def execute(self, context):
dm = {}
dm['mcell'] = examples.variable_rate_constant.variable_rate_constant_dm
cellblender.replace_data_model(dm, geometry=True)
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.dynamic_geometry.dynamic_geometry_dm
cellblender.replace_data_model(dm, geometry=True, scripts=True)
# load object with shape keys from blend file
blendfile = os.path.join(os.path.dirname(__file__),
"./examples/dynamic_geometry.blend")
section = "/Object/"
obj = "Cube"
filepath = blendfile + section + obj
directory = blendfile + section
filename = obj
bpy.ops.wm.append(filepath=filepath,
filename=filename,
directory=directory)
# set it to be dynamic and make transparent
bpy.context.scene.mcell.model_objects.object_list[0].dynamic = True
bpy.data.objects["Cube"].show_transparent = True
bpy.data.materials["Cube_mat"].use_transparency = True
bpy.data.materials["Cube_mat"].alpha = 0.2
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.direct_transport_BNGL.direct_transport_bngl_dm
cellblender.replace_data_model(dm, geometry=True)
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.lipid_raft.lipid_raft_dm
cellblender.replace_data_model(dm, geometry=True)
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.mind_mine_system.mind_mine_dm
cellblender.replace_data_model(dm, geometry=True)
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.ficks_laws.ficks_law_3D_dm
cellblender.replace_data_model(dm, geometry=True, scripts=True)
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.tlbr_mcell3r.tlbr_mcell3r_dm
cellblender.replace_data_model(dm, geometry=True, scripts=False)
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.simple_coil_mcell3r.simple_coil_mcell3r_dm
cellblender.replace_data_model(dm, geometry=True)
view_all()
bpy.ops.view3d.viewnumpad(type='TOP')
hide_manipulator(hide=True)
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.pbc.pbc_dm
clear_texts()
mdl_name = 'pbc.mdl'
pbc_txt = bpy.data.texts.new(mdl_name)
pbc_txt.write(dm['mcell']['scripting']['script_texts'][mdl_name])
cellblender.replace_data_model(dm, geometry=True)
bpy.ops.view3d.snap_cursor_to_center()
bpy.ops.mesh.primitive_cube_add()
bpy.context.scene.objects.active.scale = (0.5, 0.1, 0.1)
bpy.context.object.draw_type = 'WIRE'
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.rat_nmj.rat_nmj_dm
clear_texts()
param_mdl_name = 'rat_nmj.parameters.mdl'
parameters_txt = bpy.data.texts.new(param_mdl_name)
parameters_txt.write(
dm['mcell']['scripting']['script_texts'][param_mdl_name])
release_mdl_name = 'rat_nmj.release_sites.mdl'
release_sites_txt = bpy.data.texts.new(release_mdl_name)
release_sites_txt.write(
dm['mcell']['scripting']['script_texts'][release_mdl_name])
cellblender.replace_data_model(dm, geometry=True)
view_all()
return {'FINISHED'}
def execute(self, context):
dm = {}
dm['mcell'] = examples.dyn_geo_conc_clamp.dyn_geo_cc_dm
cellblender.replace_data_model(dm, geometry=True, scripts=True)
# Default frame_start is 1, set to 0 to match model
context.scene.frame_start = 0
context.scene.update()
# Set the frame to 50 (large cube) so the view all operator will fit at max size (not really needed for scripting)
context.scene.frame_current = 50
# Set the view to show the selected object
context.scene.update()
# Add a cube tepmorarily to use for centering the view
bpy.ops.mesh.primitive_cube_add()
bpy.context.scene.objects.active.location.z = 3
view_all()
# This zooming seems to have no effect
# zoom_view(-500)
# Remove the temporary cube that was used for centering the view
bpy.ops.object.delete(use_global=False)
# Re-select the original cube
bpy.data.objects[
'Cube'].select = True # This selects it (enables manipulator on the object)
context.scene.objects.active = bpy.data.objects[
'Cube'] # This makes it active for material display etc
# Return the current frame to 0 (small cube) after viewing large cube (not really needed for scripting)
context.scene.frame_current = 0
return {'FINISHED'}
def execute(self, context):
# Start by loading the data model and placing into CellBlender properties
dm = {}
dm['mcell'] = examples.shape_key_dyn_geo.shape_key_dyn_geo_dm
cellblender.replace_data_model(dm, geometry=True, scripts=False)
# Select the Cube object (created by the data model)
obj = bpy.data.objects['Cube']
obj.select = True
context.scene.objects.active = obj
# Remove all previous shape keys (otherwise this can't be run twice!!)
# Suggestion from cmomoney:
# https://blenderartists.org/forum/showthread.php?243733-Shape-Key-Removal&p=3177866&viewfull=1#post3177866
#if obj.data.shape_keys:
# This is never executed because obj.data.shape_keys is None
# The problem isn't how to delete from the object, but how to delete from bpy.data.shape_keys
# for k in obj.data.shape_keys.key_blocks:
# obj.shape_key_remove(k)
# https://blender.stackexchange.com/questions/27193/how-do-i-delete-one-single-shape-key
# Shape keys can be added and deleted through the Properties editor (the on the right ) under the Data tab in Shape keys.
# Note that you have to be in Object Mode for this to work... otherwise the minus sign will be greyed out!
# https://blenderartists.org/forum/showthread.php?283867-Delete-All-Shape-Keys
# Try this in the python console:
# [bpy.ops.object.shape_key_remove() for x in range(50)]
# It's a hack, but it should work!
# https://blenderartists.org/forum/showthread.php?233730-delete-shape-key-by-name-via-python
# delete shape key by name via python
# Q. how to delete shapekey by name from python...
# foreach_get_howto.jpgforeach_get_howto.jpg
# i can get shapekey names via
# #### iterate over existing shapekeys
# obj = bpy.context.object
# sk = obj.data.shape_keys
# skNamesArr = sk.key_blocks
# for each in skNamesArr:
# print each
# ##########################
# #### adding shape keys
# obj.shape_key_add("nameStr")
# ##########################
# #### removing by name seems hard...
# bpy.ops.object.shape_key_remove() # this will remove selected shape key.
# # how to give it parameter/ datapath from above lines(where i m iterating over sk)
# or how to select a shapekey from list by name, ??
# another question(thanks in advance for taking time n helping me out)
# Q. how to use function "foreach_get" or "foreach_set" in most of blender returned data objects.??
#you could wrap it like this:
#Code:
#import bpy
#def deleteShapekeyByName(oObject, sShapekeyName):
#
# # setting the active shapekey
# iIndex = oObject.data.shape_keys.key_blocks.keys().index(sShapekeyName)
# oObject.active_shape_key_index = iIndex
#
# # delete it
# bpy.ops.object.shape_key_remove()
#
#oActiveObject = bpy.context.active_object
#deleteShapekeyByName(oActiveObject, "MyShapeKey")
try:
# This currently fails with:
# RuntimeError: Operator bpy.ops.object.shape_key_remove.poll() failed, context is incorrect
# Keep it here until we figure out how to make it work!!
bpy.ops.object.shape_key_remove(all=True)
except:
pass
# Add two shape keys
bpy.ops.object.shape_key_add(from_mix=False) # Adds "Basis" Shape Key
bpy.ops.object.shape_key_add(from_mix=False) # Adds "Key 1" Shape Key
# Temp fix - this works,
# but additional shape keys are added to:
# bpy.data.shape_keys.keys
# every time the example is loaded.
# key_to_modify = bpy.data.shape_keys['Key']
key_to_modify = bpy.data.shape_keys[-1]
print("Current bpy.data.shape_keys.keys() = " +
str(bpy.data.shape_keys.keys()))
# Enter Edit Mode and deselect all
bpy.ops.object.mode_set(mode="EDIT")
bpy.ops.mesh.select_all(action='DESELECT')
# Move the top 4 points when on "Key 1" (the default key after the previous adds)
obj = context.object
mesh = obj.data
bm = bmesh.from_edit_mesh(mesh)
bm.verts.ensure_lookup_table()
verts = bm.verts
for v in verts:
if v.co[2] > 0:
# This is a positive (top) vertex so stretch it
v.co[0] = v.co[0] * 0.25
v.co[1] = v.co[1] * 0.25
v.co[2] = 3.0
bmesh.update_edit_mesh(mesh)
# Return to Object Mode
bpy.ops.object.mode_set(mode="OBJECT")
# Default frame_start is 1, set to 0 to match shape key assignments
context.scene.frame_start = 0
# Assign the shape keys to complete one cycle every 100 frames
context.scene.frame_current = 0
key_to_modify.key_blocks["Key 1"].value = 0.0
mesh.shape_keys.key_blocks['Key 1'].keyframe_insert(data_path='value')
context.scene.frame_current = 100
key_to_modify.key_blocks["Key 1"].value = 1.0
mesh.shape_keys.key_blocks['Key 1'].keyframe_insert(data_path='value')
context.scene.frame_current = 200
key_to_modify.key_blocks["Key 1"].value = 0.0
mesh.shape_keys.key_blocks['Key 1'].keyframe_insert(data_path='value')
# Set the frame to 50 (large cube) so the view all operator will fit at max size
context.scene.frame_current = 100
# Switch area type to set the F-Curve modifier to "CYCLES"
area = bpy.context.area
old_type = area.type
area.type = 'GRAPH_EDITOR'
bpy.ops.graph.fmodifier_add(type='CYCLES')
area.type = old_type
# Set the view to show the selected object
context.scene.update()
view_all()
# Return the current frame to 0 (small cube) after viewing large cube
context.scene.frame_current = 0
return {'FINISHED'}
'data_model_version' : "DM_2014_10_24_1638",
'fwd_rate' : "fr",
'name' : "r_%d -> NULL" % (i+1),
'products' : "NULL",
'reactants' : "m_%d" % ((i%nmols)+1),
'rxn_name' : "",
'rxn_type' : "irreversible",
'variable_rate' : "",
'variable_rate_switch' : False,
'variable_rate_text' : "",
'variable_rate_valid' : False
}
rlist.append ( r )
i += 1
path += delta
mcell['initialization']['iterations'] = str(i)
patterns['release_pattern_list'] = plist
mcell['define_release_patterns'] = patterns
sites['release_site_list'] = slist
mcell['release_sites'] = sites
reactions['reaction_list'] = rlist
mcell['define_reactions'] = reactions
mcell['geometrical_objects'] = { 'object_list' : [] }
mcell['model_objects'] = { 'data_model_version' : "DM_2014_10_24_1638", 'model_object_list' : [] }
cb.replace_data_model ( dm, geometry=True )
