Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv31595
Modified Files:
pymol-py-apbstools.patch
Log Message:
update to 1.6.0
Index: pymol-py-apbstools.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py-apbstools.patch,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- pymol-py-apbstools.patch 21 Aug 2013 21:09:21 -0000 1.2
+++ pymol-py-apbstools.patch 23 Aug 2013 17:53:53 -0000 1.3
@@ -1,6 +1,6 @@
---- modules/pmg_tk/startup/apbs_tools.py.orig 2013-08-16 20:29:27.000000000
-0400
-+++ modules/pmg_tk/startup/apbs_tools.py 2013-08-16 20:31:35.000000000
-0400
-@@ -560,7 +560,8 @@
+--- pymol-1.6.0/modules/pmg_tk/startup/apbs_tools.py.orig 2013-08-23
11:59:00.000000000 -0400
++++ pymol-1.6.0/modules/pmg_tk/startup/apbs_tools.py 2013-08-23
12:00:59.000000000 -0400
+@@ -612,7 +612,8 @@
# Set up the Main page
page = self.notebook.add('Main')
group = Pmw.Group(page,tag_text='Main options')
@@ -10,7 +10,7 @@
self.selection = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Selection to use: ',
-@@ -606,7 +607,8 @@
+@@ -658,7 +659,8 @@
page = self.notebook.add('Configuration')
group = Pmw.Group(page,tag_text='Dielectric Constants')
@@ -20,7 +20,7 @@
group.grid(column=0, row=0)
self.interior_dielectric =
Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Protein Dielectric:',
-@@ -625,7 +627,8 @@
+@@ -677,7 +679,8 @@
#entry.pack(side='left',fill='both',expand=1,padx=4) #
side-by-side
entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical
group = Pmw.Group(page,tag_text='Other')
@@ -30,7 +30,7 @@
group.grid(column=1, row=1,columnspan=4)
self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Maximum Memory
Allowed (MB):',
-@@ -683,7 +686,8 @@
+@@ -735,7 +738,8 @@
group = Pmw.Group(page,tag_text='Ions')
@@ -40,7 +40,7 @@
group.grid(column=0, row=1, )
self.ion_plus_one_conc = Pmw.EntryField(group.interior(),
labelpos='w',
-@@ -742,7 +746,8 @@
+@@ -794,7 +798,8 @@
entry.pack(fill='x',expand=1,padx=4)
group = Pmw.Group(page,tag_text = 'Coarse Mesh Length')
@@ -50,7 +50,7 @@
group.grid(column = 1, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -757,7 +762,8 @@
+@@ -809,7 +814,8 @@
group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
@@ -60,7 +60,7 @@
group.grid(column = 2, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -772,7 +778,8 @@
+@@ -824,7 +830,8 @@
group = Pmw.Group(page,tag_text = 'Grid Center')
@@ -70,7 +70,7 @@
group.grid(column = 3, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -786,7 +793,8 @@
+@@ -838,7 +845,8 @@
getattr(self,'grid_center_%s'%coord).pack(fill='x', expand=1,
padx=4, pady=1)
group = Pmw.Group(page,tag_text = 'Grid Points')
@@ -80,7 +80,7 @@
group.grid(column = 4, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -804,7 +812,8 @@
+@@ -856,7 +864,8 @@
page.grid_columnconfigure(5,weight=1)
page = self.notebook.add('Program Locations')
group = Pmw.Group(page,tag_text='Locations')
@@ -90,7 +90,7 @@
def quickFileValidation(s):
if s == '': return Pmw.PARTIAL
elif os.path.isfile(s): return Pmw.OK
-@@ -867,7 +876,8 @@
+@@ -955,7 +964,8 @@
page = self.notebook.add('Temp File Locations')
group = Pmw.Group(page,tag_text='Locations')
@@ -100,7 +100,7 @@
self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
labelpos = 'w',
label_pyclass =
FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
-@@ -915,17 +925,20 @@
+@@ -1003,17 +1013,20 @@
page = self.notebook.add('Visualization (1)')
group =
VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
self.visualization_group_1 = group
@@ -124,7 +124,7 @@
text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS
(http://www.poissonboltzmann.org/apbs/).
Documentation may be found at
-@@ -2158,7 +2171,8 @@
+@@ -2267,7 +2280,8 @@
self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(),
padx=0)
self.update_buttonbox.pack(side=LEFT)
self.update_buttonbox.add('Update',command=self.refresh)
@@ -134,43 +134,63 @@
self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular
Surface')
self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(),
padx=0)
-@@ -2209,7 +2223,8 @@
+@@ -2317,8 +2331,9 @@
+ )
bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
Pmw.alignlabels(bars)
- for bar in bars: bar.pack(side=LEFT)
+- for bar in bars: bar.pack(side=LEFT)
- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5,
side=LEFT)
++ for bar in bars: bar.pack(expand = 1, side=LEFT)
+ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady =
5, side=LEFT)
-+ self.ms_group.grid(row=1, padx = 4, pady = 5, sticky=(W))
++ self.ms_group.grid(column=0, row=1, padx = 4, pady = 5, rowspan =
2, sticky=(N, S, E, W))
self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(),
padx=0)
-@@ -2224,7 +2239,8 @@
+@@ -2333,11 +2348,13 @@
text = """Follows same coloring as
surface.""",
)
label.pack()
- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5,
side=TOP)
+ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady =
5, side=TOP)
-+ self.fl_group.grid(row=1, padx = 4, pady = 5, sticky=(E))
++ self.fl_group.grid(column = 1, row=0, padx = 4, pady = 5)
self.pi_group = Pmw.Group(self.interior(),tag_text='Positive
Isosurface')
self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(),
padx=0)
-@@ -2243,7 +2259,8 @@
+- self.pi_buttonbox.pack()
++ #self.pi_buttonbox.pack()
++ self.pi_buttonbox.grid()
+ self.pi_buttonbox.add('Show',command=self.showPosSurface)
+ self.pi_buttonbox.add('Hide',command=self.hidePosSurface)
+ self.pi_buttonbox.add('Update',command=self.updatePosSurface)
+@@ -2351,12 +2368,15 @@
+ datatype = 'real',
entryfield_validate =
{'validator' : 'real', 'min':0}
)
- self.pos_surf_val.pack(side=LEFT)
+- self.pos_surf_val.pack(side=LEFT)
- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5,
side=LEFT)
++ #self.pos_surf_val.pack(side=LEFT)
++ self.pos_surf_val.grid()
+ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady =
5, side=LEFT)
-+ self.pi_group.grid(row=2, padx = 4, pady = 5, sticky=(W))
++ self.pi_group.grid(column = 1, row = 1, padx = 4, pady = 5,
sticky=(N, S, E, W))
self.ni_group = Pmw.Group(self.interior(),tag_text='Negative
Isosurface')
self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(),
padx=0)
-@@ -2262,7 +2279,8 @@
+- self.ni_buttonbox.pack()
++ #self.ni_buttonbox.pack()
++ self.ni_buttonbox.grid()
+ self.ni_buttonbox.add('Show',command=self.showNegSurface)
+ self.ni_buttonbox.add('Hide',command=self.hideNegSurface)
+ self.ni_buttonbox.add('Update',command=self.updateNegSurface)
+@@ -2370,8 +2390,10 @@
+ datatype = 'real',
entryfield_validate =
{'validator' : 'real', 'max':0}
)
- self.neg_surf_val.pack(side=LEFT)
+- self.neg_surf_val.pack(side=LEFT)
- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5,
side=LEFT)
++ #self.neg_surf_val.pack(side=LEFT)
++ self.neg_surf_val.grid()
+ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady =
5, side=LEFT)
-+ self.ni_group.grid(row=2, padx = 4, pady = 5, sticky=(E))
++ self.ni_group.grid(column = 1, row=2, padx = 4, pady = 5,
sticky=(N, S, E, W))
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