diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/pymol/ChangeLog | 3 | ||||
| -rw-r--r-- | sci-chemistry/pymol/files/pymol-9999-tk8.6.patch | 129 |
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)) - - - |