def apply(self):
cmd = self.cmd
pymol = cmd._pymol
if self.status == 1:
# find the name of the object which contains the selection
new_name = None
obj_list = cmd.get_names("objects")
for a in obj_list:
if cmd.get_type(a) == "object:molecule":
if cmd.count_atoms("(%s and %s)" % (a, src_sele)):
new_name = a
break
src_frame = cmd.get_state()
if new_name == None:
print " Mutagenesis: object not found."
else:
auto_zoom = cmd.get_setting_text("auto_zoom")
cmd.set("auto_zoom", "0", quiet=1)
if self.lib_mode != "current":
# create copy w/o residue
cmd.create(tmp_obj1, "(%s and not %s)" % (new_name, src_sele))
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)" % (tmp_obj1, src_sele))
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)" % (tmp_obj1, src_sele))
# save copy for bonded atom reference
cmd.create(tmp_obj3, new_name)
# transfer the selection to copy
cmd.select(src_sele, "(%s in %s)" % (tmp_obj3, src_sele))
# create copy with mutant in correct frame
cmd.create(tmp_obj2, obj_name, src_frame, 1)
cmd.set_title(tmp_obj2, 1, "")
cmd.delete(new_name)
# create the merged molecule
cmd.create(new_name, "(%s or %s)" % (tmp_obj1, tmp_obj2), 1) # only one state in merged object...
# now connect them
cmd.select(mut_sele, "(byres (%s like %s))" % (new_name, src_sele))
# bond N+0 to C-1
if (cmd.select(tmp_sele1, "(name C and (%s in (neighbor %s)))" % (new_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "((%s in %s) and n;N)" % (mut_sele, tmp_obj2)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.set_geometry(tmp_sele1, 3, 3) # make amide planer
cmd.set_geometry(tmp_sele2, 3, 3) # make amide planer
# bond C+0 to N+1
if (cmd.select(tmp_sele1, "(name N and (%s in (neighbor %s)))" % (new_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "((%s in %s) and n;C)" % (mut_sele, tmp_obj2)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.set_geometry(tmp_sele1, 3, 3) # make amide planer
cmd.set_geometry(tmp_sele2, 3, 3) # make amide planer
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
# fix N-H hydrogen position (if any exists)
cmd.h_fix("(name N and bound_to (%s in %s and n;H))" % (new_name, tmp_obj2))
# now transfer selection back to the modified object
cmd.delete(tmp_obj1)
cmd.delete(tmp_obj2)
cmd.delete(tmp_obj3)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2, obj_name, src_frame, 1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)" % (new_name, src_sele))
cmd.remove("(%s) and name OXT" % src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)" % (new_name, src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("(" + src_sele + ")")
# modify the conformation
cmd.update(new_name, tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set("auto_zoom", auto_zoom, quiet=1)
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 apply(self):
cmd=self.cmd
if self.status==1:
# find the name of the object which contains the selection
src_frame = cmd.get_state()
try:
new_name = cmd.get_object_list(src_sele)[0]
except IndexError:
print(" Mutagenesis: object not found.")
return
if True:
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
if self.lib_mode!="current":
# create copy with mutant in correct frame
state = cmd.get_object_state(new_name)
cmd.create(tmp_obj2, obj_name, src_frame, state)
cmd.set_title(tmp_obj2, state, '')
cmd.color(self.stored.identifiers[4], "?%s & elem C" % tmp_obj2)
cmd.alter(tmp_obj2, 'ID = -1')
# select backbone connection atoms
cmd.select(tmp_sele1, 'neighbor ?%s' % (src_sele), 0)
# remove residue and neighboring c-cap/n-cap (if any)
cmd.remove("?%s | byres (?%s & "
"(name N & resn NME+NHH | name C & resn ACE))" % (src_sele, tmp_sele1))
# create the merged molecule
cmd.create(new_name, "?%s | ?%s" % (new_name, tmp_obj2), state, state)
# now connect them
cmd.select(tmp_sele2, '/%s/%s/%s/%s' % ((new_name,) + self.stored.identifiers[:3]))
cmd.bond('?%s & name C' % (tmp_sele1), '?%s & name N' % (tmp_sele2), quiet=1)
cmd.bond('?%s & name N' % (tmp_sele1), '?%s & name C' % (tmp_sele2), quiet=1)
cmd.set_geometry('(?%s | ?%s) & name C+N' % (tmp_sele1, tmp_sele2), 3, 3) # make amide planer
# fix N-H hydrogen position (if any exists)
cmd.h_fix('?%s & name N' % (tmp_sele2))
# delete temporary objects/selections
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2,obj_name,src_frame,1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn NME+NHH)"%
(new_name,src_sele))
cmd.remove("(%s) and name OXT"%src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ACE)"%
(new_name,src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("("+src_sele+")")
# modify the conformation
cmd.update(new_name,tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set('auto_zoom',auto_zoom,quiet=1)
def apply(self):
cmd=self.cmd
pymol=cmd._pymol
if self.status==1:
# find the name of the object which contains the selection
new_name = None
obj_list = cmd.get_names('objects')
for a in obj_list:
if cmd.get_type(a)=="object:molecule":
if cmd.count_atoms("(%s and %s)"%(a,src_sele)):
new_name = a
break
src_frame = cmd.get_state()
if new_name==None:
print " Mutagenesis: object not found."
else:
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
if self.lib_mode!="current":
# create copy w/o residue
cmd.create(tmp_obj1,"(%s and not %s)"%(new_name,src_sele))
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)"%
(tmp_obj1,src_sele))
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)"%
(tmp_obj1,src_sele))
# save copy for bonded atom reference
cmd.create(tmp_obj3,new_name)
# transfer the selection to copy
cmd.select(src_sele,"(%s in %s)"%(tmp_obj3,src_sele))
# create copy with mutant in correct frame
cmd.create(tmp_obj2,obj_name,src_frame,1)
cmd.set_title(tmp_obj2,1,'')
cmd.delete(new_name)
# create the merged molecule
cmd.create(new_name,"(%s or %s)"%(tmp_obj1,tmp_obj2),1) # only one state in merged object...
# now connect them
cmd.select(mut_sele,"(byres (%s like %s))"%(new_name,src_sele))
# bond N+0 to C-1
if ((cmd.select(tmp_sele1, "(name C and (%s in (neighbor %s)))"%
(new_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "((%s in %s) and n;N)"%
(mut_sele,tmp_obj2)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.set_geometry(tmp_sele1,3,3) # make amide planer
cmd.set_geometry(tmp_sele2,3,3) # make amide planer
# bond C+0 to N+1
if ((cmd.select(tmp_sele1, "(name N and (%s in (neighbor %s)))"%
(new_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"((%s in %s) and n;C)"%
(mut_sele,tmp_obj2)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.set_geometry(tmp_sele1,3,3) # make amide planer
cmd.set_geometry(tmp_sele2,3,3) # make amide planer
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
# fix N-H hydrogen position (if any exists)
cmd.h_fix("(name N and bound_to (%s in %s and n;H))"%(new_name,tmp_obj2))
# now transfer selection back to the modified object
cmd.delete(tmp_obj1)
cmd.delete(tmp_obj2)
cmd.delete(tmp_obj3)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2,obj_name,src_frame,1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)"%
(new_name,src_sele))
cmd.remove("(%s) and name OXT"%src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)"%
(new_name,src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("("+src_sele+")")
# modify the conformation
cmd.update(new_name,tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set('auto_zoom',auto_zoom,quiet=1)
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 apply(self):
cmd=self.cmd
if self.status==1:
# find the name of the object which contains the selection
src_frame = cmd.get_state()
try:
new_name = cmd.get_object_list(src_sele)[0]
except IndexError:
print(" Mutagenesis: object not found.")
return
if True:
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
if self.lib_mode!="current":
# create copy with mutant in correct frame
state = cmd.get_object_state(new_name)
cmd.create(tmp_obj2, obj_name, src_frame, state)
cmd.set_title(tmp_obj2, state, '')
cmd.color(self.stored.identifiers[4], "?%s & elem C" % tmp_obj2)
cmd.alter(tmp_obj2, 'ID = -1')
# select backbone connection atoms
cmd.select(tmp_sele1, 'neighbor ?%s' % (src_sele), 0)
# remove residue and neighboring c-cap/n-cap (if any)
cmd.remove("?%s | byres (?%s & "
"(name N & resn NME+NHH | name C & resn ACE))" % (src_sele, tmp_sele1))
# create the merged molecule
cmd.create(new_name, "?%s | ?%s" % (new_name, tmp_obj2), state, state)
# now connect them
cmd.select(tmp_sele2, '/%s/%s/%s/%s' % ((new_name,) + self.stored.identifiers[:3]))
cmd.bond('?%s & name C' % (tmp_sele1), '?%s & name N' % (tmp_sele2), quiet=1)
cmd.bond('?%s & name N' % (tmp_sele1), '?%s & name C' % (tmp_sele2), quiet=1)
cmd.set_geometry('(?%s | ?%s) & name C+N' % (tmp_sele1, tmp_sele2), 3, 3) # make amide planer
# fix N-H hydrogen position (if any exists)
cmd.h_fix('?%s & name N' % (tmp_sele2))
# delete temporary objects/selections
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2,obj_name,src_frame,1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn NME+NHH)"%
(new_name,src_sele))
cmd.remove("(%s) and name OXT"%src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ACE)"%
(new_name,src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("("+src_sele+")")
# modify the conformation
cmd.update(new_name,tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set('auto_zoom',auto_zoom,quiet=1)
