol/modules/chempy/tinker/amber.pyo
 share/pymol/modules/chempy/tinker/keyword.py
-share/pymol/modules/chempy/tinker/keyword.pyc
-share/pymol/modules/chempy/tinker/keyword.pyo
 share/pymol/modules/chempy/tinker/realtime.py
-share/pymol/modules/chempy/tinker/realtime.pyc
-share/pymol/modules/chempy/tinker/realtime.pyo
 share/pymol/modules/chempy/tinker/state.py
+share/pymol/modules/chempy/tinker/__init__.pyc
+share/pymol/modules/chempy/tinker/amber.pyc
+share/pymol/modules/chempy/tinker/keyword.pyc
+share/pymol/modules/chempy/tinker/realtime.pyc
 share/pymol/modules/chempy/tinker/state.pyc
+share/pymol/modules/chempy/tinker/__init__.pyo
+share/pymol/modules/chempy/tinker/amber.pyo
+share/pymol/modules/chempy/tinker/keyword.pyo
+share/pymol/modules/chempy/tinker/realtime.pyo
 share/pymol/modules/chempy/tinker/state.pyo
-share/pymol/modules/chempy/water_amber.py
+share/pymol/modules/chempy/__init__.pyc
+share/pymol/modules/chempy/arc.pyc
+share/pymol/modules/chempy/bond_amber.pyc
+share/pymol/modules/chempy/bond_mmff.pyc
+share/pymol/modules/chempy/bonds.pyc
+share/pymol/modules/chempy/brick.pyc
+share/pymol/modules/chempy/cc1.pyc
+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
+share/pymol/modules/chempy/io.pyc
+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
+share/pymol/modules/chempy/protein_amber.pyc
+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
 share/pymol/modules/chempy/water_amber.pyc
-share/pymol/modules/chempy/water_amber.pyo
-share/pymol/modules/chempy/water_residues.py
 share/pymol/modules/chempy/water_residues.pyc
-share/pymol/modules/chempy/water_residues.pyo
-share/pymol/modules/chempy/xyz.py
 share/pymol/modules/chempy/xyz.pyc
+share/pymol/modules/chempy/__init__.pyo
+share/pymol/modules/chempy/arc.pyo
+share/pymol/modules/chempy/bond_amber.pyo
+share/pymol/modules/chempy/bond_mmff.pyo
+share/pymol/modules/chempy/bonds.pyo
+share/pymol/modules/chempy/brick.pyo
+share/pymol/modules/chempy/cc1.pyo
+share/pymol/modules/chempy/cex.pyo
+share/pymol/modules/chempy/charge.pyo
+share/pymol/modules/chempy/cpv.pyo
+share/pymol/modules/chempy/dictdb.pyo
+share/pymol/modules/chempy/gamess1.pyo
+share/pymol/modules/chempy/gms.pyo
+share/pymol/modules/chempy/hetatm.pyo
+share/pymol/modules/chempy/io.pyo
+share/pymol/modules/chempy/lst.pyo
+share/pymol/modules/chempy/mae.pyo
+share/pymol/modules/chempy/map.pyo
+share/pymol/modules/chempy/mass.pyo
+share/pymol/modules/chempy/mmd.pyo
+share/pymol/modules/chempy/models.pyo
+share/pymol/modules/chempy/mol.pyo
+share/pymol/modules/chempy/neighbor.pyo
+share/pymol/modules/chempy/pdb.pyo
+share/pymol/modules/chempy/pkl.pyo
+share/pymol/modules/chempy/place.pyo
+share/pymol/modules/chempy/protein.pyo
+share/pymol/modules/chempy/protein_amber.pyo
+share/pymol/modules/chempy/protein_amber99.pyo
+share/pymol/modules/chempy/protein_mmff.pyo
+share/pymol/modules/chempy/protein_residues.pyo
+share/pymol/modules/chempy/sdf.pyo
+share/pymol/modules/chempy/solvate.pyo
+share/pymol/modules/chempy/water_amber.pyo
+share/pymol/modules/chempy/water_residues.pyo
 share/pymol/modules/chempy/xyz.pyo
 share/pymol/modules/compile_pymol.py
-share/pymol/modules/compile_pymol.pyc
-share/pymol/modules/compile_pymol.pyo
 share/pymol/modules/launch_pymol.py
-share/pymol/modules/launch_pymol.pyc
-share/pymol/modules/launch_pymol.pyo
+share/pymol/modules/pmg_tk/startup/__init__.py
+share/pymol/modules/pmg_tk/startup/apbs_tools.py
+share/pymol/modules/pmg_tk/startup/remote_pdb_load.py
+share/pymol/modules/pmg_tk/startup/__init__.pyc
+share/pymol/modules/pmg_tk/startup/apbs_tools.pyc
+share/pymol/modules/pmg_tk/startup/remote_pdb_load.pyc
+share/pymol/modules/pmg_tk/startup/__init__.pyo
+share/pymol/modules/pmg_tk/startup/apbs_tools.pyo
+share/pymol/modules/pmg_tk/startup/remote_pdb_load.pyo
 share/pymol/modules/pmg_tk/AbstractApp.py
-share/pymol/modules/pmg_tk/AbstractApp.pyc
-share/pymol/modules/pmg_tk/AbstractApp.pyo
 share/pymol/modules/pmg_tk/ColorEditor.py
-share/pymol/modules/pmg_tk/ColorEditor.pyc
-share/pymol/modules/pmg_tk/ColorEditor.pyo
 share/pymol/modules/pmg_tk/Demo.py
-share/pymol/modules/pmg_tk/Demo.pyc
-share/pymol/modules/pmg_tk/Demo.pyo
 share/pymol/modules/pmg_tk/PMGApp.py
-share/pymol/modules/pmg_tk/PMGApp.pyc
-share/pymol/modules/pmg_tk/PMGApp.pyo
 share/pymol/modules/pmg_tk/SetEditor.py
-share/pymol/modules/pmg_tk/SetEditor.pyc
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 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
+share/pymol/test/ref/C0700odd.log
 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