Source code for simularium_readdy_models.actin.actin_test_data
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
from simularium_readdy_models.actin import FiberData, ArpData
[docs]class ActinTestData:
[docs] def linear_actin_fiber():
return [
FiberData(
28,
[
np.array([-70, 0, 0]),
np.array([10, 0, 0]),
],
"Actin-Polymer",
)
]
[docs] def complex_branched_actin_fiber():
return [
FiberData(
fiber_id=0,
points=[
np.array([-50, 0, 0]),
np.array([50, 0, 0]),
],
type_name="Actin-Polymer",
nucleated_arps=[
ArpData(
arp_id=0,
position=np.array([-19, 0, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=1,
points=[
np.array([-19, 0, 0]),
np.array([0.8, 54.5, 0]),
],
type_name="Actin-Polymer",
is_daughter=True,
nucleated_arps=[
ArpData(
arp_id=1,
position=np.array([-6, 35.7, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=2,
points=[
np.array([-6, 35.7, 0]),
np.array([14, 35.7, 0]),
],
type_name="Actin-Polymer",
is_daughter=True,
),
),
],
),
),
ArpData(
arp_id=3,
position=np.array([0, 0, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=3,
points=[
np.array([0, 0, 0]),
np.array([16.4, -45.1, 0]),
],
type_name="Actin-Polymer",
is_daughter=True,
nucleated_arps=[
ArpData(
arp_id=4,
position=np.array([6.5, -17.9, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=4,
points=[
np.array([6.5, -17.9, 0]),
np.array([-30.3, -48.7, 0]),
],
type_name="Actin-Polymer",
is_daughter=True,
nucleated_arps=[
ArpData(
arp_id=5,
position=np.array([-22.6, -42.3, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=5,
points=[
np.array([-22.6, -42.3, 0]),
np.array([-15.8, -61.1, 0]),
],
type_name="Actin-Polymer",
is_daughter=True,
),
),
],
),
),
ArpData(
arp_id=6,
position=np.array([13, -35.7, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=6,
points=[
np.array([13, -35.7, 0]),
np.array([33, -35.7, 0]),
],
type_name="Actin-Polymer",
is_daughter=True,
),
),
],
),
),
ArpData(
arp_id=7,
position=np.array([9.5, 0, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=7,
points=[
np.array([9.5, 0, 0]),
np.array([16.3, 0, 18.8]),
],
type_name="Actin-Polymer",
is_daughter=True,
),
),
ArpData(
arp_id=8,
position=np.array([19, 0, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=8,
points=[
np.array([19, 0, 0]),
np.array([29.3, 28.2, 0]),
],
type_name="Actin-Polymer",
is_daughter=True,
bound_arps=[
ArpData(
arp_id=9,
position=np.array([25.9, 18.8, 0]),
),
],
),
),
],
bound_arps=[
ArpData(
arp_id=2,
position=np.array([-10, 0, 0]),
),
ArpData(
arp_id=10,
position=np.array([30, 0, 0]),
),
],
)
]
[docs] def simple_branched_actin_fiber():
return [
FiberData(
fiber_id=0,
points=[
np.array([-50, 0, 0]),
np.array([50, 0, 0]),
],
type_name="Actin-Polymer",
nucleated_arps=[
ArpData(
arp_id=0,
position=np.array([0, 0, 0]),
nucleated=True,
daughter_fiber=FiberData(
fiber_id=1,
points=[
np.array([0, 0, 0]),
np.array([16.4, -45.1, 0]),
],
type_name="Actin-Polymer",
is_daughter=True,
),
),
],
)
]
[docs] def linear_actin_monomers():
return {
"topologies": {
28: {
"type_name": "Actin-Polymer",
"particle_ids": [
0,
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
22,
23,
24,
25,
26,
27,
],
}
},
"particles": {
0: {
"unique_id": 0,
"type_name": "actin#pointed_ATP_1",
"position": np.array([-67.19690124, -1.44136597, -0.73486099]),
"neighbor_ids": [1],
},
1: {
"unique_id": 1,
"type_name": "actin#ATP_2",
"position": np.array([-64.39380247, 1.23818016, 1.04137719]),
"neighbor_ids": [0, 2],
},
2: {
"unique_id": 2,
"type_name": "actin#mid_ATP_3",
"position": np.array([-61.59070371, -0.97102348, -1.29409039]),
"neighbor_ids": [1, 3],
},
3: {
"unique_id": 3,
"type_name": "actin#mid_ATP_1",
"position": np.array([-58.78760495, 0.65369866, 1.47994412]),
"neighbor_ids": [2, 4],
},
4: {
"unique_id": 4,
"type_name": "actin#mid_ATP_2",
"position": np.array([-55.98450619, -0.30260035, -1.58933621]),
"neighbor_ids": [3, 5],
},
5: {
"unique_id": 5,
"type_name": "actin#mid_ATP_3",
"position": np.array([-53.18140742, -0.06413188, 1.61661487]),
"neighbor_ids": [4, 6],
},
6: {
"unique_id": 6,
"type_name": "actin#mid_ATP_1",
"position": np.array([-50.37830866, 0.42755072, -1.56037077]),
"neighbor_ids": [5, 7],
},
7: {
"unique_id": 7,
"type_name": "actin#mid_ATP_2",
"position": np.array([-47.5752099, -0.76888006, 1.42350975]),
"neighbor_ids": [6, 8],
},
8: {
"unique_id": 8,
"type_name": "actin#mid_ATP_3",
"position": np.array([-44.77211113, 1.07048503, -1.21310278]),
"neighbor_ids": [7, 9],
},
9: {
"unique_id": 9,
"type_name": "actin#mid_ATP_1",
"position": np.array([-41.96901237, -1.31678315, 0.94002058]),
"neighbor_ids": [8, 10],
},
10: {
"unique_id": 10,
"type_name": "actin#mid_ATP_2",
"position": np.array([-39.16591361, 1.49504937, -0.618372]),
"neighbor_ids": [9, 11],
},
11: {
"unique_id": 11,
"type_name": "actin#mid_ATP_3",
"position": np.array([-36.36281484, -1.59607353, 0.26477509]),
"neighbor_ids": [10, 12],
},
12: {
"unique_id": 12,
"type_name": "actin#mid_ATP_1",
"position": np.array([-33.55971608, 1.61463618, 0.10250148]),
"neighbor_ids": [11, 13],
},
13: {
"unique_id": 13,
"type_name": "actin#mid_ATP_2",
"position": np.array([-30.75661732, -1.54977829, -0.46448229]),
"neighbor_ids": [12, 14],
},
14: {
"unique_id": 14,
"type_name": "actin#mid_ATP_3",
"position": np.array([-27.95351855, 1.40485076, 0.80246552]),
"neighbor_ids": [13, 15],
},
15: {
"unique_id": 15,
"type_name": "actin#mid_ATP_1",
"position": np.array([-25.15041979, -1.18734129, -1.09898918]),
"neighbor_ids": [14, 16],
},
16: {
"unique_id": 16,
"type_name": "actin#mid_ATP_2",
"position": np.array([-22.34732103, 0.90848756, 1.33873332]),
"neighbor_ids": [15, 17],
},
17: {
"unique_id": 17,
"type_name": "actin#mid_ATP_3",
"position": np.array([-19.54422227, -0.58269662, -1.5093115]),
"neighbor_ids": [16, 18],
},
18: {
"unique_id": 18,
"type_name": "actin#mid_ATP_1",
"position": np.array([-16.7411235, 0.22680052, 1.60191076]),
"neighbor_ids": [17, 19],
},
19: {
"unique_id": 19,
"type_name": "actin#mid_ATP_2",
"position": np.array([-13.93802474, 0.14081327, -1.61174693]),
"neighbor_ids": [18, 20],
},
20: {
"unique_id": 20,
"type_name": "actin#mid_ATP_3",
"position": np.array([-11.13492598, -0.50115192, 1.53831184]),
"neighbor_ids": [19, 21],
},
21: {
"unique_id": 21,
"type_name": "actin#mid_ATP_1",
"position": np.array([-8.33182721, 0.83559844, -1.38539951]),
"neighbor_ids": [20, 22],
},
22: {
"unique_id": 22,
"type_name": "actin#mid_ATP_2",
"position": np.array([-5.52872845, -1.12687357, 1.1609102]),
"neighbor_ids": [21, 23],
},
23: {
"unique_id": 23,
"type_name": "actin#mid_ATP_3",
"position": np.array([-2.72562969, 1.35992853, -0.87644221]),
"neighbor_ids": [22, 24],
},
24: {
"unique_id": 24,
"type_name": "actin#mid_ATP_1",
"position": np.array([0.07746908, -1.52272247, 0.54669263]),
"neighbor_ids": [23, 25],
},
25: {
"unique_id": 25,
"type_name": "actin#mid_ATP_2",
"position": np.array([2.88056784, 1.60684461, -0.18869805]),
"neighbor_ids": [24, 26],
},
26: {
"unique_id": 26,
"type_name": "actin#mid_ATP_3",
"position": np.array([5.6836666, -1.60794876, -0.17904566]),
"neighbor_ids": [25, 27],
},
27: {
"unique_id": 27,
"type_name": "actin#barbed_ATP_1",
"position": np.array([8.48676536, 1.52597787, 0.53753893]),
"neighbor_ids": [26],
},
},
}
[docs] def complex_branched_actin_monomers():
return {
"topologies": {
126: {
"type_name": "Actin-Polymer",
"particle_ids": [
10,
9,
8,
7,
6,
5,
4,
3,
2,
1,
0,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
22,
23,
24,
25,
26,
27,
28,
29,
30,
31,
32,
33,
34,
35,
58,
59,
60,
36,
37,
38,
39,
40,
41,
42,
43,
44,
45,
46,
47,
48,
49,
50,
51,
55,
56,
57,
52,
53,
54,
102,
103,
104,
61,
62,
63,
64,
65,
66,
67,
68,
69,
70,
71,
72,
73,
93,
94,
95,
74,
75,
76,
77,
78,
79,
80,
81,
82,
83,
84,
85,
86,
90,
91,
92,
87,
88,
89,
99,
100,
101,
96,
97,
98,
108,
109,
110,
105,
106,
107,
119,
120,
121,
111,
112,
113,
114,
115,
116,
117,
118,
122,
123,
124,
125,
],
}
},
"particles": {
0: {
"unique_id": 0,
"type_name": "actin#ATP_2",
"position": np.array([-20.26714464, -1.57293361, -0.37872999]),
"neighbor_ids": [1, 11],
},
1: {
"unique_id": 1,
"type_name": "actin#mid_ATP_1",
"position": np.array(
[-2.30702434e01, 1.61782814e00, 1.37352874e-02]
),
"neighbor_ids": [0, 2],
},
2: {
"unique_id": 2,
"type_name": "actin#mid_ATP_3",
"position": np.array([-25.87334216, -1.57913721, 0.35196905]),
"neighbor_ids": [1, 3],
},
3: {
"unique_id": 3,
"type_name": "actin#mid_ATP_2",
"position": np.array([-28.67644092, 1.4588598, -0.69948883]),
"neighbor_ids": [2, 4],
},
4: {
"unique_id": 4,
"type_name": "actin#mid_ATP_1",
"position": np.array([-31.47953969, -1.26321007, 1.01086936]),
"neighbor_ids": [3, 5],
},
5: {
"unique_id": 5,
"type_name": "actin#mid_ATP_3",
"position": np.array([-34.28263845, 1.0022963, -1.2700231]),
"neighbor_ids": [4, 6],
},
6: {
"unique_id": 6,
"type_name": "actin#mid_ATP_2",
"position": np.array([-37.08573721, -0.68959867, 1.4635608]),
"neighbor_ids": [5, 7],
},
7: {
"unique_id": 7,
"type_name": "actin#mid_ATP_1",
"position": np.array([-39.88883598, 0.34127276, -1.58148331]),
"neighbor_ids": [6, 8],
},
8: {
"unique_id": 8,
"type_name": "actin#mid_ATP_3",
"position": np.array(
[-4.26919347e01, 2.46850777e-02, 1.61769812e00]
),
"neighbor_ids": [7, 9],
},
9: {
"unique_id": 9,
"type_name": "actin#ATP_2",
"position": np.array([-45.4950335, -0.38936756, -1.57033419]),
"neighbor_ids": [8, 10],
},
10: {
"unique_id": 10,
"type_name": "actin#pointed_ATP_1",
"position": np.array([-48.29813227, 0.73393327, 1.44183858]),
"neighbor_ids": [9],
},
11: {
"unique_id": 11,
"type_name": "actin#ATP_3",
"position": np.array([-17.46404587, 1.44677311, 0.72415752]),
"neighbor_ids": [0, 12, 58],
},
12: {
"unique_id": 12,
"type_name": "actin#ATP_1",
"position": np.array([-14.66094711, -1.24586475, -1.0321713]),
"neighbor_ids": [13, 11, 59],
},
13: {
"unique_id": 13,
"type_name": "actin#ATP_2",
"position": np.array([-11.85784835, 0.9805885, 1.2868577]),
"neighbor_ids": [12, 14],
},
14: {
"unique_id": 14,
"type_name": "actin#ATP_3",
"position": np.array([-9.05474958, -0.66464992, -1.47505831]),
"neighbor_ids": [13, 15, 122],
},
15: {
"unique_id": 15,
"type_name": "actin#ATP_1",
"position": np.array([-6.25165082, 0.31437206, 1.5870497]),
"neighbor_ids": [14, 16, 123],
},
16: {
"unique_id": 16,
"type_name": "actin#ATP_2",
"position": np.array([-3.44855206, 0.05214791, -1.61704581]),
"neighbor_ids": [15, 17],
},
17: {
"unique_id": 17,
"type_name": "actin#ATP_3",
"position": np.array([-0.64545329, -0.41597364, 1.56349688]),
"neighbor_ids": [16, 18, 102],
},
18: {
"unique_id": 18,
"type_name": "actin#ATP_1",
"position": np.array([2.15764547, 0.758308, -1.42916952]),
"neighbor_ids": [17, 19, 103],
},
19: {
"unique_id": 19,
"type_name": "actin#ATP_2",
"position": np.array([4.96074423, -1.06146421, 1.2210038]),
"neighbor_ids": [18, 20],
},
20: {
"unique_id": 20,
"type_name": "actin#ATP_3",
"position": np.array([7.76384299, 1.30977963, -0.94975464]),
"neighbor_ids": [19, 21],
},
21: {
"unique_id": 21,
"type_name": "actin#ATP_1",
"position": np.array([10.56694176, -1.49042498, 0.62943619]),
"neighbor_ids": [20, 22, 108],
},
22: {
"unique_id": 22,
"type_name": "actin#ATP_2",
"position": np.array([13.37004052, 1.59406719, -0.27659778]),
"neighbor_ids": [21, 23, 109],
},
23: {
"unique_id": 23,
"type_name": "actin#ATP_3",
"position": np.array([16.17313928, -1.61535156, -0.09053112]),
"neighbor_ids": [22, 24],
},
24: {
"unique_id": 24,
"type_name": "actin#ATP_1",
"position": np.array([18.97623805, 1.55317842, 0.45298271]),
"neighbor_ids": [23, 25, 119],
},
25: {
"unique_id": 25,
"type_name": "actin#ATP_2",
"position": np.array([21.77933681, -1.41075997, -0.79203084]),
"neighbor_ids": [24, 26, 120],
},
26: {
"unique_id": 26,
"type_name": "actin#ATP_3",
"position": np.array([24.58243557, 1.19545429, 1.09015852]),
"neighbor_ids": [25, 27],
},
27: {
"unique_id": 27,
"type_name": "actin#ATP_1",
"position": np.array([27.38553434, -0.91838518, -1.33196292]),
"neighbor_ids": [26, 28],
},
28: {
"unique_id": 28,
"type_name": "actin#ATP_2",
"position": np.array([30.1886331, 0.5938675, 1.50495114]),
"neighbor_ids": [27, 29, 124],
},
29: {
"unique_id": 29,
"type_name": "actin#ATP_3",
"position": np.array([32.99173186, -0.23866752, -1.60018573]),
"neighbor_ids": [28, 30, 125],
},
30: {
"unique_id": 30,
"type_name": "actin#ATP_1",
"position": np.array([35.79483062, -0.12886327, 1.61274636]),
"neighbor_ids": [29, 31],
},
31: {
"unique_id": 31,
"type_name": "actin#ATP_2",
"position": np.array([38.59792939, 0.48973632, -1.54198408]),
"neighbor_ids": [30, 32],
},
32: {
"unique_id": 32,
"type_name": "actin#mid_ATP_3",
"position": np.array([41.40102815, -0.82530702, 1.39155484]),
"neighbor_ids": [31, 33],
},
33: {
"unique_id": 33,
"type_name": "actin#mid_ATP_1",
"position": np.array([44.20412691, 1.11823805, -1.16923061]),
"neighbor_ids": [32, 34],
},
34: {
"unique_id": 34,
"type_name": "actin#mid_ATP_2",
"position": np.array([47.00722568, -1.35339506, 0.88649781]),
"neighbor_ids": [33, 35],
},
35: {
"unique_id": 35,
"type_name": "actin#barbed_ATP_3",
"position": np.array([49.81032444, 1.5186286, -0.5579639]),
"neighbor_ids": [34],
},
36: {
"unique_id": 36,
"type_name": "actin#ATP_2",
"position": np.array([-13.92101264, 13.23481985, 1.59774927]),
"neighbor_ids": [37, 60],
},
37: {
"unique_id": 37,
"type_name": "actin#mid_ATP_3",
"position": np.array([-13.77514447, 16.16418153, -1.4990095]),
"neighbor_ids": [36, 38],
},
38: {
"unique_id": 38,
"type_name": "actin#mid_ATP_1",
"position": np.array([-11.37034585, 18.27286757, 1.32282307]),
"neighbor_ids": [37, 39],
},
39: {
"unique_id": 39,
"type_name": "actin#mid_ATP_2",
"position": np.array([-12.42236595, 21.63742535, -1.07829268]),
"neighbor_ids": [38, 40],
},
40: {
"unique_id": 40,
"type_name": "actin#mid_ATP_3",
"position": np.array([-8.99827637, 23.37580018, 0.77805206]),
"neighbor_ids": [39, 41],
},
41: {
"unique_id": 41,
"type_name": "actin#mid_ATP_1",
"position": np.array([-10.8383282, 27.02665206, -0.4376132]),
"neighbor_ids": [40, 42],
},
42: {
"unique_id": 42,
"type_name": "actin#mid_ATP_2",
"position": np.array([-6.89817996, 28.57754135, 0.07456496]),
"neighbor_ids": [41, 43],
},
43: {
"unique_id": 43,
"type_name": "actin#ATP_3",
"position": np.array([-8.95565511, 32.30738372, 0.2923357]),
"neighbor_ids": [42, 44],
},
44: {
"unique_id": 44,
"type_name": "actin#ATP_1",
"position": np.array([-5.10795212, 33.89185863, -0.64413277]),
"neighbor_ids": [43, 45, 55],
},
45: {
"unique_id": 45,
"type_name": "actin#ATP_2",
"position": np.array([-6.76788964, 37.47727449, 0.96265057]),
"neighbor_ids": [44, 46, 56],
},
46: {
"unique_id": 46,
"type_name": "actin#ATP_3",
"position": np.array([-3.60227777, 39.30955497, -1.23143282]),
"neighbor_ids": [45, 47],
},
47: {
"unique_id": 47,
"type_name": "actin#ATP_1",
"position": np.array([-4.33081108, 42.55658912, 1.4365928]),
"neighbor_ids": [46, 48],
},
48: {
"unique_id": 48,
"type_name": "actin#mid_ATP_2",
"position": np.array([-2.29779532, 44.80034489, -1.5675309]),
"neighbor_ids": [47, 49],
},
49: {
"unique_id": 49,
"type_name": "actin#mid_ATP_3",
"position": np.array([-1.75105645, 47.58406914, 1.61748215]),
"neighbor_ids": [48, 50],
},
50: {
"unique_id": 50,
"type_name": "actin#mid_ATP_1",
"position": np.array([-1.0701017, 50.3190324, -1.58386582]),
"neighbor_ids": [49, 51],
},
51: {
"unique_id": 51,
"type_name": "actin#barbed_ATP_2",
"position": np.array([0.83563247, 52.60902992, 1.46841871]),
"neighbor_ids": [50],
},
52: {
"unique_id": 52,
"type_name": "actin#ATP_2",
"position": np.array([8.14704791, 35.94934191, -1.59855721]),
"neighbor_ids": [53, 57],
},
53: {
"unique_id": 53,
"type_name": "actin#mid_ATP_3",
"position": np.array([10.95014667, 35.09610162, 1.50095413]),
"neighbor_ids": [52, 54],
},
54: {
"unique_id": 54,
"type_name": "actin#barbed_ATP_1",
"position": np.array([13.75324544, 36.6272543, -1.32580391]),
"neighbor_ids": [53],
},
55: {
"unique_id": 55,
"type_name": "arp2#branched",
"position": np.array([2.49594049, 34.90795338, -0.11552341]),
"neighbor_ids": [56, 57, 44],
},
56: {
"unique_id": 56,
"type_name": "arp3#ATP",
"position": np.array([-0.10863178, 37.20492983, 2.68579493]),
"neighbor_ids": [55, 45],
},
57: {
"unique_id": 57,
"type_name": "actin#branch_ATP_1",
"position": np.array([5.34394915, 35.91925943, 2.99576567]),
"neighbor_ids": [55, 52],
},
58: {
"unique_id": 58,
"type_name": "arp2#branched",
"position": np.array([-16.84336419, 8.28402437, 0.11552341]),
"neighbor_ids": [59, 60, 11],
},
59: {
"unique_id": 59,
"type_name": "arp3#ATP",
"position": np.array([-15.57382277, 5.05166268, -2.68579493]),
"neighbor_ids": [58, 12],
},
60: {
"unique_id": 60,
"type_name": "actin#branch_ATP_1",
"position": np.array([-14.92034518, 10.61552413, -2.99576567]),
"neighbor_ids": [58, 36],
},
61: {
"unique_id": 61,
"type_name": "actin#ATP_2",
"position": np.array([5.08457938, -13.23277245, -1.59746502]),
"neighbor_ids": [62, 104],
},
62: {
"unique_id": 62,
"type_name": "actin#mid_ATP_3",
"position": np.array([5.22807177, -16.16326884, 1.49833101]),
"neighbor_ids": [61, 63],
},
63: {
"unique_id": 63,
"type_name": "actin#ATP_1",
"position": np.array([7.63644269, -18.27017304, -1.32178538]),
"neighbor_ids": [62, 64],
},
64: {
"unique_id": 64,
"type_name": "actin#ATP_2",
"position": np.array([6.58290355, -21.63595362, 1.07694941]),
"neighbor_ids": [63, 65, 93],
},
65: {
"unique_id": 65,
"type_name": "actin#ATP_3",
"position": np.array([10.00944563, -23.37261376, -0.77647261]),
"neighbor_ids": [64, 66, 94],
},
66: {
"unique_id": 66,
"type_name": "actin#ATP_1",
"position": np.array([8.16919975, -27.02446952, 0.43587917]),
"neighbor_ids": [65, 67],
},
67: {
"unique_id": 67,
"type_name": "actin#ATP_2",
"position": np.array([12.11033878, -28.57400349, -0.07276593]),
"neighbor_ids": [66, 68],
},
68: {
"unique_id": 68,
"type_name": "actin#ATP_3",
"position": np.array([10.05419251, -32.30436849, -0.29410677]),
"neighbor_ids": [67, 69],
},
69: {
"unique_id": 69,
"type_name": "actin#ATP_1",
"position": np.array([13.90138082, -33.88806636, 0.64578438]),
"neighbor_ids": [68, 70, 99],
},
70: {
"unique_id": 70,
"type_name": "actin#ATP_2",
"position": np.array([12.24418239, -37.47335941, -0.96409739]),
"neighbor_ids": [69, 71, 100],
},
71: {
"unique_id": 71,
"type_name": "actin#ATP_3",
"position": np.array([15.40803747, -39.30554209, 1.23260009]),
"neighbor_ids": [70, 72],
},
72: {
"unique_id": 72,
"type_name": "actin#ATP_1",
"position": np.array([14.68325309, -42.55177549, -1.43742023]),
"neighbor_ids": [71, 73],
},
73: {
"unique_id": 73,
"type_name": "actin#barbed_ATP_2",
"position": np.array([16.71378668, -44.79607508, 1.56797573]),
"neighbor_ids": [72],
},
74: {
"unique_id": 74,
"type_name": "actin#ATP_2",
"position": np.array([-4.20199346, -27.18397212, -1.598351]),
"neighbor_ids": [75, 95],
},
75: {
"unique_id": 75,
"type_name": "actin#mid_ATP_3",
"position": np.array([-6.9008281, -28.32679417, 1.50045548]),
"neighbor_ids": [74, 76],
},
76: {
"unique_id": 76,
"type_name": "actin#mid_ATP_1",
"position": np.array([-8.06616828, -31.30184336, -1.3250386]),
"neighbor_ids": [75, 77],
},
77: {
"unique_id": 77,
"type_name": "actin#mid_ATP_2",
"position": np.array([-11.58406273, -31.4660485, 1.08116329]),
"neighbor_ids": [76, 78],
},
78: {
"unique_id": 78,
"type_name": "actin#mid_ATP_3",
"position": np.array([-12.05188835, -35.27449171, -0.78142944]),
"neighbor_ids": [77, 79],
},
79: {
"unique_id": 79,
"type_name": "actin#mid_ATP_1",
"position": np.array([-16.10971487, -34.7935832, 0.44132286]),
"neighbor_ids": [78, 80],
},
80: {
"unique_id": 80,
"type_name": "actin#mid_ATP_2",
"position": np.array([-16.22308663, -39.02552973, -0.07841523]),
"neighbor_ids": [79, 81],
},
81: {
"unique_id": 81,
"type_name": "actin#ATP_3",
"position": np.array([-20.43157585, -38.36460864, -0.28854374]),
"neighbor_ids": [80, 82],
},
82: {
"unique_id": 82,
"type_name": "actin#ATP_1",
"position": np.array([-20.60586008, -42.52377663, 0.64059503]),
"neighbor_ids": [81, 83, 90],
},
83: {
"unique_id": 83,
"type_name": "actin#ATP_2",
"position": np.array([-24.54500873, -42.18466507, -0.95954983]),
"neighbor_ids": [82, 84, 91],
},
84: {
"unique_id": 84,
"type_name": "actin#ATP_3",
"position": np.array([-25.18314611, -45.7896189, 1.22892927]),
"neighbor_ids": [83, 85],
},
85: {
"unique_id": 85,
"type_name": "actin#ATP_1",
"position": np.array([-28.4878941, -46.20849253, -1.4348158]),
"neighbor_ids": [84, 86],
},
86: {
"unique_id": 86,
"type_name": "actin#barbed_ATP_2",
"position": np.array([-29.89820318, -48.89085161, 1.56657225]),
"neighbor_ids": [85],
},
87: {
"unique_id": 87,
"type_name": "actin#ATP_2",
"position": np.array([-18.03089005, -55.68578739, 1.59745526]),
"neighbor_ids": [88, 92],
},
88: {
"unique_id": 88,
"type_name": "actin#mid_ATP_3",
"position": np.array([-16.26239191, -58.02694477, -1.49830776]),
"neighbor_ids": [87, 89],
},
89: {
"unique_id": 89,
"type_name": "actin#barbed_ATP_1",
"position": np.array([-16.76038871, -61.18789819, 1.32174985]),
"neighbor_ids": [88],
},
90: {
"unique_id": 90,
"type_name": "arp2#branched",
"position": np.array([-18.95888232, -50.01060018, 0.11552341]),
"neighbor_ids": [91, 92, 82],
},
91: {
"unique_id": 91,
"type_name": "arp3#ATP",
"position": np.array([-22.00703713, -48.34667415, -2.68579493]),
"neighbor_ids": [90, 83],
},
92: {
"unique_id": 92,
"type_name": "actin#branch_ATP_1",
"position": np.array([-18.93714594, -53.03275516, -2.99576567]),
"neighbor_ids": [90, 87],
},
93: {
"unique_id": 93,
"type_name": "arp2#branched",
"position": np.array([-0.5402271, -22.7548803, -0.11552341]),
"neighbor_ids": [94, 95, 64],
},
94: {
"unique_id": 94,
"type_name": "arp3#ATP",
"position": np.array([2.93138214, -22.8433498, 2.68579493]),
"neighbor_ids": [93, 65],
},
95: {
"unique_id": 95,
"type_name": "actin#branch_ATP_1",
"position": np.array([-2.07417683, -25.35889479, 2.99576567]),
"neighbor_ids": [93, 74],
},
96: {
"unique_id": 96,
"type_name": "actin#ATP_2",
"position": np.array([27.15763386, -35.95314688, 1.59795908]),
"neighbor_ids": [97, 101],
},
97: {
"unique_id": 97,
"type_name": "actin#mid_ATP_3",
"position": np.array([29.96073263, -35.09253002, -1.49951218]),
"neighbor_ids": [96, 98],
},
98: {
"unique_id": 98,
"type_name": "actin#barbed_ATP_1",
"position": np.array([32.76383139, -36.63040801, 1.32359264]),
"neighbor_ids": [97],
},
99: {
"unique_id": 99,
"type_name": "arp2#branched",
"position": np.array([21.50622855, -34.9016237, 0.11552341]),
"neighbor_ids": [100, 101, 69],
},
100: {
"unique_id": 100,
"type_name": "arp3#ATP",
"position": np.array([18.90233327, -37.19936757, -2.68579493]),
"neighbor_ids": [99, 70],
},
101: {
"unique_id": 101,
"type_name": "actin#branch_ATP_1",
"position": np.array([24.3545351, -35.91209045, -2.99576567]),
"neighbor_ids": [99, 96],
},
102: {
"unique_id": 102,
"type_name": "arp2#branched",
"position": np.array([2.15663581, -8.28402437, -0.11552341]),
"neighbor_ids": [103, 104, 17],
},
103: {
"unique_id": 103,
"type_name": "arp3#ATP",
"position": np.array([3.42617723, -5.05166268, 2.68579493]),
"neighbor_ids": [102, 18],
},
104: {
"unique_id": 104,
"type_name": "actin#branch_ATP_1",
"position": np.array([4.07965482, -10.61552413, 2.99576567]),
"neighbor_ids": [102, 61],
},
105: {
"unique_id": 105,
"type_name": "actin#ATP_2",
"position": np.array([14.55212534, -1.59908567, 13.24460638]),
"neighbor_ids": [106, 110],
},
106: {
"unique_id": 106,
"type_name": "actin#mid_ATP_3",
"position": np.array([14.70941526, 1.50223942, 16.1685412]),
"neighbor_ids": [105, 107],
},
107: {
"unique_id": 107,
"type_name": "actin#barbed_ATP_1",
"position": np.array([17.09703399, -1.32777964, 18.28576133]),
"neighbor_ids": [106],
},
108: {
"unique_id": 108,
"type_name": "arp2#branched",
"position": np.array([11.65663581, -0.11552341, 8.28402437]),
"neighbor_ids": [109, 110, 21],
},
109: {
"unique_id": 109,
"type_name": "arp3#ATP",
"position": np.array([12.92617723, 2.68579493, 5.05166268]),
"neighbor_ids": [108, 22],
},
110: {
"unique_id": 110,
"type_name": "actin#branch_ATP_1",
"position": np.array([13.57965482, 2.99576567, 10.61552413]),
"neighbor_ids": [108, 105],
},
111: {
"unique_id": 111,
"type_name": "actin#ATP_2",
"position": np.array([24.11156452, 13.22284346, 1.59606406]),
"neighbor_ids": [112, 121],
},
112: {
"unique_id": 112,
"type_name": "actin#ATP_3",
"position": np.array([24.24360216, 16.15883948, -1.49502728]),
"neighbor_ids": [111, 113],
},
113: {
"unique_id": 113,
"type_name": "actin#ATP_1",
"position": np.array([26.66919128, 18.25711988, 1.31674956]),
"neighbor_ids": [112, 114, 117],
},
114: {
"unique_id": 114,
"type_name": "actin#ATP_2",
"position": np.array([25.60835594, 21.62881064, -1.07044169]),
"neighbor_ids": [113, 115, 118],
},
115: {
"unique_id": 115,
"type_name": "actin#ATP_3",
"position": np.array([29.04669112, 23.35718734, 0.7688292]),
"neighbor_ids": [114, 116],
},
116: {
"unique_id": 116,
"type_name": "actin#barbed_ATP_1",
"position": np.array([27.20556039, 27.0138796, -0.42749497]),
"neighbor_ids": [115],
},
117: {
"unique_id": 117,
"type_name": "arp2",
"position": np.array([28.7247819, 19.80230706, 9.48231305]),
"neighbor_ids": [113, 118],
},
118: {
"unique_id": 118,
"type_name": "arp3#ATP",
"position": np.array([26.08942261, 22.11644092, 6.72424345]),
"neighbor_ids": [114, 117],
},
119: {
"unique_id": 119,
"type_name": "arp2#branched",
"position": np.array([21.15663581, 8.28402437, 0.11552341]),
"neighbor_ids": [120, 121, 24],
},
120: {
"unique_id": 120,
"type_name": "arp3#ATP",
"position": np.array([22.42617723, 5.05166268, -2.68579493]),
"neighbor_ids": [119, 25],
},
121: {
"unique_id": 121,
"type_name": "actin#branch_ATP_1",
"position": np.array([23.07965482, 10.61552413, -2.99576567]),
"neighbor_ids": [119, 111],
},
122: {
"type_name": "arp2",
"position": np.array([-6.89811378, -7.01551544, -6.79529446]),
"neighbor_ids": [14, 123],
},
123: {
"type_name": "arp3#ATP",
"position": np.array([-5.62857235, -6.27778874, -2.58206459]),
"neighbor_ids": [15, 122],
},
124: {
"type_name": "arp2",
"position": np.array([32.3452689, 6.6849766, 7.12071425]),
"neighbor_ids": [28, 125],
},
125: {
"type_name": "arp3#ATP",
"position": np.array([33.61481033, 6.14811778, 2.8772099]),
"neighbor_ids": [29, 124],
},
},
}