def accept(self):
# accept compound and advance
if self.object is None:
print(" Filter-Error: Please choose an object first")
else:
state = cmd.get_object_state(self.object)
ident = self.get_ident(self.object,state)
print(" Filter: Accepting '%s'"%ident)
self.count(ident,accept_str)
cmd.forward()
cmd.refresh_wizard()
def defer(self):
# defer compound and advance
if self.object is None:
print(" Filter-Error: Please choose an object first")
else:
state = cmd.get_object_state(self.object)
ident = self.get_ident(self.object,state)
print(" Filter: Deferring '%s'"%ident)
self.check_object_dict()
self.count(ident,defer_str)
cmd.forward()
cmd.refresh_wizard()
def get_prompt(self):
# returns text prompt
self.prompt = None
if self.object is None:
self.prompt = [ 'Please select a multi-state object...' ]
else:
self.prompt = [ '%s: %d accepted, %d rejected, %d deferred, %d remaining'%(
self.object,self.acce,self.reje,self.defe,self.togo) ]
state = cmd.get_object_state(self.object)
ident = self.get_ident(self.object,state)
sdo=self.dict[self.object]
if ident in sdo:
self.prompt.append('%s: %s'%(ident,sdo[ident]))
else:
self.prompt.append('%s?'%(ident))
return self.prompt
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
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)
