def __init__(self):
self.prefs = preferences.addCategory("write PDB dialog",
preferences.HiddenCategory,
optDict={"multiSavePDB": "multiple"})
self.haveTraj = False
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("PDB", "*.pdb", ".pdb")])
openModels.addAddHandler(self._modelsChange, None),
openModels.addRemoveHandler(self._modelsChange, None)
self._modelsChange()
def __init__(self):
self.prefs = preferences.addCategory("write Mol2 dialog",
preferences.HiddenCategory,
optDict={"multiSaveMol2": "multiple",
"hydrogen naming": "sybyl",
"residue numbers": True})
SaveModeless.__init__(self, clientPos='s', clientSticky='ewns',
filters=[("Mol2", "*.mol2", ".mol2")])
openModels.addAddHandler(self._modelsChange, None)
openModels.addRemoveHandler(self._modelsChange, None)
self._modelsChange()
def listen(mode, what, prefix=None): from chimera import replyobj mode = findBestMatch(mode, ["start", "stop"]) what = findBestMatch(what, ["models", "selection"]) if what == "models": from chimera import openModels global modelHandler if mode == "start": if modelHandler is not None: msg = "already listening for models\n" else: if prefix is None: prefix = "ModelChanged" modelHandler = openModels.addAddHandler( _alertModel, prefix) msg = "listening for models\n" else: if modelHandler is None: msg = "not listening for models\n" else: openModels.deleteAddHandler(modelHandler) modelHandler = None msg = "stopped listening for models\n" replyobj.info(msg) elif what == "selection": import chimera global selectionHandler if mode == "start": if selectionHandler is not None: msg = "already listening for selection\n" else: if prefix is None: prefix = "SelectionChanged" selectionHandler = chimera.triggers.addHandler( "selection changed", _alertSelection, prefix) msg = "listening for selection\n" else: if selectionHandler is None: msg = "not listening for selection\n" else: chimera.triggers.deleteHandler( "selection changed", selectionHandler) selectionHandler = None msg = "stopped listening for selection\n" replyobj.info(msg)
def register_cap_handlers(self):
t = self.trigger_handlers
for (name, callback), handler in t.items():
if handler == None:
import chimera
h = chimera.triggers.addHandler(name, callback, None)
t[(name, callback)] = h
#
# Using SurfacePiece trigger instead of geometry change callback
# can lead to continuous updating when surface color auto-update is
# also used. Happens because trigger reasons are not associated
# with specific objects.
#
for s in self.surface_models():
s.addGeometryChangedCallback(self.geometry_changed_cb)
from chimera import openModels as om
self.new_model_handler = om.addAddHandler(self.new_model_cb, None)
def update_model(self, open=True):
create_volume = self.volume is None
if create_volume:
self.volume = self.make_model()
v = self.volume
v.set_array_coordinates(self.transform)
v.color_mode = self.c_mode
v.set_modulation_rgba(self.luminance_color())
v.projection_mode = self.p_mode
if self.dim_transparent_voxels:
bmode = v.SRC_ALPHA_DST_1_MINUS_ALPHA
else:
bmode = v.SRC_1_DST_1_MINUS_ALPHA
v.transparency_blend_mode = bmode
v.brightness_and_transparency_correction = self.bt_correction
v.minimal_texture_memory = self.minimal_texture_memory
v.maximum_intensity_projection = self.maximum_intensity_projection
v.linear_interpolation = self.linear_interpolation
v.show_outline_box = self.show_outline_box
v.outline_box_rgb = self.outline_box_rgb
v.outline_box_linewidth = self.outline_box_linewidth
if create_volume or self.update_colors:
self.update_colors = False
self.update_coloring()
self.volume.display = True
if create_volume and open:
am = self.attached_model
from chimera import openModels
if am and not am in openModels.list():
# Defer adding model to model list until attached model is added so
# that the solid model with have the same id number as attached model.
self.add_handler = openModels.addAddHandler(
self.open_model_cb, None)
else:
self.open_model()
def update_model(self, open = True):
create_volume = self.volume is None
if create_volume:
self.volume = self.make_model()
v = self.volume
v.set_array_coordinates(self.transform)
v.color_mode = self.c_mode
v.set_modulation_rgba(self.luminance_color())
v.projection_mode = self.p_mode
if self.dim_transparent_voxels:
bmode = v.SRC_ALPHA_DST_1_MINUS_ALPHA
else:
bmode = v.SRC_1_DST_1_MINUS_ALPHA
v.transparency_blend_mode = bmode
v.brightness_and_transparency_correction = self.bt_correction
v.minimal_texture_memory = self.minimal_texture_memory
v.maximum_intensity_projection = self.maximum_intensity_projection
v.linear_interpolation = self.linear_interpolation
v.show_outline_box = self.show_outline_box
v.outline_box_rgb = self.outline_box_rgb
v.outline_box_linewidth = self.outline_box_linewidth
if create_volume or self.update_colors:
self.update_colors = False
self.update_coloring()
self.volume.display = True
if create_volume and open:
am = self.attached_model
from chimera import openModels
if am and not am in openModels.list():
# Defer adding model to model list until attached model is added so
# that the solid model with have the same id number as attached model.
self.add_handler = openModels.addAddHandler(self.open_model_cb, None)
else:
self.open_model()
def fillInUI(self, parent):
self.last_xy = None
import Tkinter
from CGLtk import Hybrid
parent.columnconfigure(0, weight = 1)
row = 0
cr = Hybrid.Checkbutton(parent, 'Constrain mouse rotations', 0)
cr.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.constrain_rotations = cr.variable
cr.callback(self.constrain_rotation_cb)
raf = Tkinter.Frame(parent)
raf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
ra = Hybrid.Entry(raf, 'Axis ', 8, '0 0 1')
ra.frame.grid(row = 0, column = 0, sticky = 'w')
self.rot_axis = ra.variable
rotx_cb = lambda v=self.rot_axis: v.set('1 0 0')
roty_cb = lambda v=self.rot_axis: v.set('0 1 0')
rotz_cb = lambda v=self.rot_axis: v.set('0 0 1')
rab = Hybrid.Button_Row(raf, ' ',
(('x', rotx_cb),
('y', roty_cb),
('z', rotz_cb)))
rab.frame.grid(row = 0, column = 1, sticky = 'w')
rof = Tkinter.Frame(parent)
rof.grid(row = row, column = 0, sticky = 'w')
row = row + 1
ro = Hybrid.Entry(rof, 'Origin ', 8, '0 0 0')
ro.frame.grid(row = 0, column = 0, sticky = 'w')
self.rot_origin = ro.variable
zorigin_cb = lambda v=self.rot_origin: v.set('0 0 0')
rob = Hybrid.Button_Row(rof, ' ',
(('zero', zorigin_cb),
('center', self.set_rotation_origin_at_center),))
rob.frame.grid(row = 0, column = 1, sticky = 'w')
sep = Tkinter.Frame(parent, relief = Tkinter.GROOVE,
borderwidth=1, height=2)
sep.grid(row = row, column = 0, sticky = 'ew', pady = 10)
row = row + 1
tr = Hybrid.Checkbutton(parent, 'Constrain mouse translations', 0)
tr.button.grid(row = row, column = 0, sticky = 'w')
row = row + 1
self.constrain_translations = tr.variable
tr.callback(self.constrain_translation_cb)
taf = Tkinter.Frame(parent)
taf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
ta = Hybrid.Entry(taf, 'Axis ', 8, '0 0 1')
ta.frame.grid(row = 0, column = 0, sticky = 'w')
self.trans_axis = ta.variable
tx_cb = lambda v=self.trans_axis: v.set('1 0 0')
ty_cb = lambda v=self.trans_axis: v.set('0 1 0')
tz_cb = lambda v=self.trans_axis: v.set('0 0 1')
tab = Hybrid.Button_Row(taf, ' ',
(('x', tx_cb),
('y', ty_cb),
('z', tz_cb)))
tab.frame.grid(row = 0, column = 1, sticky = 'w')
ttf = Tkinter.Frame(parent)
ttf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
tt = Hybrid.Option_Menu(ttf, 'Allow only ',
'parallel', 'perpendicular')
tt.variable.set('parallel')
tt.frame.grid(row = 0, column = 0, sticky = 'w')
self.translation_type = tt.variable
tl = Tkinter.Label(ttf, text = ' motion')
tl.grid(row = 0, column = 1, sticky = 'w')
sep = Tkinter.Frame(parent, relief = Tkinter.GROOVE,
borderwidth=1, height=2)
sep.grid(row = row, column = 0, sticky = 'ew', pady = 10)
row = row + 1
rl = Tkinter.Label(parent, text = 'Axis and origin relative to')
rl.grid(row = row, column = 0, sticky = 'w')
row = row + 1
mmf = Tkinter.Frame(parent)
mmf.grid(row = row, column = 0, sticky = 'w')
row = row + 1
mm = Hybrid.Option_Menu(mmf, 'model ')
mm.frame.grid(row = 0, column = 0, sticky = 'w')
self.model_menu = mm
self.model_name = mm.variable
from chimera import openModels
openModels.addAddHandler(self.model_list_changed_cb, None)
openModels.addRemoveHandler(self.model_list_changed_cb, None)
ml = Tkinter.Label(mmf, text = ' coordinates.')
ml.grid(row = 0, column = 1, sticky = 'w')
self.update_model_menu()
self.register_mouse_modes()
def add_marker_set_opened_callback(self, cb):
if self.open_handler is None:
from chimera import openModels as om
self.open_handler = om.addAddHandler(self.open_models_cb, None)
self.open_callbacks.append(cb)