def setAtoms(self, atomlist): #bruce 080208 split this out of __init__ so copy is simpler
Jig.setAtoms(self, atomlist)
if len(atomlist) == _NUMBER_OF_MARKER_ATOMS:
marked_atom, next_atom = atomlist
self.marked_atom = marked_atom
self.next_atom = next_atom
assert not self._length_1_chain
elif len(atomlist) == 1 and self._length_1_chain:
#bruce 080216, for 1-atom wholechains
# (the flag test is to make sure it's only used then)
self.marked_atom = self.next_atom = atomlist[0]
else:
# We are probably being called by _copy_fixup_at_end
# with fewer or no atoms, or by __init__ in first stage of copy
# (Jig.copy_full_in_mapping) with no atoms.
# todo: would be better to make those callers tell us for sure.
# for now: print bug warning if fewer atoms but not none
# (i don't know if that can happen), and assert not too many atoms.
assert len(atomlist) <= _NUMBER_OF_MARKER_ATOMS
if atomlist:
print "bug? %r.setAtoms(%r), len != _NUMBER_OF_MARKER_ATOMS or 0" % \
(self, atomlist)
self.marked_atom = self.next_atom = None #bruce 080216
self._check_atom_order() #bruce 080216 do in all cases, was just main one
return
def setAtoms(
self, atomlist
): #bruce 080208 split this out of __init__ so copy is simpler
Jig.setAtoms(self, atomlist)
if len(atomlist) == _NUMBER_OF_MARKER_ATOMS:
marked_atom, next_atom = atomlist
self.marked_atom = marked_atom
self.next_atom = next_atom
assert not self._length_1_chain
elif len(atomlist) == 1 and self._length_1_chain:
#bruce 080216, for 1-atom wholechains
# (the flag test is to make sure it's only used then)
self.marked_atom = self.next_atom = atomlist[0]
else:
# We are probably being called by _copy_fixup_at_end
# with fewer or no atoms, or by __init__ in first stage of copy
# (Jig.copy_full_in_mapping) with no atoms.
# todo: would be better to make those callers tell us for sure.
# for now: print bug warning if fewer atoms but not none
# (i don't know if that can happen), and assert not too many atoms.
assert len(atomlist) <= _NUMBER_OF_MARKER_ATOMS
if atomlist:
print "bug? %r.setAtoms(%r), len != _NUMBER_OF_MARKER_ATOMS or 0" % \
(self, atomlist)
self.marked_atom = self.next_atom = None #bruce 080216
self._check_atom_order(
) #bruce 080216 do in all cases, was just main one
return
def readmmp_info_leaf_setitem(self, key, val, interp):
import string, Numeric
if key == ['handle']:
self.handle_offset = Numeric.array(map(
string.atof, val.split())) - self.center()
else:
Jig.readmmp_info_leaf_setitem(self, key, val, interp)
def __init__(self, assy, atomlist):
Jig.__init__(self, assy, atomlist)
self.font_name = "Helvetica"
self.font_size = 10.0 # pt size
self.color = black # This is the "draw" color. When selected, this will become highlighted red.
self.normcolor = black # This is the normal (unselected) color.
self.cancelled = True # We will assume the user will cancel
self.handle_offset = V(0.0, 0.0, 0.0)
def __init__(self, assy, atomlist):
Jig.__init__(self, assy, atomlist)
self.font_name = "Helvetica"
self.font_size = 10.0 # pt size
self.color = black # This is the "draw" color. When selected, this will become highlighted red.
self.normcolor = black # This is the normal (unselected) color.
self.cancelled = True # We will assume the user will cancel
self.handle_offset = V(0.0, 0.0, 0.0)
def edit(self): # in class ESPImage
"""
Force into 'Build' mode before opening the dialog
"""
#bruce 060403 changes: force Build, not Select Atoms as before; only do this if current mode is not Build.
# (But why do we need to force it into any particular mode? I don't know. [bruce 070608])
commandSequencer = self.assy.w.commandSequencer #bruce 071008
if commandSequencer.currentCommand.commandName != 'DEPOSIT':
commandSequencer.userEnterCommand('DEPOSIT')
Jig.edit(self)
def edit(self): # in class ESPImage
"""
Force into 'Build' mode before opening the dialog
"""
#bruce 060403 changes: force Build, not Select Atoms as before; only do this if current mode is not Build.
# (But why do we need to force it into any particular mode? I don't know. [bruce 070608])
commandSequencer = self.assy.w.commandSequencer #bruce 071008
if commandSequencer.currentCommand.commandName != 'DEPOSIT':
commandSequencer.userEnterCommand('DEPOSIT')
Jig.edit(self)
def __init__(self, assy, list, READ_FROM_MMP):
Jig.__init__(self, assy, list)
self.width = 20
self.height = 20
self.assy = assy
self.cancelled = True # We will assume the user will cancel
self.atomPos = []
if not READ_FROM_MMP:
self.__init_quat_center(list)
def __init__(self, assy, list, READ_FROM_MMP):
Jig.__init__(self, assy, list)
self.width = 20
self.height = 20
self.assy = assy
self.cancelled = True # We will assume the user will cancel
self.atomPos = []
if not READ_FROM_MMP:
self.__init_quat_center(list)
def __init__(self, assy, atomlist = []): #bruce 050526 added optional atomlist arg
assert atomlist == [] # whether from default arg value or from caller -- for now
Jig.__init__(self, assy, atomlist)
self.quat = Q(1, 0, 0, 0)
# is self.quat ever set to other values? if not, remove it; if so, add it to mutable_attrs. [bruce 060228 comment]
#The motor is usually drawn as an opaque object. However when it is
#being previewed, it is drawn as a transparent object - Ninad 2007-10-09
self.previewOpacity = 0.4
self.defaultOpacity = 1.0
self.opacity = self.defaultOpacity
def __init__(self, win):
self.win = win
#Node.__init__(self, win.assy, gensym("%s" % self.sym, win.assy))
Jig.__init__(self, win.assy, self.atoms) # note: that sets self.glname
self.glpane = self.assy.o
#@@Geometry object with a visible direction arrow
#(at present used in Plane only) This saves the last geometry object
#for which the Direction arrow was drawn
#(that decides the direction of a plane offset to the object)
#The program needs to skip the arrow drawing (which is done inside the
# objects _draw_geometry method) when prop manager is closed or when the
#Offset option is no more requested. -- ninad 20070612
self.offsetParentGeometry = None
def __init__(self, assy, list):
Jig.__init__(self, assy, list)
self.cancelled = False
# set default color of new gamess jig to magenta
self.color = magenta # This is the "draw" color. When selected, this will become highlighted red.
self.normcolor = magenta # This is the normal (unselected) color.
#bruce 050913 thinks self.history is no longer needed:
## self.history = env.history
#self.psets = [] # list of parms set objects [as of circa 050704, only the first of these is ever defined (thinks bruce)]
self.pset = gamessParms('Parameter Set 1')
self.gmsjob = GamessJob(Gamess.job_parms, jig=self)
## bruce 050701 removing this: self.gmsjob.edit()
self.outputfile = '' # Name of jig's most recent output file. [this attr is intentionally not copied -- bruce 050704]
def __init__(self, assy, list):
Jig.__init__(self, assy, list)
self.cancelled = False
# set default color of new gamess jig to magenta
self.color = magenta # This is the "draw" color. When selected, this will become highlighted red.
self.normcolor = magenta # This is the normal (unselected) color.
#bruce 050913 thinks self.history is no longer needed:
## self.history = env.history
#self.psets = [] # list of parms set objects [as of circa 050704, only the first of these is ever defined (thinks bruce)]
self.pset = gamessParms('Parameter Set 1')
self.gmsjob = GamessJob(Gamess.job_parms, jig=self)
## bruce 050701 removing this: self.gmsjob.edit()
self.outputfile = '' # Name of jig's most recent output file. [this attr is intentionally not copied -- bruce 050704]
def __init__(self, win):
self.win = win
#Node.__init__(self, win.assy, gensym("%s" % self.sym, win.assy))
Jig.__init__(self, win.assy, self.atoms) # note: that sets self.glname
self.glpane = self.assy.o
#@@Geometry object with a visible direction arrow
#(at present used in Plane only) This saves the last geometry object
#for which the Direction arrow was drawn
#(that decides the direction of a plane offset to the object)
#The program needs to skip the arrow drawing (which is done inside the
# objects _draw_geometry method) when prop manager is closed or when the
#Offset option is no more requested. -- ninad 20070612
self.offsetParentGeometry = None
def is_disabled(self):
"""
Which is called when model tree is updated?
"""
val = Jig.is_disabled(self)
self.gmsjob.edit_cntl.run_job_btn.setEnabled(not val)
return val
def is_disabled(self):
"""
Which is called when model tree is updated?
"""
val = Jig.is_disabled(self)
self.gmsjob.edit_cntl.run_job_btn.setEnabled(not val)
return val
def __init__(self, assy, atomlist):
"""
"""
if len(atomlist) == 2 and atomlist[0] is atomlist[1]:
# let caller pass two atoms the same, but reduce it to one copy
# (compensating in setAtoms)
# (this is to make length-1 wholechains easier) [bruce 080216]
atomlist = atomlist[:1]
self._length_1_chain = True
elif len(atomlist) == 1:
# [bruce 080227 to support mmp read of 1-atom case]
# TODO: print warning unless this is called from mmp read
# (which is the only time it's not an error, AFAIK)
# and mark self invalid unless we verify that marked_atom
# is indeed on a length-1 chain (this might need to be
# done later by dna updater).
self._length_1_chain = True
Jig.__init__(self, assy, atomlist) # calls self.setAtoms
return
def __init__(self, assy, atomlist):
"""
"""
if len(atomlist) == 2 and atomlist[0] is atomlist[1]:
# let caller pass two atoms the same, but reduce it to one copy
# (compensating in setAtoms)
# (this is to make length-1 wholechains easier) [bruce 080216]
atomlist = atomlist[:1]
self._length_1_chain = True
elif len(atomlist) == 1:
# [bruce 080227 to support mmp read of 1-atom case]
# TODO: print warning unless this is called from mmp read
# (which is the only time it's not an error, AFAIK)
# and mark self invalid unless we verify that marked_atom
# is indeed on a length-1 chain (this might need to be
# done later by dna updater).
self._length_1_chain = True
Jig.__init__(self, assy, atomlist) # calls self.setAtoms
return
def make_selobj_cmenu_items(self, menu_spec):
"""
Add Motor-specific context menu items to <menu_spec> list when self is the selobj.
"""
Jig.make_selobj_cmenu_items(self, menu_spec)
#bruce 060313 share this code (it is identical to the following commented out code)
## item = ('Hide', self.Hide)
## menu_spec.append(item)
## if self.disabled_by_user_choice:
## item = ('Disabled', self.toggleJigDisabled, 'checked')
## else:
## item = ('Disable', self.toggleJigDisabled, 'unchecked')
## menu_spec.append(item)
## menu_spec.append(None) # Separator
## item = ('Properties...', self.edit)
## menu_spec.append(item)
item = ('Align to Chunk', self.__CM_Align_to_chunk)
menu_spec.append(item)
item = ('Recenter on Atoms', self.__CM_Recenter_on_atoms)
menu_spec.append(item)
item = ('Reverse Direction', self.__CM_Reverse_direction)
menu_spec.append(item)
def writemmp(self, mapping):
"""
[extends superclass method]
"""
# check a few things, then call superclass method
try:
assert not self.is_homeless() # redundant as of 080111, that's ok
assert len(self.atoms) in (1, _NUMBER_OF_MARKER_ATOMS)
self._check_atom_order()
except:
#bruce 080317, for debugging the save file traceback in
# "assert not self.is_homeless()" (above) in bug 2673,
# happens when saving after region select + delete of any
# duplex; fixed now
msg = "\n*** BUG: exception in checks before DnaMarker.writemmp; " \
"continuing, but beware of errors when reopening the file"
print_compact_traceback( msg + ": ")
pass
return Jig.writemmp(self, mapping)
def writemmp(self, mapping):
"""
[extends superclass method]
"""
# check a few things, then call superclass method
try:
assert not self.is_homeless() # redundant as of 080111, that's ok
assert len(self.atoms) in (1, _NUMBER_OF_MARKER_ATOMS)
self._check_atom_order()
except:
#bruce 080317, for debugging the save file traceback in
# "assert not self.is_homeless()" (above) in bug 2673,
# happens when saving after region select + delete of any
# duplex; fixed now
msg = "\n*** BUG: exception in checks before DnaMarker.writemmp; " \
"continuing, but beware of errors when reopening the file"
print_compact_traceback(msg + ": ")
pass
return Jig.writemmp(self, mapping)
def __CM_Calculate_Energy__options(self):
if Jig.is_disabled(self):
return ['disabled']
else:
return []
pass
def __CM_Optimize_Geometry__options(self):
if Jig.is_disabled(self):
return ['disabled']
else:
return []
def __CM_Calculate_Energy__options(self):
if Jig.is_disabled(self):
return ['disabled']
else:
return []
pass
def readmmp_info_leaf_setitem(self, key, val, interp):
import string, numpy.oldnumeric
if key == ['handle']:
self.handle_offset = Numeric.array(map(string.atof, val.split())) - self.center()
else:
Jig.readmmp_info_leaf_setitem(self, key, val, interp)
def __CM_Optimize_Geometry__options(self):
if Jig.is_disabled(self):
return ['disabled']
else:
return []
def remove_atom(self, *args, **opts):
self._initial_posns = None #bruce 050518; needed in RotaryMotor, harmless in others
return Jig.remove_atom(self, *args, **opts)
