def solid_volume(vm):
from VolumeViewer import volume_list
for v in volume_list():
if vm in v.models():
return v
return None
def solid_volume(vm):
from VolumeViewer import volume_list
for v in volume_list():
if vm in v.models():
return v
return None
def make_molecule_map(atoms, resolution, step, pad, cutoff_range,
sigma_factor, display_threshold, model_id, replace,
show_dialog):
atoms = tuple(atoms)
grid, molecules = molecule_grid_data(atoms, resolution, step, pad,
cutoff_range, sigma_factor)
from chimera import openModels as om
if replace:
from VolumeViewer import volume_list
vlist = [v for v in volume_list()
if getattr(v, 'molmap_atoms', None) == atoms]
om.close(vlist)
from VolumeViewer import volume_from_grid_data
v = volume_from_grid_data(grid, open_model = False,
show_dialog = show_dialog)
v.initialize_thresholds(mfrac = (display_threshold, 1), replace = True)
v.show()
v.molmap_atoms = tuple(atoms) # Remember atoms used to calculate volume
v.molmap_parameters = (resolution, step, pad, cutoff_range, sigma_factor)
if len(molecules) == 1 and model_id is None:
om.add([v], sameAs = tuple(molecules)[0])
else:
if model_id is None:
model_id = (om.Default, om.Default)
om.add([v], baseId = model_id[0], subid = model_id[1])
v.openState.xform = atoms[0].molecule.openState.xform
return v
def make_molecule_map(atoms, resolution, step, pad, cutoff_range, sigma_factor,
display_threshold, model_id, replace, show_dialog):
atoms = tuple(atoms)
grid, molecules = molecule_grid_data(atoms, resolution, step, pad,
cutoff_range, sigma_factor)
from chimera import openModels as om
if replace:
from VolumeViewer import volume_list
vlist = [
v for v in volume_list()
if getattr(v, 'molmap_atoms', None) == atoms
]
om.close(vlist)
from VolumeViewer import volume_from_grid_data
v = volume_from_grid_data(grid, open_model=False, show_dialog=show_dialog)
v.initialize_thresholds(mfrac=(display_threshold, 1), replace=True)
v.show()
v.molmap_atoms = tuple(atoms) # Remember atoms used to calculate volume
v.molmap_parameters = (resolution, step, pad, cutoff_range, sigma_factor)
if len(molecules) == 1 and model_id is None:
om.add([v], sameAs=tuple(molecules)[0])
else:
if model_id is None:
model_id = (om.Default, om.Default)
om.add([v], baseId=model_id[0], subid=model_id[1])
v.openState.xform = atoms[0].molecule.openState.xform
return v
def find_simulated_map(self, atoms, res, mwm):
a = tuple(atoms)
from VolumeViewer import volume_list
for v in volume_list():
if hasattr(v, 'fitsim_params') and v.fitsim_params == (a, res, mwm):
return v
return None
def find_simulated_map(self, atoms, res, mwm):
a = tuple(atoms)
from VolumeViewer import volume_list
for v in volume_list():
if hasattr(v,
'fitsim_params') and v.fitsim_params == (a, res, mwm):
return v
return None
def interpolated_map(self, create=True):
v1 = self.map_menu_1.volume()
v2 = self.map_menu_2.volume()
if v1 is None or v2 is None:
self.message('Need to select two volume data sets.')
return None
im = None
mm = self.morph_maps
if (v1, v2) in mm:
im = mm[(v1, v2)]
# Check that volume is still opened in volume viewer.
from VolumeViewer import volume_list
if not im.result in volume_list():
im = None
else:
# Check that map size matches current v1 subregion
ijk_min, ijk_max = v1.region[:2]
v1_size = tuple(map(lambda a, b: b - a + 1, ijk_min, ijk_max))
if im.result.data.size != v1_size:
im = None
if not create and im is None:
return None
sf = (1.0, self.second_map_multiplier())
adj = self.adjust_thresholds.get()
am = self.add_maps.get()
if im is None:
if v1 == v2:
self.message('Two maps are the same.')
return None
if v1.data.size != v2.data.size:
self.message('Map sizes differ.')
return None
import morph
im = morph.Interpolated_Map((v1, v2),
scale_factors=sf,
adjust_thresholds=adj,
add_mode=am,
subregion=v1.region[:2])
mm[(v1, v2)] = mm[(v2, v1)] = im
else:
im.adjust_thresholds = adj
im.add_mode = am
im.scale_factors = sf
if self.undisplay_maps.get():
v1.unshow()
v2.unshow()
self.message('')
return im
def interpolated_map(self, create = True):
v1 = self.map_menu_1.volume()
v2 = self.map_menu_2.volume()
if v1 is None or v2 is None:
self.message('Need to select two volume data sets.')
return None
im = None
mm = self.morph_maps
if (v1,v2) in mm:
im = mm[(v1,v2)]
# Check that volume is still opened in volume viewer.
from VolumeViewer import volume_list
if not im.result in volume_list():
im = None
else:
# Check that map size matches current v1 subregion
ijk_min, ijk_max = v1.region[:2]
v1_size = tuple(map(lambda a,b: b-a+1, ijk_min, ijk_max))
if im.result.data.size != v1_size:
im = None
if not create and im is None:
return None
sf = (1.0, self.second_map_multiplier())
adj = self.adjust_thresholds.get()
am = self.add_maps.get()
if im is None:
if v1 == v2:
self.message('Two maps are the same.')
return None
if v1.data.size != v2.data.size:
self.message('Map sizes differ.')
return None
import morph
im = morph.Interpolated_Map((v1,v2), scale_factors = sf,
adjust_thresholds = adj,
add_mode = am,
subregion = v1.region[:2])
mm[(v1,v2)] = mm[(v2,v1)] = im
else:
im.adjust_thresholds = adj
im.add_mode = am
im.scale_factors = sf
if self.undisplay_maps.get():
v1.unshow()
v2.unshow()
self.message('')
return im
def data_regions_volume_viewer_list():
"""data_regions_volume_viewer_list()
Output:
data_regions list of Volume Viewer data regions
Return a list of data regions in Volume Viewer dialog, if it
is open, else return None.
"""
from VolumeViewer import volume_list
return volume_list()
def outline_box():
'Toggle outline boxes for selected volumes'
from VolumeViewer import volume_list, Volume
from chimera import selection
if selection.currentEmpty():
vlist = volume_list()
else:
vlist = [v for v in selection.currentGraphs() if isinstance(v, Volume)]
for v in vlist:
if v.display:
shown = v.rendering_options.show_outline_box
v.set_parameters(show_outline_box=not shown)
v.show()
def outline_box():
'Toggle outline boxes for selected volumes'
from VolumeViewer import volume_list, Volume
from chimera import selection
if selection.currentEmpty():
vlist = volume_list()
else:
vlist = [v for v in selection.currentGraphs() if isinstance(v, Volume)]
for v in vlist:
if v.display:
shown = v.rendering_options.show_outline_box
v.set_parameters(show_outline_box = not shown)
v.show()
def fillInUI(self, parent):
self.morph_maps = {} # Writable maps for pairs of end-point maps.
self.default_f_range = (0.0, 1.0, 0.1)
self.play_stop_button = self.buttonWidgets['Play']
import Tkinter
from CGLtk import Hybrid
frame = parent
frame.columnconfigure(0, weight=1)
row = 0
h = Tkinter.Label(parent, text='Interpolate between two maps')
h.grid(row=row, column=0, sticky='w')
row += 1
from VolumeViewer import volume_list, Volume_Menu
vlist = volume_list()
vm1 = Volume_Menu(parent,
'First map',
open_button=True,
show_on_open=True)
vm1.frame.grid(row=row, column=0, sticky='w')
if len(vlist) >= 1:
vm1.set_volume(vlist[0])
row += 1
self.map_menu_1 = vm1
vm2 = Volume_Menu(parent,
'Second map',
open_button=True,
show_on_open=True)
vm2.frame.grid(row=row, column=0, sticky='w')
if len(vlist) >= 2:
vm2.set_volume(vlist[1])
row += 1
self.map_menu_2 = vm2
self.scale = Hybrid.Scale(parent, 'Fraction ', 0.0, 1.0, 0.01, 0)
self.scale.frame.grid(row=row, column=0, sticky='ew')
self.scale.callback(self.scale_changed_cb)
self.scale.entry.bind('<KeyPress-Return>', self.scale_changed_cb)
row += 1
op = Hybrid.Popup_Panel(parent)
opf = op.frame
opf.grid(row=row, column=0, sticky='news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.options_panel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row=orow, column=1, sticky='e')
fr = Tkinter.Frame(opf)
fr.grid(row=orow, column=0, sticky='w')
orow += 1
fmin, fmax, fstep = self.default_f_range
fn = Hybrid.Entry(fr, 'Movie start ', 5, fmin)
fn.frame.grid(row=0, column=0, sticky='w')
fx = Hybrid.Entry(fr, ' end ', 5, fmax)
fx.frame.grid(row=0, column=1, sticky='w')
fs = Hybrid.Entry(fr, ' step ', 5, fstep)
fs.frame.grid(row=0, column=2, sticky='w')
self.f_range_variables = (fn.variable, fx.variable, fs.variable)
um = Hybrid.Checkbutton(opf, 'Undisplay original maps', True)
um.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.undisplay_maps = um.variable
mu = Hybrid.Checkbutton_Entries(opf, False,
'Multiplier for second map',
(4, '1.0'))
mu.frame.grid(row=orow, column=0, sticky='w')
orow += 1
self.use_multiplier, self.map_2_multiplier = mu.variables
ta = Hybrid.Checkbutton(opf, 'Adjust threshold for constant volume',
False)
ta.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.adjust_thresholds = ta.variable
am = Hybrid.Checkbutton(opf,
'Add to first map instead of interpolating',
False)
am.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.add_maps = am.variable
am.callback(self.add_mode_cb)
rt = Hybrid.Checkbutton(opf, 'Round trip when recording movie', True)
rt.button.grid(row=orow, column=0, sticky='w')
orow += 1
self.roundtrip = rt.variable
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width=40, anchor='w', justify='left')
msg.grid(row=row, column=0, sticky='ew')
row = row + 1
self.message_label = msg
def getMapInfo(model): from VolumeViewer import volume_list for v in volume_list(): if v.data.name == volume_name.strip(): return (v.data.size, v.data.origin) return (None, None)
def volume_data_set(model): from VolumeViewer import volume_list for v in volume_list(): if model in v.models(): return v return None
def fillInUI(self, parent ):
self.morph_maps = {} # Writable maps for pairs of end-point maps.
self.default_f_range = (0.0, 1.0, 0.1)
self.play_stop_button = self.buttonWidgets['Play']
import Tkinter
from CGLtk import Hybrid
frame = parent
frame.columnconfigure(0, weight = 1)
row = 0
h = Tkinter.Label(parent, text = 'Interpolate between two maps')
h.grid(row = row, column = 0, sticky = 'w')
row += 1
from VolumeViewer import volume_list, Volume_Menu
vlist = volume_list()
vm1 = Volume_Menu(parent, 'First map', open_button = True,
show_on_open = True)
vm1.frame.grid(row = row, column = 0, sticky = 'w')
if len(vlist) >= 1:
vm1.set_volume(vlist[0])
row += 1
self.map_menu_1 = vm1
vm2 = Volume_Menu(parent, 'Second map', open_button = True,
show_on_open = True)
vm2.frame.grid(row = row, column = 0, sticky = 'w')
if len(vlist) >= 2:
vm2.set_volume(vlist[1])
row += 1
self.map_menu_2 = vm2
self.scale = Hybrid.Scale(parent, 'Fraction ', 0.0, 1.0, 0.01, 0)
self.scale.frame.grid(row = row, column = 0, sticky = 'ew')
self.scale.callback(self.scale_changed_cb)
self.scale.entry.bind('<KeyPress-Return>', self.scale_changed_cb)
row += 1
op = Hybrid.Popup_Panel(parent)
opf = op.frame
opf.grid(row = row, column = 0, sticky = 'news')
opf.grid_remove()
opf.columnconfigure(0, weight=1)
self.options_panel = op.panel_shown_variable
row += 1
orow = 0
cb = op.make_close_button(opf)
cb.grid(row = orow, column = 1, sticky = 'e')
fr = Tkinter.Frame(opf)
fr.grid(row=orow, column=0, sticky='w')
orow += 1
fmin, fmax, fstep = self.default_f_range
fn = Hybrid.Entry(fr, 'Movie start ', 5, fmin)
fn.frame.grid(row=0, column=0, sticky='w')
fx = Hybrid.Entry(fr, ' end ', 5, fmax)
fx.frame.grid(row=0, column=1, sticky='w')
fs = Hybrid.Entry(fr, ' step ', 5, fstep)
fs.frame.grid(row=0, column=2, sticky='w')
self.f_range_variables = (fn.variable, fx.variable, fs.variable)
um = Hybrid.Checkbutton(opf, 'Undisplay original maps', True)
um.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.undisplay_maps = um.variable
mu = Hybrid.Checkbutton_Entries(opf, False, 'Multiplier for second map',
(4, '1.0'))
mu.frame.grid(row=orow, column=0, sticky='w')
orow += 1
self.use_multiplier, self.map_2_multiplier = mu.variables
ta = Hybrid.Checkbutton(opf, 'Adjust threshold for constant volume',
False)
ta.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.adjust_thresholds = ta.variable
am = Hybrid.Checkbutton(opf, 'Add to first map instead of interpolating',
False)
am.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.add_maps = am.variable
am.callback(self.add_mode_cb)
rt = Hybrid.Checkbutton(opf, 'Round trip when recording movie', True)
rt.button.grid(row = orow, column = 0, sticky = 'w')
orow += 1
self.roundtrip = rt.variable
#
# Specify a label width so dialog is not resized for long messages.
#
msg = Tkinter.Label(parent, width = 40, anchor = 'w', justify = 'left')
msg.grid(row = row, column = 0, sticky = 'ew')
row = row + 1
self.message_label = msg
