def __init__(self):
Wizard.__init__(self)
# some attributes to do with picking
self.pick_count = 0
self.object_count = 0
self.object_prefix = "pw"
self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
cmd.deselect()
def __init__(self, _self=cmd):
Wizard.__init__(self, _self)
self.memory = 0
self.n_pair = 0
self.status = 0 # 0 node not selected, 1 node selected
self.message = None
self.selection_mode = cmd.get_setting_legacy("process_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
cmd.deselect() # disable the active selection (if any)
def __init__(self,_self=cmd):
Wizard.__init__(self,_self)
self.memory = 0
self.n_pair = 0
self.status = 0 # 0 no atoms selections, 1 atom selected
self.message = None
self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
cmd.set("mouse_selection_mode",0) # set selection mode to atomic
cmd.deselect() # disable the active selection (if any)
def __init__(self,_self=cmd):
cmd.unpick();
Wizard.__init__(self,_self)
self.status = 0 # 0 no atoms selections, 1 atom selected
self.error = None
self.object_name = None
# mode selection subsystem
self.mode = default_mode
self.modes = [
'polar',
'heavy',
'neigh',
'pairs',
]
self.mode_name = {
'polar':'Polar Neighbors',
'heavy':'Heavy Neighbors',
'neigh':'Neighbors',
'pairs':'Pairwise Distances',
}
smm = []
smm.append([ 2, 'Measurement Mode', '' ])
for a in self.modes:
smm.append([ 1, self.mode_name[a], 'cmd.get_wizard().set_mode("'+a+'")'])
self.menu['mode']=smm
# overwrite mode selection subsystem
self.object_mode=default_object_mode
self.object_modes = [
'overwr',
'append',
]
self.object_mode_name = {
'overwr':'Replace Previous',
'append':'Create New',
}
smm = []
smm.append([ 2, 'New Distances?', '' ])
for a in self.object_modes:
smm.append([ 1, self.object_mode_name[a], 'cmd.get_wizard().set_object_mode("'+a+'")'])
self.menu['object_mode']=smm
self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
cmd.set("mouse_selection_mode",0) # set selection mode to atomic
cmd.deselect() # disable the active selection (if any)
def __init__(self):
Wizard.__init__(self)
# some attributes to do with picking
self.pick_count = 0
self.object_count = 0
self.object_prefix = "pw"
# the plane facet size (the 'radius' of the section of plane we show)
self.facetSize = 5
self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
cmd.set("mouse_selection_mode",0) # set selection mode to atomic
cmd.deselect()
def __init__(self):
Wizard.__init__(self)
# some attributes to do with picking
self.pick_count = 0
self.object_count = 0
self.object_prefix = "pw"
# the plane facet size (the 'radius' of the section of plane we show)
self.facetSize = 5
self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
cmd.deselect()
def __init__(self, parent, bondForceParams, atoms_def):
Wizard.__init__(self)
self.parent = parent
self.atoms_def = atoms_def
self.params_str = [
'r_aA', 'th_a', "th_A1'", 'phi_ba', 'phi_aA', 'phi_AB'
]
self.indexes_list = [
'atom_c', 'atom_b', 'atom_a', "atom_A1", "atom_B1", "atom_C1"
]
self.bondForceParams = bondForceParams
# some attributes to do with picking
self.pick_count = 0
self.pick_count_max = 5
self.object_prefix = "pw"
self.error = None
self.selection_mode = cmd.get_setting_legacy("mouse_selection_mode")
cmd.set("mouse_selection_mode", 0) # set selection mode to atomic
cmd.deselect()
def __init__(self, _self=cmd):
cmd.unpick();
Wizard.__init__(self, _self)
self.mouse_selection_mode = cmd.get_setting_legacy('mouse_selection_mode')
cmd.set('mouse_selection_mode',0) # set selection mode to atomic
cmd.deselect() # disable the active selection (if any)
self.error = None
self.selection_mode = 1 if self.mouse_selection_mode == 6 else 0
self.selection_modes = [
'Residues',
'C-alphas',
]
smm = []
smm.append([ 2, 'Selection Mode', '' ])
for i, label in enumerate(self.selection_modes):
smm.append([1, label, 'cmd.get_wizard().set_mode(%d)' % i])
self.menu['selection_mode'] = smm
self.name = None
def __init__(self, _self=cmd):
Wizard.__init__(self, _self)
cmd = self.cmd
pymol = cmd._pymol
cmd.unpick()
self.dep = default_dep
self.ind_library = io.pkl.fromFile(os.environ["PYMOL_PATH"] + "/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 = 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_legacy("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()
def attach_amino_acid(selection,amino_acid,phi,psi):
if not selection in cmd.get_names("selections"):
if amino_acid in cmd.get_names("objects"):
print " Error: an object with than name already exists"
raise QuietException
cmd.fragment(amino_acid)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(hydro and %s)"%amino_acid)
if cmd.count_atoms("((%s) and name c)"%amino_acid,quiet=1):
cmd.edit("((%s) and name c)"%amino_acid)
else:
cmd.fragment(amino_acid,tmp_editor)
if cmd.count_atoms("((%s) and elem n)"%selection,quiet=1):
cmd.select(tmp_ed_save,"(%s)"%selection)
cmd.iterate("(%s)"%selection,"stored.resv=resv")
stored.resi = str(stored.resv-1)
cmd.alter(tmp_editor,"resi=stored.resi")
cmd.fuse("(%s and name C)"%(tmp_editor),"(pk1)",2)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(pkmol and hydro)")
cmd.set_dihedral("(name ca and neighbor pk2)",
"(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
cmd.set_geometry("pk2",3,3) # make nitrogen planer
cmd.select(tpk1,"pk2")
cmd.select(tpk2,"pk1")
if amino_acid[0:3]!='pro':
cmd.set_dihedral( # PHI
"(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
"(name ca and neighbor "+tpk1+")", # CA
tpk1, # N
tpk2, # C
phi)
cmd.set_dihedral( # PSI (n-1)
tpk1, # N
tpk2, # C
"(name ca and neighbor "+tpk2+")", # CA
"(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
psi)
cmd.delete(tpk1)
cmd.delete(tpk2)
sele = ("(name N and (byres neighbor %s) and not (byres %s))"%
(tmp_ed_save,tmp_ed_save))
if cmd.count_atoms(sele,quiet=1):
cmd.edit(sele)
cmd.delete(tmp_ed_save)
elif cmd.count_atoms("((%s) and elem c)"%selection,quiet=1):
cmd.select(tmp_ed_save,"(%s)"%selection)
cmd.iterate("(%s)"%selection,"stored.resv=resv")
stored.resi = str(stored.resv+1)
cmd.alter(tmp_editor,"resi=stored.resi")
cmd.fuse("(%s and name N)"%(tmp_editor),"(pk1)",2)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(pkmol and hydro)")
cmd.set_dihedral("(name ca and neighbor pk2)",
"(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
cmd.set_geometry("pk1",3,3) # make nitrogen planar
cmd.select(tpk1,"pk1")
cmd.select(tpk2,"pk2")
if amino_acid[0:3]!='pro':
cmd.set_dihedral( # PHI
tpk2, # C
tpk1, # N
"(name ca and neighbor "+tpk1+")", # CA
"(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
phi)
cmd.set_dihedral( # PSI (n-1)
"(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
"(name ca and neighbor "+tpk2+")", # CA
tpk2, # C
tpk1, # N
psi)
cmd.delete(tpk1)
cmd.delete(tpk2)
sele = ("(name C and (byres neighbor %s) and not (byres %s))"%
(tmp_ed_save,tmp_ed_save))
if cmd.count_atoms(sele,quiet=1):
cmd.edit(sele)
cmd.delete(tmp_ed_save)
elif cmd.count_atoms("((%s) and elem h)"%selection,quiet=1):
print " Error: please pick a nitrogen or carbonyl carbon to grow from."
cmd.delete(tmp_editor)
raise QuietException
cmd.delete(tmp_editor)
def __init__(self,_self=cmd):
Wizard.__init__(self,_self)
cmd=self.cmd
pymol=cmd._pymol
cmd.unpick()
self.dep = default_dep
self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
"/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 = 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_legacy("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()
def attach_amino_acid(selection,amino_acid,phi,psi):
if not selection in cmd.get_names("selections"):
if amino_acid in cmd.get_names("objects"):
print " Error: an object with than name already exists"
raise QuietException
cmd.fragment(amino_acid)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(hydro and %s)"%amino_acid)
if cmd.count_atoms("((%s) and name c)"%amino_acid,quiet=1):
cmd.edit("((%s) and name c)"%amino_acid)
else:
cmd.fragment(amino_acid,tmp_editor)
if cmd.count_atoms("((%s) and elem n)"%selection,quiet=1):
cmd.select(tmp_ed_save,"(%s)"%selection)
cmd.iterate("(%s)"%selection,"stored.resv=resv")
stored.resi = str(stored.resv-1)
cmd.alter(tmp_editor,"resi=stored.resi")
cmd.fuse("(%s and name C)"%(tmp_editor),"(pk1)",2)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(pkmol and hydro)")
cmd.set_dihedral("(name ca and neighbor pk2)",
"(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
cmd.set_geometry("pk2",3,3) # make nitrogen planer
# if ss:
cmd.select(tpk1,"pk2")
cmd.select(tpk2,"pk1")
if amino_acid[0:3]!='pro':
cmd.set_dihedral( # PHI
"(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
"(name ca and neighbor "+tpk1+")", # CA
tpk1, # N
tpk2, # C
phi)
cmd.set_dihedral( # PSI (n-1)
tpk1, # N
tpk2, # C
"(name ca and neighbor "+tpk2+")", # CA
"(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
psi)
cmd.delete(tpk1)
cmd.delete(tpk2)
sele = ("(name N and (byres neighbor %s) and not (byres %s))"%
(tmp_ed_save,tmp_ed_save))
if cmd.count_atoms(sele,quiet=1):
cmd.edit(sele)
cmd.delete(tmp_ed_save)
elif cmd.count_atoms("((%s) and elem c)"%selection,quiet=1):
cmd.select(tmp_ed_save,"(%s)"%selection)
cmd.iterate("(%s)"%selection,"stored.resv=resv")
stored.resi = str(stored.resv+1)
cmd.alter(tmp_editor,"resi=stored.resi")
cmd.fuse("(%s and name N)"%(tmp_editor),"(pk1)",2)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(pkmol and hydro)")
cmd.set_dihedral("(name ca and neighbor pk2)",
"(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
cmd.set_geometry("pk1",3,3) # make nitrogen planer
# if ss:
cmd.select(tpk1,"pk1")
cmd.select(tpk2,"pk2")
if amino_acid[0:3]!='pro':
cmd.set_dihedral( # PHI
tpk2, # C
tpk1, # N
"(name ca and neighbor "+tpk1+")", # CA
"(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
phi)
cmd.set_dihedral( # PSI (n-1)
"(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
"(name ca and neighbor "+tpk2+")", # CA
tpk2, # C
tpk1, # N
psi)
cmd.delete(tpk1)
cmd.delete(tpk2)
sele = ("(name C and (byres neighbor %s) and not (byres %s))"%
(tmp_ed_save,tmp_ed_save))
if cmd.count_atoms(sele,quiet=1):
cmd.edit(sele)
cmd.delete(tmp_ed_save)
elif cmd.count_atoms("((%s) and elem h)"%selection,quiet=1):
print " Error: please pick a nitrogen or carbonyl carbon to grow from."
cmd.delete(tmp_editor)
raise QuietException
cmd.delete(tmp_editor)
def __init__(self,_self=cmd):
Wizard.__init__(self,_self)
cmd=self.cmd
pymol=cmd._pymol
cmd.unpick()
self.dep = default_dep
self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+
"/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 = 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_legacy("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()