[arch-commits] Commit in pymol/trunk (PKGBUILD apbstools_tcltk8.6.patch)
Evgeniy Alekseev
arcanis at nymeria.archlinux.org
Tue Mar 18 18:03:09 UTC 2014
Date: Tuesday, March 18, 2014 @ 19:03:09
Author: arcanis
Revision: 107718
upgpkg: pymol 1.7.0.0-3
fix FS#39526
Added:
pymol/trunk/apbstools_tcltk8.6.patch
Modified:
pymol/trunk/PKGBUILD
--------------------------+
PKGBUILD | 14 ++-
apbstools_tcltk8.6.patch | 176 +++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 186 insertions(+), 4 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2014-03-18 17:59:58 UTC (rev 107717)
+++ PKGBUILD 2014-03-18 18:03:09 UTC (rev 107718)
@@ -1,11 +1,11 @@
# $Id$
-# Maintainer: Evgeniy Alekseev <arcanis.arch at gmail dot com>
+# Maintainer: Evgeniy Alekseev <arcanis dot arch at gmail dot com>
# Contributor: graysky
# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com>
pkgname=pymol
pkgver=1.7.0.0
-pkgrel=2
+pkgrel=3
pkgdesc="Molecular visualization system on an Open Source foundation"
arch=('i686' 'x86_64')
url="http://pymol.org/"
@@ -13,10 +13,12 @@
depends=('glew' 'glut' 'mesa' 'python2-numpy' 'python2-pmw' 'tcsh')
makedepends=('desktop-file-utils' 'gendesk')
source=("http://downloads.sourceforge.net/project/pymol/pymol/1.7/pymol-v${pkgver}.tar.bz2"
- "${pkgname}-38899.patch")
+ "${pkgname}-38899.patch"
+ "apbstools_tcltk8.6.patch")
install="${pkgname}.install"
md5sums=('36fc735f6104e59802f109d0d25b6676'
- '1f8152c4604ba2939b24e25a022937ca')
+ '1f8152c4604ba2939b24e25a022937ca'
+ 'a3c1544017762613bebc3f5763a434a9')
prepare() {
# create desktop file
@@ -33,6 +35,10 @@
# fix FS#38899
patch -p0 -i "${pkgname}-38899.patch"
mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb"
+
+ # fix FS#39526
+ cd "${srcdir}/${pkgname}"
+ patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
}
build() {
Added: apbstools_tcltk8.6.patch
===================================================================
--- apbstools_tcltk8.6.patch (rev 0)
+++ apbstools_tcltk8.6.patch 2014-03-18 18:03:09 UTC (rev 107718)
@@ -0,0 +1,176 @@
+--- 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 @@
+ # 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.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: ',
+@@ -606,7 +607,8 @@
+ page = self.notebook.add('Configuration')
+
+ group = Pmw.Group(page,tag_text='Dielectric Constants')
+- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++ #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:',
+@@ -625,7 +627,8 @@
+ #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')
+- group.pack(fill='both',expand=1, padx=4, pady=5)
++ #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):',
+@@ -683,7 +686,8 @@
+
+
+ group = Pmw.Group(page,tag_text='Ions')
+- group.pack(fill='both',expand=1, padx=4, pady=5)
++ #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',
+@@ -742,7 +746,8 @@
+ 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.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(),
+@@ -757,7 +762,8 @@
+
+
+ group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
+- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++ #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(),
+@@ -772,7 +778,8 @@
+
+
+ group = Pmw.Group(page,tag_text = 'Grid Center')
+- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++ #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(),
+@@ -786,7 +793,8 @@
+ 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.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(),
+@@ -804,7 +812,8 @@
+ 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.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
+@@ -867,7 +876,8 @@
+
+ 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.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),
+@@ -915,17 +925,20 @@
+ 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.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.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.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
+@@ -2158,7 +2171,8 @@
+ 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)
+- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
++ #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)
+@@ -2209,7 +2223,8 @@
+ 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.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)
+@@ -2224,7 +2239,8 @@
+ 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(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)
+@@ -2243,7 +2259,8 @@
+ 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.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)
+@@ -2262,7 +2279,8 @@
+ 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.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
++ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
+
+
+
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