| 1 |
jlec 13/11/22 13:38:23 |
| 2 |
|
| 3 |
Added: pymol-apbs-plugin-2.1_p26-tcltk8.6.patch |
| 4 |
Log: |
| 5 |
sci-chemistry/pymol-apbs-plugin: Version BUmp, add fix for tcltk8.6 support |
| 6 |
|
| 7 |
(Portage version: 2.2.7/cvs/Linux x86_64, RepoMan options: --force, signed Manifest commit with key B9D4F231BD1558AB!) |
| 8 |
|
| 9 |
Revision Changes Path |
| 10 |
1.1 sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch |
| 11 |
|
| 12 |
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch?rev=1.1&view=markup |
| 13 |
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/pymol-apbs-plugin/files/pymol-apbs-plugin-2.1_p26-tcltk8.6.patch?rev=1.1&content-type=text/plain |
| 14 |
|
| 15 |
Index: pymol-apbs-plugin-2.1_p26-tcltk8.6.patch |
| 16 |
=================================================================== |
| 17 |
--- pymol-apbs-plugin-2.1_p26.py.orig 2013-08-16 20:29:27.000000000 -0400 |
| 18 |
+++ pymol-apbs-plugin-2.1_p26.py 2013-08-16 20:31:35.000000000 -0400 |
| 19 |
@@ -560,7 +560,8 @@ |
| 20 |
# Set up the Main page |
| 21 |
page = self.notebook.add('Main') |
| 22 |
group = Pmw.Group(page,tag_text='Main options') |
| 23 |
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 24 |
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 25 |
+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) |
| 26 |
self.selection = Pmw.EntryField(group.interior(), |
| 27 |
labelpos='w', |
| 28 |
label_text='Selection to use: ', |
| 29 |
@@ -606,7 +607,8 @@ |
| 30 |
page = self.notebook.add('Configuration') |
| 31 |
|
| 32 |
group = Pmw.Group(page,tag_text='Dielectric Constants') |
| 33 |
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 34 |
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 35 |
+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 36 |
group.grid(column=0, row=0) |
| 37 |
self.interior_dielectric = Pmw.EntryField(group.interior(),labelpos='w', |
| 38 |
label_text = 'Protein Dielectric:', |
| 39 |
@@ -625,7 +627,8 @@ |
| 40 |
#entry.pack(side='left',fill='both',expand=1,padx=4) # side-by-side |
| 41 |
entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical |
| 42 |
group = Pmw.Group(page,tag_text='Other') |
| 43 |
- group.pack(fill='both',expand=1, padx=4, pady=5) |
| 44 |
+ #group.pack(fill='both',expand=1, padx=4, pady=5) |
| 45 |
+ group.grid(padx=4, pady=5, sticky=(N, S, E, W)) |
| 46 |
group.grid(column=1, row=1,columnspan=4) |
| 47 |
self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w', |
| 48 |
label_text = 'Maximum Memory Allowed (MB):', |
| 49 |
@@ -683,7 +686,8 @@ |
| 50 |
|
| 51 |
|
| 52 |
group = Pmw.Group(page,tag_text='Ions') |
| 53 |
- group.pack(fill='both',expand=1, padx=4, pady=5) |
| 54 |
+ #group.pack(fill='both',expand=1, padx=4, pady=5) |
| 55 |
+ group.grid(padx=4, pady=5, sticky=(N, S, E, W)) |
| 56 |
group.grid(column=0, row=1, ) |
| 57 |
self.ion_plus_one_conc = Pmw.EntryField(group.interior(), |
| 58 |
labelpos='w', |
| 59 |
@@ -742,7 +746,8 @@ |
| 60 |
entry.pack(fill='x',expand=1,padx=4) |
| 61 |
|
| 62 |
group = Pmw.Group(page,tag_text = 'Coarse Mesh Length') |
| 63 |
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 64 |
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 65 |
+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 66 |
group.grid(column = 1, row = 0) |
| 67 |
for coord in 'x y z'.split(): |
| 68 |
setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(), |
| 69 |
@@ -757,7 +762,8 @@ |
| 70 |
|
| 71 |
|
| 72 |
group = Pmw.Group(page,tag_text = 'Fine Mesh Length') |
| 73 |
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 74 |
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 75 |
+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 76 |
group.grid(column = 2, row = 0) |
| 77 |
for coord in 'x y z'.split(): |
| 78 |
setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(), |
| 79 |
@@ -772,7 +778,8 @@ |
| 80 |
|
| 81 |
|
| 82 |
group = Pmw.Group(page,tag_text = 'Grid Center') |
| 83 |
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 84 |
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 85 |
+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 86 |
group.grid(column = 3, row = 0) |
| 87 |
for coord in 'x y z'.split(): |
| 88 |
setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(), |
| 89 |
@@ -786,7 +793,8 @@ |
| 90 |
getattr(self,'grid_center_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1) |
| 91 |
|
| 92 |
group = Pmw.Group(page,tag_text = 'Grid Points') |
| 93 |
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 94 |
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5) |
| 95 |
+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 96 |
group.grid(column = 4, row = 0) |
| 97 |
for coord in 'x y z'.split(): |
| 98 |
setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(), |
| 99 |
@@ -804,7 +812,8 @@ |
| 100 |
page.grid_columnconfigure(5,weight=1) |
| 101 |
page = self.notebook.add('Program Locations') |
| 102 |
group = Pmw.Group(page,tag_text='Locations') |
| 103 |
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 104 |
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 105 |
+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) |
| 106 |
def quickFileValidation(s): |
| 107 |
if s == '': return Pmw.PARTIAL |
| 108 |
elif os.path.isfile(s): return Pmw.OK |
| 109 |
@@ -867,7 +876,8 @@ |
| 110 |
|
| 111 |
page = self.notebook.add('Temp File Locations') |
| 112 |
group = Pmw.Group(page,tag_text='Locations') |
| 113 |
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 114 |
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 115 |
+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) |
| 116 |
self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(), |
| 117 |
labelpos = 'w', |
| 118 |
label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename), |
| 119 |
@@ -915,17 +925,20 @@ |
| 120 |
page = self.notebook.add('Visualization (1)') |
| 121 |
group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1) |
| 122 |
self.visualization_group_1 = group |
| 123 |
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 124 |
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 125 |
+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) |
| 126 |
|
| 127 |
page = self.notebook.add('Visualization (2)') |
| 128 |
group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2) |
| 129 |
self.visualization_group_2 = group |
| 130 |
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 131 |
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 132 |
+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) |
| 133 |
|
| 134 |
# Create a couple of other empty pages |
| 135 |
page = self.notebook.add('About') |
| 136 |
group = Pmw.Group(page, tag_text='About PyMOL APBS Tools') |
| 137 |
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 138 |
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5) |
| 139 |
+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W)) |
| 140 |
text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/). |
| 141 |
|
| 142 |
Documentation may be found at |
| 143 |
@@ -2158,7 +2171,8 @@ |
| 144 |
self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0) |
| 145 |
self.update_buttonbox.pack(side=LEFT) |
| 146 |
self.update_buttonbox.add('Update',command=self.refresh) |
| 147 |
- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) |
| 148 |
+ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) |
| 149 |
+ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 150 |
|
| 151 |
self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface') |
| 152 |
self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0) |
| 153 |
@@ -2209,7 +2223,8 @@ |
| 154 |
bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high) |
| 155 |
Pmw.alignlabels(bars) |
| 156 |
for bar in bars: bar.pack(side=LEFT) |
| 157 |
- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) |
| 158 |
+ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) |
| 159 |
+ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 160 |
|
| 161 |
self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines') |
| 162 |
self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0) |
| 163 |
@@ -2224,7 +2239,8 @@ |
| 164 |
text = """Follows same coloring as surface.""", |
| 165 |
) |
| 166 |
label.pack() |
| 167 |
- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) |
| 168 |
+ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP) |
| 169 |
+ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 170 |
|
| 171 |
self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface') |
| 172 |
self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0) |
| 173 |
@@ -2243,7 +2259,8 @@ |
| 174 |
entryfield_validate = {'validator' : 'real', 'min':0} |
| 175 |
) |
| 176 |
self.pos_surf_val.pack(side=LEFT) |
| 177 |
- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) |
| 178 |
+ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) |
| 179 |
+ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
| 180 |
|
| 181 |
self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface') |
| 182 |
self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0) |
| 183 |
@@ -2262,7 +2279,8 @@ |
| 184 |
entryfield_validate = {'validator' : 'real', 'max':0} |
| 185 |
) |
| 186 |
self.neg_surf_val.pack(side=LEFT) |
| 187 |
- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) |
| 188 |
+ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT) |
| 189 |
+ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W)) |
Archives