updated assembly

Tried reconfiguring the dictionary with connector to ipMT correspondance. The alternative list based solution has to be tested yet

SpindleAssembly/PositionConnectors.py

@@ -96,6 +96,7 @@ def pick_vertices(ConnectorData, **kwargs):
     v2 = []
     connector_point1 = []
     connector_point2 = []
+    # TODO: Resolve the issue with ipMT and connector sorting
     print(len(ConnectorDataSorted1))
     for value in ConnectorDataSorted1:
         for index in range(len(a.instances[value[1][0]])):
@@ -197,34 +198,3 @@ def connect_nodes(MTname1, MTname2, connectorname, i, modelname, a, MTnumber):
     region = mdb.models[modelname].rootAssembly.sets[ConnectionRegion]
     csa = a.SectionAssignment(sectionName=SectionName,
                               region=region)
-
-
-def connect_ipMT_pair( MTname1, MTname2, pos1, pos2, **kwargs ):
-    """
-    Connect two ipMTs via MT connectors. The connectors are attached to each ipMT at the
-    partition points
-    :param MTname1: name of the 1-st ipMT of the pair to be connected
-    :param MTname2 name of the 2-nd ipMT of the pair to be connected
-    :param pos1: (x, y, z) of the 1-st ipMT of the pair to be connected
-    :param pos2: (x, y, z) of the 2-nd ipMT of the pair to be connected
-    :param kwargs: dictionary -> keyword arguments
-    :return:
-    """
-    modelname = kwargs['modelname']
-
-    # Make each ipMT independent
-    a = ah.return_assembly(**kwargs)
-    a.makeIndependent(instances=(a.instances[MTname1],))
-    a.makeIndependent(instances=(a.instances[MTname2],))
-
-    # Generate partition points coordinates
-    z1, z2 = generate_connector_positions(pos1, pos2, **kwargs)
-
-    # Partition ipMT pair using generated partition points
-    partition_names1, partition_names2 = partiotion_MT_pair( MTname1, MTname2, z1, z2, **kwargs )
-
-    # Add and position connectors
-    connectornames = position_connectors(pos1, pos2, MTname1, MTname2, z1, **kwargs)
-
-    # Attach connectors
-    # attach_connectors(connectornames, MTname1, MTname2, **kwargs)

SpindleAssembly/assembly_random.py

@@ -74,23 +74,6 @@ def add_and_position_astral_mts(**kwargs):
     return aMTnames, kwargs
 
 
-# def partition_microtubules( **kwargs ):
-#     ipMTnames = kwargs['ipMTnames']
-#     modelname = kwargs['modelname']
-#
-#     # Partition each MT in the collection of ipMTs
-#     for name in ipMTnames:
-#         p = mdb.models[modelname].parts[name]
-#         e = p.edges
-#         pickedEdges = e.getSequenceFromMask(mask=('[#1 ]',), )
-#         p.PartitionEdgeByParam(edges=pickedEdges, parameter=0.5)
-#         p = mdb.models[modelname].parts[name]
-#         p.regenerate()
-#
-#     a = ac.return_assembly(**kwargs)
-#     a.regenerate()
-
-
 def assign_ipMTs(**kwargs):
     # Create dictionary to store MT metadata
     MTdata = {'MTnames': [],
@@ -205,6 +188,7 @@ def assign_ipMTs(**kwargs):
                                          MTname6, (pos6[0], pos6[1], z65[index], z65_global[index])]})
 
     # Create partitions that correspond to connector attachment sites
+    # TODO: Think if it is possible to use lists instead of dictionaries for simplicity
     MTpoints = {}
     for i in range(len(MTdata['MTnames'])):
         MTpoints.update({str(i+1): []})