from Parts import standard_parts as sparts
from Parts import GeometryBuilder as gb
from abaqus import *
from abaqusConstants import *
import math
[docs]def return_assembly(**kwargs):
"""
Return the current assembly
:param kwargs: object
:return: a -> (object) current assembly
"""
modelname = kwargs['modelname']
a = mdb.models[modelname].rootAssembly
return a
[docs]def add_centrosome(position, **kwargs):
"""
Generate and add centrosome
:param position: 'right' or 'left' -> positioning of centrosome in the spindle
:param kwargs: object
:return: Null
"""
modelname = kwargs['modelname']
if position == 'right':
sparts.centrosome(**kwargs)
p = mdb.models[modelname].parts['centrosome']
a = return_assembly(**kwargs)
a.Instance(name='centrosome-right', part=p, dependent=ON)
a = mdb.models[modelname].rootAssembly
a.rotate(
instanceList=('centrosome-right',),
axisPoint=(0.0, 0.0, 0.0),
axisDirection=(1.0, 0.0, 0.0),
angle=90)
elif position == 'left':
sparts.centrosome(**kwargs)
p = mdb.models[modelname].parts['centrosome']
a = return_assembly(**kwargs)
a.Instance(name='centrosome-left', part=p, dependent=ON)
a = mdb.models[modelname].rootAssembly
# Translate left centrosome and position it at the left pole
a.translate(
instanceList=('centrosome-left',),
vector=(0, 0, kwargs['spindleLength']))
a.rotate(
instanceList=('centrosome-left',),
axisPoint=(0.0, 0.0, kwargs['spindleLength']),
axisDirection=(1.0, 0.0, kwargs['spindleLength']),
angle=90)
[docs]def add_microtubule(l, type, i, **kwargs):
"""
Generate and add microtubules to the assembly
:param l: length of the microtubule
:param type: 'ipMT' or 'aMT' -> Either interpolar or astral microtubule
:param i: number of MT
:param kwargs: object
:return: p -> microtubule part, MTname -> (string) name of the MT
"""
# generate name for microtubule:
MTname = gb.create_mt_name(l, type, i)
# generate microtubule
modelname = kwargs['modelname']
sparts.microtubule(type, l, i, **kwargs)
p = mdb.models[modelname].parts[MTname]
return p, MTname
[docs]def add_connectors(pos1, pos2, MTname1, MTname2, z, **kwargs):
"""
Generate and add connectors to couple ipMT pair
: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 z: numpy array of connector positions along z coordinate
:param kwargs: dictionary -> keyword arguments
:return: list -> list of connector names, float -> angle of connector orientation
"""
# Calculate orientation and length of connector
alpha = math.degrees(math.atan((pos2[1] - pos1[1]) / (pos2[0] - pos1[0])))
length = math.sqrt((pos2[0] - pos1[0])**2 + (pos2[1] - pos1[1])**2)
# Add connectors
modelname = kwargs['modelname']
connectornames = []
for i in range(len(z)):
connectorname = 'connector-' + MTname1 + '-' + MTname2 + '-' + str(i)
sparts.connector(i, length, connectorname, **kwargs)
p = mdb.models[modelname].parts[connectorname]
a = return_assembly(**kwargs)
a.Instance(name=connectorname, part=p, dependent=OFF)
connectornames.append(connectorname)
return connectornames, alpha
[docs]def generate_MT_length( type, **kwargs ):
"""
calculate length of an MT based on its type
:param type: 'ipMT' or 'aMT' -> interpolar or astral microtubules
:param kwargs: object
:return: l -> (float) length of the MT
"""
import random
if type == 'ipMT':
l = kwargs['lengthInterval'][0] * random.random() + kwargs['lengthInterval'][1]
elif type == 'aMT':
l = kwargs['aMTlength']
else:
raise ValueError('Only ipMT and aMT are valid types')
return l
[docs]def create_MT_instance(type, i, **kwargs):
"""
create abaqus instance that contain a single microtubule
:param type: 'ipMT' or 'aMT' -> interpolar or astral microtubule
:param i: number of microtubule
:param kwargs: object
:return: l -> (float) length of MT,
p -> (object) MT part,
MTname -> (string) name of MT
"""
# Calculate a random length of MT
l = generate_MT_length(type, **kwargs)
# Create MT part
p, MTname = add_microtubule(l, type, i, **kwargs)
# Create MT instance
a = return_assembly(**kwargs)
a.Instance(name=MTname, part=p, dependent=ON)
return l, p, MTname
