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authorJustin Lecher <jlec@gentoo.org>2014-10-31 08:19:20 +0100
committerJustin Lecher <jlec@gentoo.org>2014-11-03 08:15:05 +0100
commitde472bbdde04ced59132ab600b63417a5f9b839c (patch)
tree7c2d8cd4ea56ab20abe08b25f8ee280a1a836b32 /sci-chemistry
parentMask Lab::Instrument and Lab::Tools for removal (diff)
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sci-chemistry/pymol: Update patch to upstream suggestion
Package-Manager: portage-2.2.14
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/pymol/ChangeLog3
-rw-r--r--sci-chemistry/pymol/files/pymol-9999-tk8.6.patch129
2 files changed, 19 insertions, 113 deletions
diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 15af521b6..c55379ba6 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 31 Oct 2014; Justin Lecher <jlec@gentoo.org> files/pymol-9999-tk8.6.patch:
+ Update patch to upstream suggestion
+
30 Oct 2014; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild,
+files/pymol-9999-tk8.6.patch:
Make it really multi py ABI ready; use internal apbs plugin
diff --git a/sci-chemistry/pymol/files/pymol-9999-tk8.6.patch b/sci-chemistry/pymol/files/pymol-9999-tk8.6.patch
index c4fa20954..529de8406 100644
--- a/sci-chemistry/pymol/files/pymol-9999-tk8.6.patch
+++ b/sci-chemistry/pymol/files/pymol-9999-tk8.6.patch
@@ -1,163 +1,66 @@
- pymol/modules/pmg_tk/startup/apbs_tools.py | 36 +++++++++++++++---------------
- 1 file changed, 18 insertions(+), 18 deletions(-)
+commit afb1c62e05d56dfbe2940f4f939428739d834f05
+Author: Thomas Holder <thomas.holder@schrodinger.com>
+Date: Thu Oct 30 17:04:45 2014 -0400
-diff --git a/pymol/modules/pmg_tk/startup/apbs_tools.py b/pymol/modules/pmg_tk/startup/apbs_tools.py
-index 9b76070..ad82df3 100644
---- a/pymol/modules/pmg_tk/startup/apbs_tools.py
-+++ b/pymol/modules/pmg_tk/startup/apbs_tools.py
-@@ -612,7 +612,7 @@ class APBSTools2:
- # Set up the Main page
- page = self.notebook.add('Main')
- group = Pmw.Group(page,tag_text='Main options')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.selection = Pmw.EntryField(group.interior(),
- labelpos='w',
- label_text='Selection to use: ',
-@@ -658,7 +658,7 @@ class APBSTools2:
+ fix apbs_tools for tcl/tk 8.6
+
+diff --git a/modules/pmg_tk/startup/apbs_tools.py b/modules/pmg_tk/startup/apbs_tools.py
+index 9b76070..c9f649c 100644
+--- a/modules/pmg_tk/startup/apbs_tools.py
++++ b/modules/pmg_tk/startup/apbs_tools.py
+@@ -658,7 +658,6 @@ class APBSTools2:
page = self.notebook.add('Configuration')
group = Pmw.Group(page,tag_text='Dielectric Constants')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column=0, row=0)
self.interior_dielectric = Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Protein Dielectric:',
-@@ -677,7 +677,7 @@ class APBSTools2:
+@@ -677,7 +676,6 @@ class APBSTools2:
#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')
- group.pack(fill='both',expand=1, padx=4, pady=5)
-+ group.grid(padx=4, pady=5, sticky=(N, S, E, W))
group.grid(column=1, row=1,columnspan=4)
self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Maximum Memory Allowed (MB):',
-@@ -735,7 +735,7 @@ class APBSTools2:
+@@ -735,7 +733,6 @@ class APBSTools2:
group = Pmw.Group(page,tag_text='Ions')
- group.pack(fill='both',expand=1, padx=4, pady=5)
-+ group.grid(padx=4, pady=5, sticky=(N, S, E, W))
group.grid(column=0, row=1, )
self.ion_plus_one_conc = Pmw.EntryField(group.interior(),
labelpos='w',
-@@ -794,7 +794,7 @@ class APBSTools2:
+@@ -794,7 +791,6 @@ class APBSTools2:
entry.pack(fill='x',expand=1,padx=4)
group = Pmw.Group(page,tag_text = 'Coarse Mesh Length')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column = 1, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -809,7 +809,7 @@ class APBSTools2:
+@@ -809,7 +805,6 @@ class APBSTools2:
group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column = 2, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -824,7 +824,7 @@ class APBSTools2:
+@@ -824,7 +819,6 @@ class APBSTools2:
group = Pmw.Group(page,tag_text = 'Grid Center')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column = 3, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -838,7 +838,7 @@ class APBSTools2:
+@@ -838,7 +832,6 @@ class APBSTools2:
getattr(self,'grid_center_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1)
group = Pmw.Group(page,tag_text = 'Grid Points')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column = 4, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -856,7 +856,7 @@ class APBSTools2:
- page.grid_columnconfigure(5,weight=1)
- page = self.notebook.add('Program Locations')
- group = Pmw.Group(page,tag_text='Locations')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- def quickFileValidation(s):
- if s == '': return Pmw.PARTIAL
- elif os.path.isfile(s): return Pmw.OK
-@@ -955,7 +955,7 @@ protein residues and AMBER charges. If wish that behavior, simply delete the "p
-
- page = self.notebook.add('Temp File Locations')
- group = Pmw.Group(page,tag_text='Locations')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
- labelpos = 'w',
- label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
-@@ -1003,17 +1003,17 @@ by setting the environment variable TEMP.
- page = self.notebook.add('Visualization (1)')
- group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
- self.visualization_group_1 = group
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
-
- page = self.notebook.add('Visualization (2)')
- group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
- self.visualization_group_2 = group
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
-
- # Create a couple of other empty pages
- page = self.notebook.add('About')
- group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
-- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
- text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
-
- Documentation may be found at
-@@ -2271,7 +2271,7 @@ class VisualizationGroup(Pmw.Group):
- 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)
-- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
- self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
-@@ -2322,7 +2322,7 @@ class VisualizationGroup(Pmw.Group):
- bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
- Pmw.alignlabels(bars)
- for bar in bars: bar.pack(side=LEFT)
-- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ms_group.grid(padx = 4, pady = 5, 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)
-@@ -2337,7 +2337,7 @@ class VisualizationGroup(Pmw.Group):
- 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.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
- self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
- self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
-@@ -2356,7 +2356,7 @@ class VisualizationGroup(Pmw.Group):
- entryfield_validate = {'validator' : 'real', 'min':0}
- )
- self.pos_surf_val.pack(side=LEFT)
-- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.pi_group.grid(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)
-@@ -2375,7 +2375,7 @@ class VisualizationGroup(Pmw.Group):
- entryfield_validate = {'validator' : 'real', 'max':0}
- )
- self.neg_surf_val.pack(side=LEFT)
-- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
-
-
-