def show_curve(self,
radius=0,
band_length=0,
segment_subdivisions=10,
circle_subdivisions=15):
m = self.molecule
if m is None:
return
import tube
s, plist = tube.tube_through_atoms(m.atoms, radius, band_length,
segment_subdivisions,
circle_subdivisions)
if s is None:
return
s.name = 'path tracer curve'
self.curve_parameters = (radius, band_length, segment_subdivisions)
self.curve_model = s
from chimera import addModelClosedCallback
addModelClosedCallback(s, self.curve_model_closed_cb)
import SimpleSession
SimpleSession.noAutoRestore(s)
def show_cb(self, event=None, model_id=None):
radius = self.radius.value(self.default_radius)
sphere_factor = self.sphere_factor.value(0)
surface_style = self.surface_style.get()
orientation = self.orientation_name()
subdivision_levels = self.subdivision_levels(radius)
if self.surface_model == None:
import _surface
sm = _surface.SurfaceModel()
sm.name = 'Icosahedron'
self.surface_model = sm
import chimera
chimera.addModelClosedCallback(sm, self.surface_closed_cb)
self.surface_piece = None
from Icosahedron import make_icosahedron_surface
p = make_icosahedron_surface(radius, orientation, subdivision_levels,
sphere_factor, surface_style,
self.color.rgba, self.surface_model)
if self.surface_piece:
self.surface_model.removePiece(self.surface_piece)
else:
from chimera import openModels as om
if model_id is None:
id = subid = om.Default
else:
id, subid = model_id
om.add([self.surface_model], baseId=id, subid=subid)
self.surface_piece = p
def show_cb(self, event = None, model_id = None):
radius = self.radius.value(self.default_radius)
sphere_factor = self.sphere_factor.value(0)
surface_style = self.surface_style.get()
orientation = self.orientation_name()
subdivision_levels = self.subdivision_levels(radius)
if self.surface_model == None:
import _surface
sm = _surface.SurfaceModel()
sm.name = 'Icosahedron'
self.surface_model = sm
import chimera
chimera.addModelClosedCallback(sm, self.surface_closed_cb)
self.surface_piece = None
from Icosahedron import make_icosahedron_surface
p = make_icosahedron_surface(radius, orientation, subdivision_levels,
sphere_factor, surface_style, self.color.rgba,
self.surface_model)
if self.surface_piece:
self.surface_model.removePiece(self.surface_piece)
else:
from chimera import openModels as om
if model_id is None:
id = subid = om.Default
else:
id, subid = model_id
om.add([self.surface_model], baseId = id, subid = subid)
self.surface_piece = p
def create_box(self):
m = chimera.Molecule()
m.name = 'Subregion Selection Box'
chimera.openModels.add([m], noprefs=True)
chimera.addModelClosedCallback(m, self.model_closed_cb)
rid = chimera.MolResId(1)
r = m.newResidue('markers', rid)
corners = []
for name in ('a000', 'a001', 'a010', 'a011', 'a100', 'a101', 'a110',
'a111'):
a = m.newAtom(name, chimera.elements.H)
r.addAtom(a)
corners.append(a)
green = chimera.MaterialColor(0, 1, 0, 1)
for a1, a2 in ((0, 1), (2, 3), (4, 5), (6, 7), (0, 2), (1, 3), (4, 6),
(5, 7), (0, 4), (1, 5), (2, 6), (3, 7)):
b = m.newBond(corners[a1], corners[a2])
b.halfbond = 0
b.drawMode = chimera.Bond.Wire
b.color = green
return corners
def __init__(self,
molecule,
category,
probeRadius=1.4,
allComponents=True,
vertexDensity=2.0):
SurfaceModel.__init__(self)
name = 'MSMS %s surface of %s' % (category, molecule.name)
SurfaceModel.__setattr__(self, 'name', name)
SurfaceModel.__setattr__(self, 'piecesAreSelectable', True)
SurfaceModel.__setattr__(self, 'oneTransparentLayer', True)
init = {
'molecule': molecule,
'colorMode': self.ByAtom,
'visibilityMode': self.ByAtom,
'density': vertexDensity,
'probeRadius': probeRadius,
'category': category,
'allComponents': allComponents,
'atomMap': None, # vertex number to Atom
'surface_piece': None,
'srf': None, # MSMS surface object
'triData': None, # MSMS triangle data
'areaSES': 0.0,
'areaSAS': 0.0,
'calculationFailed': False,
}
self.__dict__.update(init)
from _surface import SurfacePiece
self.surface_piece_defaults = {
'drawMode': self.Filled,
'lineWidth': 1.0,
'pointSize': 1.0,
'useLighting': True,
'twoSidedLighting': True,
'smoothLines': False,
'transparencyBlendMode': SurfacePiece.SRC_ALPHA_DST_1_MINUS_ALPHA,
}
self.update_surface()
# Detect changes in atom color, atom surfaceColor, atom surfaceOpacity,
# molecule color, atom surfaceDisplay.
from chimera import triggers as t
self.molecule_handler = t.addHandler('Molecule', self.molecule_cb,
None)
# Detect when surface or molecule deleted.
from chimera import addModelClosedCallback
addModelClosedCallback(self, self.surface_closed_cb)
addModelClosedCallback(self.molecule, self.molecule_closed_cb)
import Surface
Surface.set_coloring_method('msms', self, self.custom_coloring)
Surface.set_visibility_method('msms', self, self.custom_visibility)
def make_model(self, length, thickness, rgb, label, xy_offset, label_rgb,
model_id):
m = chimera.Molecule()
m.name = 'scale bar'
#
# Need to create a residue because atom without residue causes
# unknown C++ exceptions.
#
rid = chimera.MolResId(1)
r = m.newResidue('sb', rid)
atoms = []
for name, pos in (('1', (-length / 2.0, 0, 0)), ('2', (length / 2.0, 0,
0)),
('label', (xy_offset[0],
xy_offset[1] + thickness / 2.0, 0))):
a = m.newAtom(name, chimera.elements.H)
r.addAtom(a)
c = chimera.Coord()
c.x, c.y, c.z = pos
a.setCoord(c) # a.coord = c does not work
a.display = 0
atoms.append(a)
m.atom1, m.atom2, m.label_atom = atoms
m.label_atom.color = background_color()
m.label_atom.display = 1
b = m.newBond(m.atom1, m.atom2)
b.display = b.Always
b.drawMode = b.Stick
b.radius = thickness / 2.0
b.color = chimera_color(rgb)
b.halfbond = 0
m.label_atom.label = label
m.label_atom.labelColor = chimera_color(label_rgb)
self.model = m
if model_id == None:
id, subid = (self.model_id(), chimera.openModels.Default)
else:
id, subid = model_id
chimera.openModels.add([m], baseId=id, subid=subid)
chimera.addModelClosedCallback(m, self.model_closed_cb)
import SimpleSession
SimpleSession.noAutoRestore(m)
m.openState.active = False
z_near, z_far = clip_plane_positions()
self.set_depth(.5 * (z_near + z_far))
self.set_screen_position(self.screen_position)
self.orientation_cb()
return m
def make_model(self, length, thickness, rgb, label, xy_offset, label_rgb,
model_id):
m = chimera.Molecule()
m.name = 'scale bar'
#
# Need to create a residue because atom without residue causes
# unknown C++ exceptions.
#
rid = chimera.MolResId(1)
r = m.newResidue('sb', rid)
atoms = []
for name, pos in (('1', (-length/2.0, 0, 0)),
('2', (length/2.0, 0, 0)),
('label',
(xy_offset[0], xy_offset[1] + thickness/2.0, 0))):
a = m.newAtom(name, chimera.elements.H)
r.addAtom(a)
c = chimera.Coord()
c.x, c.y, c.z = pos
a.setCoord(c) # a.coord = c does not work
a.display = 0
atoms.append(a)
m.atom1, m.atom2, m.label_atom = atoms
m.label_atom.color = background_color()
m.label_atom.display = 1
b = m.newBond(m.atom1, m.atom2)
b.display = b.Always
b.drawMode = b.Stick
b.radius = thickness/2.0
b.color = chimera_color(rgb)
b.halfbond = 0
m.label_atom.label = label
m.label_atom.labelColor = chimera_color(label_rgb)
self.model = m
if model_id == None:
id, subid = (self.model_id(), chimera.openModels.Default)
else:
id, subid = model_id
chimera.openModels.add([m], baseId = id, subid = subid)
chimera.addModelClosedCallback(m, self.model_closed_cb)
import SimpleSession
SimpleSession.noAutoRestore(m)
m.openState.active = False
z_near, z_far = clip_plane_positions()
self.set_depth(.5 * (z_near + z_far))
self.set_screen_position(self.screen_position)
self.orientation_cb()
return m
def auto_recolor(self, model, color_source, caps_only):
add_callback = not self.models.has_key(model)
self.models[model] = (color_source, caps_only)
from Surface import set_coloring_method
set_coloring_method('surface color', model, self.stop_coloring)
if add_callback:
model.addGeometryChangedCallback(self.surface_changed_cb)
from chimera import addModelClosedCallback
addModelClosedCallback(model, self.model_closed_cb)
def auto_dust(self, model, method, limit):
add_callback = not self.models.has_key(model)
self.models[model] = (method, limit)
from Surface import set_visibility_method
set_visibility_method('hide dust', model, self.stop_hiding_dust)
if add_callback:
model.addGeometryChangedCallback(self.surface_changed_cb)
import chimera
chimera.addModelClosedCallback(model, self.model_closed_cb)
def auto_zone(self, model, points, colors, distance):
add_callback = not self.models.has_key(model)
self.models[model] = (points, colors, distance)
from Surface import set_coloring_method
set_coloring_method('color zone', model, self.stop_zone)
if add_callback:
model.addGeometryChangedCallback(self.surface_changed_cb)
import chimera
chimera.addModelClosedCallback(model, self.model_closed_cb)
def auto_recolor(self, model, color_source, caps_only):
add_callback = not self.models.has_key(model)
self.models[model] = (color_source, caps_only)
from Surface import set_coloring_method
set_coloring_method('surface color', model, self.stop_coloring)
if add_callback:
model.addGeometryChangedCallback(self.surface_changed_cb)
from chimera import addModelClosedCallback
addModelClosedCallback(model, self.model_closed_cb)
def auto_zone(self, model, points, colors, distance):
add_callback = not self.models.has_key(model)
self.models[model] = (points, colors, distance)
from Surface import set_coloring_method
set_coloring_method('color zone', model, self.stop_zone)
if add_callback:
model.addGeometryChangedCallback(self.surface_changed_cb)
import chimera
chimera.addModelClosedCallback(model, self.model_closed_cb)
def auto_dust(self, model, method, limit):
add_callback = not self.models.has_key(model)
self.models[model] = (method, limit)
from Surface import set_visibility_method
set_visibility_method('hide dust', model, self.stop_hiding_dust)
if add_callback:
model.addGeometryChangedCallback(self.surface_changed_cb)
import chimera
chimera.addModelClosedCallback(model, self.model_closed_cb)
def __init__(self, molecule, category, probeRadius = 1.4,
allComponents = True, vertexDensity = 2.0):
SurfaceModel.__init__(self)
name = 'MSMS %s surface of %s' % (category, molecule.name)
SurfaceModel.__setattr__(self, 'name', name)
SurfaceModel.__setattr__(self, 'piecesAreSelectable', True)
SurfaceModel.__setattr__(self, 'oneTransparentLayer', True)
init = {
'molecule': molecule,
'colorMode': self.ByAtom,
'visibilityMode': self.ByAtom,
'density': vertexDensity,
'probeRadius': probeRadius,
'category': category,
'allComponents': allComponents,
'atomMap': None, # vertex number to Atom
'surface_piece': None,
'srf': None, # MSMS surface object
'triData': None, # MSMS triangle data
'areaSES': 0.0,
'areaSAS': 0.0,
'calculationFailed': False,
}
self.__dict__.update(init)
from _surface import SurfacePiece
self.surface_piece_defaults = {
'drawMode': self.Filled,
'lineWidth': 1.0,
'pointSize': 1.0,
'useLighting': True,
'twoSidedLighting': True,
'smoothLines': False,
'transparencyBlendMode': SurfacePiece.SRC_ALPHA_DST_1_MINUS_ALPHA,
}
self.update_surface()
# Detect changes in atom color, atom surfaceColor, atom surfaceOpacity,
# molecule color, atom surfaceDisplay.
from chimera import triggers as t
self.molecule_handler = t.addHandler('Molecule', self.molecule_cb, None)
# Detect when surface or molecule deleted.
from chimera import addModelClosedCallback
addModelClosedCallback(self, self.surface_closed_cb)
addModelClosedCallback(self.molecule, self.molecule_closed_cb)
import Surface
Surface.set_coloring_method('msms', self, self.custom_coloring)
Surface.set_visibility_method('msms', self, self.custom_visibility)
def __init__(self,
name,
matrix,
matrix_id,
transform,
align=None,
message_cb=None):
self.name = name
self.matrix = matrix
self.matrix_id = matrix_id # indicates if matrix changed
self.matrix_range = None
self.transform = transform
self.volume = None # Volume_Model
self.add_handler = None
from chimera import Model, addModelClosedCallback
if isinstance(align, Model):
self.attached_model = align
addModelClosedCallback(self.attached_model,
self.attached_model_closed_cb)
else:
self.attached_model = None
self.message_cb = message_cb
self.transfer_function = ()
self.brightness_factor = 1
self.transparency_depth = 0
self.colormap_size = 256
self.clamp = False
self.color_mode = 'auto8'
self.c_mode = 'rgba8'
self.projection_mode = 'auto'
self.p_mode = '2d-xyz'
self.use_plane_callback = True # Avoids allocating 3d color array
self.dim_transparent_voxels = True
self.bt_correction = False
self.minimal_texture_memory = False
self.maximum_intensity_projection = False
self.linear_interpolation = True
self.show_outline_box = True
self.outline_box_rgb = (1, 1, 1)
self.outline_box_linewidth = 1
self.update_colors = False
def settings_changed_cb(self, event=None):
if not self.have_phantom():
return
phantom_on = self.phantom_on.get()
if not phantom_on:
if self.cursor_model:
chimera.openModels.close([self.cursor_model])
return
phantom_range_mm = float_variable_value(self.phantom_range)
box_size_mm = (phantom_range_mm, phantom_range_mm, phantom_range_mm)
shape = self.cursor_shape.get()
from _phantomcursor import Cursor_Model
cursor_shape = {
'cross': Cursor_Model.Cross,
'jack': Cursor_Model.Jack,
'sphere': Cursor_Model.Sphere,
'volume crosshair': Cursor_Model.Cross,
}[shape]
cursor_size = float_variable_value(self.cursor_size)
r, g, b = self.cursor_color.rgb
cursor_color = chimera.MaterialColor(r, g, b)
pd = self.phantom_device
cm = self.cursor_model
if pd == None or cm == None:
pd, cm = self.make_phantom_cursor_model(box_size_mm, cursor_shape,
cursor_size, cursor_color)
self.phantom_device = pd
self.cursor_model = cm
chimera.addModelClosedCallback(cm, self.model_closed_cb)
else:
pd.box_size_mm = box_size_mm
cm.cursor_style = cursor_shape
cm.cursor_size = cursor_size
cm.cursor_color = cursor_color
crosshair_on = (self.cursor_shape.get() == 'volume crosshair')
cm.show_crosshair = crosshair_on
self.update_force_field()
def settings_changed_cb(self, event = None):
if not self.have_phantom():
return
phantom_on = self.phantom_on.get()
if not phantom_on:
if self.cursor_model:
chimera.openModels.close([self.cursor_model])
return
phantom_range_mm = float_variable_value(self.phantom_range)
box_size_mm = (phantom_range_mm, phantom_range_mm, phantom_range_mm)
shape = self.cursor_shape.get()
from _phantomcursor import Cursor_Model
cursor_shape = {'cross': Cursor_Model.Cross,
'jack': Cursor_Model.Jack,
'sphere': Cursor_Model.Sphere,
'volume crosshair': Cursor_Model.Cross,
}[shape]
cursor_size = float_variable_value(self.cursor_size)
r,g,b = self.cursor_color.rgb
cursor_color = chimera.MaterialColor(r,g,b)
pd = self.phantom_device
cm = self.cursor_model
if pd == None or cm == None:
pd, cm = self.make_phantom_cursor_model(box_size_mm, cursor_shape,
cursor_size, cursor_color)
self.phantom_device = pd
self.cursor_model = cm
chimera.addModelClosedCallback(cm, self.model_closed_cb)
else:
pd.box_size_mm = box_size_mm
cm.cursor_style = cursor_shape
cm.cursor_size = cursor_size
cm.cursor_color = cursor_color
crosshair_on = (self.cursor_shape.get() == 'volume crosshair')
cm.show_crosshair = crosshair_on
self.update_force_field()
def __init__(self, name, matrix, matrix_id, transform,
align = None, message_cb = None):
self.name = name
self.matrix = matrix
self.matrix_id = matrix_id # indicates if matrix changed
self.matrix_range = None
self.transform = transform
self.volume = None # Volume_Model
self.add_handler = None
from chimera import Model, addModelClosedCallback
if isinstance(align, Model):
self.attached_model = align
addModelClosedCallback(self.attached_model, self.attached_model_closed_cb)
else:
self.attached_model = None
self.message_cb = message_cb
self.transfer_function = ()
self.brightness_factor = 1
self.transparency_depth = 0
self.colormap_size = 256
self.clamp = False
self.color_mode = 'auto8'
self.c_mode = 'rgba8'
self.projection_mode = 'auto'
self.p_mode = '2d-xyz'
self.use_plane_callback = True # Avoids allocating 3d color array
self.dim_transparent_voxels = True
self.bt_correction = False
self.minimal_texture_memory = False
self.maximum_intensity_projection = False
self.linear_interpolation = True
self.show_outline_box = True
self.outline_box_rgb = (1,1,1)
self.outline_box_linewidth = 1
self.update_colors = False
def show_in_volume_viewer(self):
data_seq = list(self.data_sets)
data_seq.sort(lambda a,b: cmp(a.time, b.time))
from VolumeViewer import volume_from_grid_data
data_regions = [volume_from_grid_data(g, show_data = False)
for g in data_seq]
self.data_regions = list(data_regions)
# Add callbacks to detect when volume data sets are closed.
import chimera
for v in data_regions:
chimera.addModelClosedCallback(v, self.volume_closed)
if data_regions:
dr = data_regions[0]
from VolumeViewer import set_active_volume
set_active_volume(dr)
dr.initialize_thresholds()
dr.show()
def show_in_volume_viewer(self):
data_seq = list(self.data_sets)
data_seq.sort(lambda a, b: cmp(a.time, b.time))
from VolumeViewer import volume_from_grid_data
data_regions = [
volume_from_grid_data(g, show_data=False) for g in data_seq
]
self.data_regions = list(data_regions)
# Add callbacks to detect when volume data sets are closed.
import chimera
for v in data_regions:
chimera.addModelClosedCallback(v, self.volume_closed)
if data_regions:
dr = data_regions[0]
from VolumeViewer import set_active_volume
set_active_volume(dr)
dr.initialize_thresholds()
dr.show()
def open_model(self):
from chimera import openModels, addModelClosedCallback
openModels.add([self.volume], sameAs=self.attached_model)
addModelClosedCallback(self.volume, self.model_closed_cb)
def set_volume(self, volume):
self.volume = volume
from chimera import addModelClosedCallback
addModelClosedCallback(volume, self.volume_closed_cb)
def set_volume(self, volume):
self.volume = volume
from chimera import addModelClosedCallback
addModelClosedCallback(volume, self.volume_closed_cb)
def set_marker_molecule(self, mol):
self.molecule = mol
mol.marker_set = self
from chimera import addModelClosedCallback
addModelClosedCallback(mol, self.model_closed_cb)
def open_model(self):
from chimera import openModels, addModelClosedCallback
openModels.add([self.volume], sameAs = self.attached_model)
addModelClosedCallback(self.volume, self.model_closed_cb)