def createlegacypmgapp():
'''
Start a Tk app in separate thread.
Returns a "fake" PMGApp instance for legacy support
'''
app = pymol.Scratch_Storage()
app.root = None
app.menuBar = pymol.Scratch_Storage()
app.menuBar.addmenuitem = \
app.menuBar.deletemenuitems = \
app.menuBar.addcascademenu = lambda *x, **y: None
def starttk():
import Tkinter
app.root = Tkinter.Tk()
app.root.withdraw()
app.root.mainloop()
import threading
t = threading.Thread(target=starttk, args=())
t.setDaemon(1)
t.start()
import time
wait, maxwait = 0.01, 1.0
while app.root is None and maxwait > 0.0:
time.sleep(wait)
maxwait -= wait
return app
def createlegacypmgapp():
'''
Start a Tk app in separate thread.
Returns a "fake" PMGApp instance for legacy support
'''
app = pymol.Scratch_Storage()
app.root = None
app.menuBar = pymol.Scratch_Storage()
app.menuBar.addmenuitem = \
app.menuBar.deletemenuitems = \
app.menuBar.addcascademenu = lambda *x, **y: None
app.execute = lambda c: eval(c) if isinstance(c, str) else c()
return app
def ff_copy(src, dst, _self=cmd):
pymol = _self._pymol
cmd = _self # NOT THREAD SAFE
pymol._rcopy = pymol.Scratch_Storage()
pymol._rcopy.pc = {}
pymol._rcopy.tt = {}
cmd.iterate("(%s)" % src, "_rcopy.pc[name]=partial_charge")
cmd.alter("(%s)" % dst, "partial_charge=_rcopy.pc[name]")
cmd.iterate("(%s)" % src, "_rcopy.tt[name]=text_type")
cmd.alter("(%s)" % dst, "text_type=_rcopy.tt[name]")
del pymol._rcopy
def __init__(self, _self=pymol.cmd): #PyMOL pattern
Wizard.__init__(self, _self) #PyMOL pattern
if self.cmd.get_movie_length() > 0:
raise pymol.wizarding.WizardError(
'Mutagenesis Wizard cannot be used with Movie')
self.cmd.unpick()
self._stored = pymol.Scratch_Storage()
self._space = {'stored': self._stored}
self._status = Status.NO_SELECTION
self._auto_center = "ON"
self.mode = DEFAULT_MODE
self.rep = DEFAULT_REP
self.selection_mode = self.cmd.get_setting_int("mouse_selection_mode")
self.cmd.set("mouse_selection_mode", 1)
tmp_menu = [[2, 'Mutant', '']]
for mode in self._mode_labels:
tmp_menu.append(
[1, mode, 'cmd.get_wizard().set_mode("' + mode + '")'])
self.menu['mode'] = tmp_menu
tmp_menu2 = [[2, 'Representation', '']]
for rep in self._reps:
tmp_menu2.append([
1, self._rep_name[rep],
'cmd.get_wizard().set_rep("' + rep + '")'
])
self.menu['rep'] = tmp_menu2
tmp_menu = [[2, 'Auto Center',
''], [1, "ON", 'cmd.get_wizard().set_auto_center("ON")'],
[1, "OFF", 'cmd.get_wizard().set_auto_center("OFF")']]
self.menu['auto_center'] = tmp_menu
def __init__(self,_self=cmd):
Wizard.__init__(self,_self)
cmd=self.cmd
if self.cmd.get_movie_length() > 0:
raise pymol.wizarding.WizardError('Mutagenesis Wizard cannot be used with Movie')
cmd.unpick()
self.stored = pymol.Scratch_Storage()
self.space = {'stored': self.stored}
self.bump_scores = []
self.dep = default_dep
self.ind_library = io.pkl.fromFile(os.environ['PYMOL_DATA']+
"/chempy/sidechains/sc_bb_ind.pkl")
self.load_library()
self.status = 0 # 0 no selection, 1 mutagenizing
self.bump_check = 1
self.auto_center = 1
self.error = None
self.object_name = None
self.modes = [
'current'
]
self.mode = default_mode
self.rep = default_rep
self.hyd = default_hyd
self.n_cap = default_n_cap
self.c_cap = default_c_cap
residues = list(self.ind_library.keys())
# could extent with additional fragments manually as below
residues.extend(['GLY','ALA'])
residues.extend(['HID','HIE','HIP'])
residues.extend(['ARGN','LYSN','ASPH','GLUH'])
residues.sort()
res_copy = deepcopy(residues)
for a in res_copy:
residues.append('NT_'+a)
residues.append('CT_'+a)
self.modes.extend(residues)
self.mode_label={}
for a in self.modes:
self.mode_label[a] = ""+a
self.mode_label['current']="No Mutant"
self.selection_mode = cmd.get_setting_int("mouse_selection_mode")
cmd.set("mouse_selection_mode",1)
smm = []
smm.append([ 2, 'Mutant', '' ])
smm.append([ 1, 'No change', 'cmd.get_wizard().set_mode("current")' ])
# smm.append([ 1, 'N-Term', [] ])
# smm.append([ 1, 'C-Term', [] ])
smm.append([ 0, '', '' ])
for a in self.modes:
if a == 'current':
pass
elif a[0:3]=='NT_':
pass
# smm[2][2].append([ 1, self.mode_label[a[3:]], 'cmd.get_wizard().set_mode("'+a+'")'])
elif a[0:3]=='CT_':
pass
# smm[3][2].append([ 1, self.mode_label[a[3:]], 'cmd.get_wizard().set_mode("'+a+'")'])
else:
smm.append([ 1, self.mode_label[a], 'cmd.get_wizard().set_mode("'+a+'")'])
# group arg, lys, his, glu, asp
for lst in [ smm ]: # [ smm, smm[2][2], smm[3][2] ]:
for a in 'ARG','LYS','HID','GLU','ASP':
ix = 0
start = 0
stop = 0
for b in lst:
if start==0:
if b[1][0:]==a:
start = ix
stop = ix + 1
elif b[1][0:3]==a[0:3] or ( b[1][0:2]==a[0:2] and a[0:2]=='HI' ):
stop = ix + 1
ix = ix + 1
if start!=0 and stop!=0:
slice = lst[start:stop]
if a != 'HID':
slice2 = [slice[0] ] + [ [0,'',''] ] + slice[1:]
lst[start:stop] = [ [1, self.mode_label[a] + "... " , slice2 ] ]
else:
slice2 = [ slice[3] ] + [ [0,'',''] ] + slice[0:3]
lst[start:stop] = [ [1, self.mode_label['HIS']+ "... ", slice2 ] ]
self.menu['mode']=smm
self.reps = [
'lines',
'sticks',
'spheres',
'dots'
]
self.rep_name = {
'lines' : "Show Lines",
'sticks' : "Show Sticks",
'spheres' : "Show Spheres",
'dots' : "Show Dots",
}
self.dep_name = {
'dep' : "Backbone Depen. Rotamers",
'ind' : "Backbone Indep. Rotamers"
}
self.hyd_name = {
'auto' : "Hydrogens: Current",
'keep' : "Hydrogens: Add & Retain",
# 'polar' : "Polar Hydrogens",
'none' : "Hydrogens: Remove",
}
self.hyds = [ 'auto', 'keep', 'none' ]
self.n_cap_name = {
'none' : 'Open',
'posi' : 'NH3+',
'acet' : 'Acetyl',
}
self.n_caps = [ 'none', 'posi', 'acet' ]
self.c_cap_name = {
'none' : 'Open',
'nega' : 'COO-',
'amin' : 'Amine',
'nmet' : 'N-methyl',
}
self.c_caps = [ 'none', 'nega', 'amin', 'nmet' ]
smm = []
smm.append([ 2, 'N-Cap', '' ])
for a in self.n_caps:
smm.append([ 1, self.n_cap_name[a], 'cmd.get_wizard().set_n_cap("'+a+'")'])
self.menu['n_cap']=smm
smm = []
smm.append([ 2, 'C-Cap', '' ])
for a in self.c_caps:
smm.append([ 1, self.c_cap_name[a], 'cmd.get_wizard().set_c_cap("'+a+'")'])
self.menu['c_cap']=smm
smm = []
smm.append([ 2, 'Hydrogens', '' ])
for a in self.hyds:
smm.append([ 1, self.hyd_name[a], 'cmd.get_wizard().set_hyd("'+a+'")'])
self.menu['hyd']=smm
smm = []
smm.append([ 2, 'Representation', '' ])
for a in self.reps:
smm.append([ 1, self.rep_name[a], 'cmd.get_wizard().set_rep("'+a+'")'])
self.menu['rep']=smm
self.deps = [ 'dep', 'ind' ]
smm = []
smm.append([ 2, 'Rotamers', '' ])
for a in self.deps:
smm.append([ 1, self.dep_name[a], 'cmd.get_wizard().set_dep("'+a+'")'])
self.menu['dep']=smm
if 'pk1' in cmd.get_names('selections'):
cmd.select(src_sele,"(byres pk1)")
cmd.unpick()
cmd.enable(src_sele)
self.status = 1
self.error = None
self.do_library()
cmd.refresh_wizard()
