# Maintainer: Evgeniy Alekseev <arcanis dot arch at gmail dot com>

# Contributor: graysky

# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com>

pkgname=pymol

pkgdesc="Molecular visualization system on an Open Source foundation"

arch=('i686' 'x86_64')

url="http://pymol.org/"

"${pkgname}-38899.patch"

"apbstools_tcltk8.6.patch")

install="${pkgname}.install"

'1f8152c4604ba2939b24e25a022937ca'

prepare() {

# create desktop file

gendesk -f --pkgname "${pkgname}" --pkgdesc "${pkgdesc}" --name="PyMOL" --categories="Science;Chemistry"

# suppress non-zero exit code that breaks makepkg

sed -i '/sys.exit/ s,2,0,' "${srcdir}/pymol/setup.py"

# change python to python2

sed -i "s|python|python2|g" "${srcdir}/pymol/test/run"

sed -i "s|python|python2|g" "${srcdir}/pymol/test/show"

sed -i "s|python|python2|g" "${srcdir}/pymol/modules/pmg_tk/startup/apbs_tools.py"

# fix FS#38899

patch -p0 -i "${pkgname}-38899.patch"

mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb"

# fix FS#39526

cd "${srcdir}/${pkgname}"

}

build() {

# 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)

self.selection = Pmw.EntryField(group.interior(),

labelpos='w',

label_text='Selection to use: ',

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(column=0, row=0)

self.interior_dielectric = Pmw.EntryField(group.interior(),labelpos='w',

label_text = 'Protein Dielectric:',

#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(column=1, row=1,columnspan=4)

self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w',

label_text = 'Maximum Memory Allowed (MB):',

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(column=0, row=1, )

self.ion_plus_one_conc = Pmw.EntryField(group.interior(),

labelpos='w',

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(column = 1, row = 0)

for coord in 'x y z'.split():

setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(),

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(column = 2, row = 0)

for coord in 'x y z'.split():

setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(),

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(column = 3, row = 0)

for coord in 'x y z'.split():

setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(),

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(column = 4, row = 0)

for coord in 'x y z'.split():

setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(),

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)

def quickFileValidation(s):

if s == '': return Pmw.PARTIAL

elif os.path.isfile(s): return Pmw.OK

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)

self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),

labelpos = 'w',

label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),

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)

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)

# 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)

text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).

Documentation may be found at

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.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')

self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)

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.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')

self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)

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.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')

self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)

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.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')

self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)

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)