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)