From 4c8a9c7f510108e26454fdb3e9a211b40955e908 Mon Sep 17 00:00:00 2001 From: Ryan Spangler Date: Tue, 15 Mar 2022 14:03:36 -0700 Subject: [PATCH] working out interaction between cytosim and medyan --- in/cytosim-buckling.cym | 66 ++++++++++--------- .../filaments.txt | 53 ++++++++------- ...019_no_tread_2mUNI_alphaA_0.1_MA_0.675.txt | 2 +- .../composites/filament_alternatives.py | 18 +++-- vivarium_models/processes/cytosim.py | 15 ++--- vivarium_models/processes/medyan.py | 2 +- 6 files changed, 83 insertions(+), 73 deletions(-) diff --git a/in/cytosim-buckling.cym b/in/cytosim-buckling.cym index 8c733ed..1188763 100644 --- a/in/cytosim-buckling.cym +++ b/in/cytosim-buckling.cym @@ -15,7 +15,7 @@ set space cell new cell { - length = 4.0, 2.0, 2.0 + length = 3.8, 1.9, 1.9 } set fiber actin @@ -24,6 +24,8 @@ set fiber actin segmentation = 0.1 display = ( point=6,1; line=10,2; ) + confine = inside, 100, cell + } set hand binder @@ -46,185 +48,185 @@ set single link new actin { mark = 1 - shape = 3.2743 -1.7332 -4.0069, 3.198 -1.7567 -3.9497, 3.1217 -1.7803 -3.8926, 3.0455 -1.804 -3.8354, 2.9693 -1.8278 -3.7782, 2.8932 -1.8514999999999997 -3.721, 2.8169 -1.8753 -3.6638999999999995, 2.7405 -1.8989 -3.6069, 2.6639 -1.9223 -3.5501, 2.5871 -1.9455 -3.4935, 2.5102 -1.9683 -3.437, 2.433 -1.9907 -3.3806, 2.3556 -2.0126 -3.3243, 2.278 -2.0342 -3.2681, 2.2004 -2.0556 -3.2119, 2.1226 -2.0767 -3.1558, 2.0446 -2.0975 -3.1, 1.9664 -2.1181 -3.0443, 1.8879 -2.1385 -2.9889, 1.8091 -2.1586 -2.934, 1.73 -2.1787 -2.8793, 1.6508 -2.1986 -2.8248, 1.5716 -2.2184 -2.7702 + shape = 0.8264 0.9149 -0.895, 0.7283 0.9135 -0.8933, 0.6301 0.9121 -0.8915, 0.532 0.9108 -0.8897, 0.4338 0.9098 -0.8878, 0.3357 0.9091 -0.8859, 0.2375 0.9086 -0.8841, 0.1393 0.9081999999999999 -0.8824, 0.0412 0.9077 -0.881, -0.057 0.9073 -0.8797, -0.1552 0.9069 -0.8786, -0.2534 0.9065 -0.8775, -0.35150000000000003 0.9062 -0.8762, -0.4497 0.9058 -0.8747, -0.5479 0.9054 -0.8731, -0.646 0.9047 -0.8713, -0.7442 0.9038 -0.8692, -0.8423 0.9025 -0.8672, -0.9405 0.9009 -0.865, -1.0386 0.8989 -0.8629, -1.1368 0.8966 -0.8607, -1.2349 0.8941 -0.8583999999999999, -1.333 0.8916 -0.8561 } new actin { mark = 2 - shape = 6.2346 -2.0193 -2.9501, 6.2872 -1.9661 -3.0137, 6.3399 -1.9129 -3.0772, 6.3928 -1.8599 -3.1407, 6.4459 -1.8067 -3.2039, 6.4994 -1.7535 -3.2667, 6.5531 -1.7001 -3.3293, 6.6068 -1.6465 -3.3916, 6.6604 -1.5928 -3.4539, 6.7139 -1.5391 -3.5163, 6.7671 -1.4853 -3.5788, 6.8202 -1.4315 -3.6415, 6.873 -1.3777 -3.7044, 6.9256 -1.3239 -3.7675, 6.9781 -1.2701 -3.8306, 7.0303 -1.2162 -3.894, 7.0824 -1.1625 -3.9576, 7.1344 -1.109 -4.0214, 7.1863 -1.0559 -4.0856, 7.238 -1.003 -4.1502, 7.2894 -0.9504 -4.2152, 7.3409 -0.8979 -4.2803, 7.3923 -0.8454 -4.3455 + shape = -0.6891 0.7503 -0.8866, -0.6314 0.7592 -0.8077, -0.5737 0.7681 -0.7287, -0.5161 0.777 -0.6497, -0.4586 0.7858 -0.5706, -0.4014 0.7946 -0.4913, -0.3445 0.8035 -0.4118, -0.2881 0.8124 -0.3319, -0.2322 0.8216 -0.2518, -0.1767 0.8310000000000001 -0.1713, -0.1216 0.8409 -0.0906, -0.0669 0.8512 -0.0097, -0.0126 0.8617 0.0714, 0.0414 0.8725 0.1526, 0.0953 0.8831 0.234, 0.1493 0.8934999999999998 0.3154, 0.2033 0.9034 0.3967, 0.2573 0.9129 0.4782, 0.3113 0.9218 0.5597, 0.36519999999999997 0.9301 0.6414, 0.419 0.9381 0.7231, 0.4728 0.9457 0.8049, 0.5265 0.9531 0.8867 } new actin { mark = 3 - shape = 0.5499 -3.6304 -5.7062, 0.5238 -3.6236 -5.8006, 0.4977 -3.6166 -5.8949, 0.4716 -3.6094000000000004 -5.9893, 0.4457 -3.6019 -6.0837, 0.4199 -3.5944 -6.1782, 0.3941 -3.5869 -6.2726, 0.3682 -3.5795 -6.367, 0.3424 -3.5723 -6.4615, 0.3164 -3.5651 -6.5559, 0.29 -3.5582 -6.6502, 0.2633 -3.5514 -6.7444, 0.2363 -3.5446 -6.8386, 0.2093 -3.5378 -6.9327, 0.1822 -3.531 -7.0269, 0.1552 -3.5243 -7.121, 0.1283 -3.5175 -7.2152, 0.1013 -3.5108 -7.3094, 0.0742 -3.5041000000000007 -7.4035, 0.0467 -3.4972 -7.4975, 0.0192 -3.4903 -7.5915, -0.0084 -3.4835 -7.6855, -0.0359 -3.4767 -7.7795 + shape = 0.892 -0.828 0.9498, 0.9388 -0.8346 0.8637, 0.9853999999999999 -0.8413 0.7776, 1.032 -0.8478 0.6912999999999999, 1.0783 -0.8542 0.605, 1.1245 -0.8603 0.5186, 1.1705 -0.8661 0.4321, 1.2167 -0.8717 0.3456, 1.2629 -0.8771 0.2592, 1.3093 -0.8825 0.1728, 1.3559 -0.8878 0.0865, 1.4025 -0.8933 0.0003, 1.449 -0.8989 -0.086, 1.4954 -0.9047 -0.1723, 1.5416 -0.9107 -0.2587, 1.5877 -0.9167 -0.3452, 1.6337 -0.9227 -0.4318, 1.6796 -0.9284 -0.5184, 1.7256 -0.9337 -0.605, 1.7716 -0.9386 -0.6915, 1.8178 -0.9431 -0.778, 1.8641 -0.9475 -0.8645, 1.9104 -0.9517 -0.951 } new actin { mark = 4 - shape = -6.3192 -0.4222 3.3755, -6.3671 -0.3373 3.3878, -6.4149 -0.2525 3.4, -6.4625 -0.1675 3.4123, -6.5098 -0.0824 3.4247, -6.5568 0.0029 3.4374, -6.6035 0.0883 3.4504, -6.6498 0.1738 3.4637, -6.6958 0.2595 3.4772, -6.7416 0.3452 3.4911, -6.7871 0.4311 3.5052, -6.8324 0.517 3.5194, -6.8776 0.603 3.5337, -6.9226 0.6891 3.548, -6.9674 0.7752 3.5621, -7.0121 0.8616 3.576, -7.0562 0.9482 3.5897, -7.0998 1.0351 3.6034, -7.1429 1.1223 3.617, -7.1856 1.2096 3.6305, -7.2281 1.2971 3.644, -7.2705 1.3846000000000003 3.6574, -7.3129 1.4722 3.6709 + shape = -0.9465 0.9127 0.8016, -0.8483 0.9118 0.8025, -0.7501 0.9108 0.8035, -0.652 0.9096 0.8045, -0.5538 0.9081999999999999 0.8056000000000001, -0.4557 0.9067 0.807, -0.3575 0.9051 0.8084, -0.2593 0.9032 0.8099, -0.1612 0.901 0.8115, -0.0631 0.8985 0.813, 0.0351 0.896 0.8144, 0.1332 0.8934 0.8158, 0.2314 0.8911 0.8172, 0.3295 0.8891 0.8185, 0.4277 0.8873 0.8199, 0.5258 0.8854 0.8214, 0.624 0.8834 0.823, 0.7221 0.8812 0.825, 0.8202 0.8785 0.8272, 0.9183 0.8754 0.8297, 1.0164 0.8719 0.8323, 1.1145 0.8680999999999999 0.8349, 1.2126 0.8642 0.8376 } new actin { mark = 5 - shape = 1.7052 2.1905 -0.8135, 1.7516 2.1591 -0.8941, 1.7981 2.1278 -0.9747, 1.8447 2.0966 -1.0553, 1.8914 2.0655 -1.1359, 1.9381 2.0345 -1.2165, 1.9848 2.0034 -1.297, 2.0317 1.9723 -1.3775, 2.0786 1.9413 -1.458, 2.1257 1.9104 -1.5384, 2.173 1.8794 -1.6187, 2.2202 1.8482 -1.6989, 2.2673 1.8168 -1.7791, 2.3143 1.7852 -1.8593, 2.3613 1.7533 -1.9394, 2.408 1.7211 -2.0195, 2.4544 1.6887 -2.0997, 2.5005 1.6561 -2.18, 2.5466 1.6234 -2.2604, 2.5926 1.5906 -2.3407, 2.6386 1.5577 -2.4209, 2.6847 1.5245 -2.501, 2.7308 1.4914 -2.581 + shape = 1.1718 -0.9598 0.22730000000000003, 1.2009 -0.8725 0.2615, 1.23 -0.7852 0.2958, 1.2591 -0.6979 0.3301, 1.2883 -0.6108 0.3646, 1.3179 -0.5236 0.3988, 1.3476 -0.4365 0.4329, 1.3775 -0.3493 0.4667, 1.4075 -0.26209999999999994 0.5003, 1.4378 -0.1749 0.5339, 1.4683 -0.0878 0.5673, 1.4992 -0.0007 0.6005, 1.5305 0.0864 0.6333, 1.5623 0.1734 0.6658, 1.5943 0.2605 0.698, 1.6265 0.3475 0.73, 1.6589 0.4346 0.7618, 1.6916 0.5216 0.7934, 1.7246 0.6086 0.8248, 1.758 0.6955 0.8559, 1.7917 0.7824 0.8868, 1.8257 0.8693 0.9173, 1.8599 0.9562 0.9478 } new actin { mark = 6 - shape = -7.3387 5.2696 -1.1384, -7.3531 5.3667 -1.1367, -7.3675 5.4638 -1.135, -7.3818 5.5609 -1.1333, -7.3958 5.6581 -1.1313, -7.4095 5.7553 -1.1293, -7.4226 5.8526 -1.1272, -7.4354 5.9499 -1.1253, -7.4479 6.0473 -1.1236, -7.4604 6.1447 -1.1221, -7.4731 6.242 -1.1209, -7.4862 6.3393 -1.1201, -7.4997 6.4366 -1.1196, -7.5138 6.5338 -1.1195, -7.5282 6.6309 -1.1198, -7.5429 6.728 -1.1205, -7.5575 6.825 -1.1217, -7.5721 6.9221 -1.1234, -7.5867 7.0192 -1.1253, -7.6012 7.1163 -1.1273, -7.6157 7.2134 -1.1292, -7.6301 7.3105 -1.131, -7.6444 7.4076 -1.1327 + shape = 1.2461 -0.0999 -0.6748, 1.1936 -0.1387 -0.6013999999999999, 1.1413 -0.1774 -0.5279, 1.089 -0.2162 -0.4544, 1.0367000000000002 -0.2549 -0.3809, 0.9844 -0.2937 -0.3074, 0.9321 -0.3324 -0.2339, 0.8798 -0.3711 -0.1603, 0.8278 -0.4098 -0.0865, 0.7762 -0.4484 -0.0125, 0.725 -0.487 0.0618, 0.6739 -0.5254 0.1363, 0.6228 -0.5635 0.2111, 0.5717 -0.6012 0.2859, 0.5205 -0.6384 0.3609, 0.469 -0.6754 0.4359, 0.4173 -0.7122 0.5109, 0.3656 -0.7489 0.5858, 0.3135 -0.7852 0.6607, 0.261 -0.8212 0.7354, 0.2082 -0.857 0.81, 0.1551 -0.8928 0.8845, 0.102 -0.9285 0.9589 } new actin { mark = 7 - shape = -3.5898 2.1058 -3.8465, -3.5163 2.1697 -3.8346, -3.4427 2.2336 -3.8228, -3.369 2.2974 -3.8109, -3.2953 2.3612 -3.7991, -3.2216 2.4249999999999994 -3.7874, -3.1479 2.4888 -3.7761, -3.0742 2.5527 -3.7651, -3.0005 2.6167 -3.7546, -2.9267 2.6807 -3.7445, -2.8528 2.7446 -3.7348, -2.7789 2.8086 -3.7255, -2.7052 2.8727 -3.7163, -2.6315 2.9369999999999994 -3.7074, -2.5581 3.0016 -3.6987, -2.4851 3.0667 -3.6905, -2.4124 3.1323 -3.6824, -2.3401 3.1981 -3.6745, -2.2678 3.2642 -3.6666, -2.1957 3.3303 -3.6586, -2.1237 3.3965 -3.6507, -2.0517 3.4628 -3.6426, -1.9797 3.529 -3.6345 + shape = 0.074 0.9553 0.7061, 0.1533 0.9371 0.6511, 0.2326 0.919 0.5961, 0.3118 0.9011 0.541, 0.3911 0.8835 0.4858, 0.4704 0.8659 0.4306, 0.5496000000000001 0.8483 0.3753, 0.6288000000000001 0.8305 0.3201, 0.7081 0.8127 0.265, 0.7876 0.7947 0.2102, 0.8673 0.7766 0.156, 0.9474 0.7582 0.1021, 1.0277 0.7398 0.04869999999999999, 1.1083 0.7213 -0.0042, 1.1890999999999998 0.7028 -0.0568, 1.2701 0.6843 -0.1091, 1.3513 0.6656 -0.1611, 1.4326 0.647 -0.2129, 1.514 0.6282 -0.2644, 1.5954999999999997 0.6094 -0.3158, 1.677 0.5904 -0.3671, 1.7586 0.5712 -0.4183, 1.8401 0.5519 -0.4695 } new actin { mark = 8 - shape = -3.0057 -0.7373 -0.8103, -2.9158 -0.7036 -0.7897, -2.826 -0.6699 -0.7691, -2.7362 -0.6361 -0.7482, -2.6464 -0.6023 -0.7272, -2.5568 -0.5683 -0.7061, -2.4673 -0.5341 -0.6846, -2.3779 -0.4999 -0.6626, -2.2888 -0.4656 -0.64, -2.1998 -0.431 -0.617, -2.1109 -0.3963 -0.5937, -2.0222 -0.3614 -0.5702, -1.9336 -0.3264 -0.5466, -1.8449 -0.2914 -0.523, -1.7563 -0.2564 -0.4995, -1.6676 -0.2215 -0.4758, -1.579 -0.1866 -0.452, -1.4904 -0.1517 -0.4283, -1.4016 -0.1169 -0.4045, -1.3129 -0.0822 -0.3809, -1.2241999999999997 -0.04730000000000001 -0.3573, -1.1356 -0.0121 -0.3337, -1.047 0.0231 -0.3103 + shape = 0.8655 -0.2791 0.9498, 0.9121 -0.2747 0.8635, 0.9588 -0.2703 0.7772, 1.0056 -0.266 0.691, 1.0523 -0.2619 0.6048, 1.099 -0.2581 0.5185, 1.1456 -0.2546 0.4321, 1.1922 -0.2516 0.3457, 1.2389 -0.2489 0.2594, 1.2859 -0.2468 0.1733, 1.333 -0.2452 0.0871, 1.3802 -0.244 0.0011, 1.4275 -0.2431 -0.085, 1.4747 -0.2425 -0.1711, 1.5219 -0.2419 -0.2572, 1.5689 -0.2413 -0.3434, 1.6157 -0.2406 -0.4297000000000001, 1.6623 -0.2399 -0.5161, 1.7088 -0.2394 -0.6026, 1.7551 -0.239 -0.6891, 1.8013 -0.2387 -0.7758, 1.8473 -0.2384 -0.8625, 1.8934 -0.238 -0.9492 } new actin { mark = 9 - shape = 3.7708 5.0758 -0.1657, 3.8605 5.1046 -0.1934, 3.9502 5.1333 -0.221, 4.0401 5.1619 -0.2484, 4.13 5.1904 -0.2755, 4.2201 5.2188 -0.3022, 4.3103 5.2471 -0.3286, 4.4007 5.2753 -0.3546, 4.4912 5.3031 -0.3803, 4.5819 5.3307 -0.4058, 4.6727 5.3581 -0.4312, 4.7635 5.3855 -0.4566, 4.8543 5.412799999999999 -0.482, 4.9451 5.44 -0.5076, 5.0358 5.4672 -0.5332, 5.1267 5.4943 -0.5587, 5.217599999999999 5.5211 -0.5842, 5.3087 5.5474 -0.6096, 5.3998 5.5734 -0.6353, 5.4909 5.5991 -0.6612, 5.582 5.6247 -0.6873, 5.673 5.6504 -0.7137, 5.764 5.6761 -0.7402 + shape = 1.872 0.9576 -0.0322, 1.8712 0.8696 0.0115, 1.8704 0.7818 0.05530000000000001, 1.8695 0.694 0.0993, 1.8685 0.6064 0.14349999999999996, 1.8671 0.5188 0.1879, 1.8651999999999997 0.4314 0.2325, 1.8627 0.3441 0.2775, 1.8598 0.2569 0.3225, 1.8566 0.1697 0.3675, 1.853 0.0825 0.4125, 1.849 -0.0047 0.4574, 1.8447 -0.0919 0.5022, 1.8401 -0.1792 0.5471, 1.8353 -0.2663 0.5921, 1.8303 -0.3533 0.6373, 1.8251 -0.4402 0.6826, 1.8197 -0.5271 0.728, 1.8142 -0.6141000000000001 0.7733, 1.8084 -0.7009999999999998 0.8186, 1.8025 -0.788 0.8638, 1.7966 -0.8749 0.909, 1.7906 -0.9618 0.9543 } new actin { mark = 10 - shape = -6.1314 -0.9171 1.4135, -6.2293 -0.9095 1.4146, -6.3272 -0.9017 1.4156, -6.425 -0.8937 1.4164, -6.5229 -0.8856 1.417, -6.6207 -0.8772 1.4174, -6.7186 -0.8689 1.4174, -6.8164 -0.8606 1.4171, -6.9143 -0.8526 1.4164, -7.0122 -0.8449 1.4152, -7.11 -0.8372 1.4135, -7.2079 -0.8295 1.4113, -7.3057 -0.8215 1.4084, -7.4035 -0.8129 1.4051, -7.5012 -0.8038 1.4012, -7.5988 -0.7943 1.397, -7.6964 -0.7843 1.3925, -7.794 -0.774 1.3879, -7.8914 -0.7631 1.383, -7.9888 -0.752 1.3778, -8.0862 -0.7405 1.3723, -8.1835 -0.7288 1.3665, -8.2808 -0.717 1.3606 + shape = 0.0426 0.6761 0.7484, 0.1268 0.688 0.6993, 0.211 0.6999 0.6502, 0.2953 0.712 0.6013999999999999, 0.3797 0.7243 0.5528, 0.4643 0.7368 0.5045, 0.5491 0.7493 0.4566, 0.6339 0.7619 0.4088, 0.7189 0.7746 0.3613, 0.8039 0.7874 0.31390000000000007, 0.8889 0.8001 0.2664, 0.9738 0.8126 0.2187, 1.0586 0.8252 0.1708, 1.1433 0.8378 0.1229, 1.2281 0.8504 0.0749, 1.313 0.8632 0.0273, 1.3981 0.876 -0.02, 1.4833 0.8889 -0.067, 1.5686 0.9017 -0.1139, 1.6539 0.9146 -0.1608, 1.7392 0.9275 -0.2076, 1.8244 0.9405 -0.2547, 1.9095 0.9534 -0.3018 } new actin { mark = 11 - shape = 1.3372 1.0912 2.8145, 1.2904 1.1673 2.7737, 1.2437 1.2434 2.7328, 1.1971 1.3196 2.6921, 1.1504 1.3958 2.6514, 1.1036 1.4719 2.6107, 1.0567 1.5479 2.57, 1.0096 1.6238 2.5293, 0.9624 1.6996 2.4883, 0.9152 1.7752 2.4472, 0.868 1.8507 2.4059, 0.8207 1.9259 2.3641, 0.7733 2.0008 2.3219, 0.7257 2.0755 2.2795, 0.678 2.15 2.2368, 0.6301 2.2243 2.1941, 0.582 2.2984 2.1514, 0.5338 2.3726 2.1087, 0.4855 2.4469 2.0664, 0.4371 2.5213 2.0244, 0.3888 2.5958 1.9826, 0.3405 2.6704 1.9409, 0.2921 2.7451 1.8994 + shape = -0.1298 0.4784999999999999 0.2305, -0.0378 0.4607 0.2599, 0.0541 0.443 0.2893, 0.1461 0.4252 0.3188, 0.2381 0.4075 0.3482, 0.33 0.3899 0.3777, 0.422 0.3726 0.4073, 0.514 0.3554 0.4371, 0.6059 0.3382 0.4671, 0.6976 0.3207 0.4974, 0.7893 0.3031 0.5277, 0.881 0.2855 0.5581, 0.9727000000000001 0.2679 0.5884, 1.0645 0.2506 0.6187, 1.1563 0.2336 0.6492, 1.2481 0.2168 0.6798, 1.3398 0.2002 0.7104, 1.4315 0.1835 0.7413, 1.5231 0.1668 0.7726, 1.6145 0.1501 0.8043, 1.7058 0.1334 0.8362, 1.7971 0.1168 0.8684, 1.8884 0.1001 0.9005 } new actin { mark = 12 - shape = -2.4439 -0.9213 -0.3224, -2.3853 -0.9948 -0.2938, -2.3267 -1.0681 -0.2651, -2.268 -1.1413 -0.2363, -2.2092 -1.2144 -0.2072, -2.1502 -1.2873 -0.1781, -2.0911 -1.36 -0.1488, -2.032 -1.4327 -0.1195, -1.9731 -1.5054 -0.0899, -1.9143 -1.5783 -0.0602, -1.8559 -1.6511 -0.03, -1.7976 -1.724 0.0005, -1.7394 -1.7968 0.0314, -1.6815 -1.8696 0.0627, -1.6236 -1.9425 0.0941, -1.5658 -2.0152 0.1258, -1.5081 -2.088 0.1577, -1.4505 -2.1607 0.1897, -1.3929 -2.2334999999999994 0.2217, -1.3354 -2.3064 0.2537, -1.2781 -2.3794 0.2856, -1.221 -2.4526 0.3175, -1.1639 -2.526 0.3493 + shape = 0.6664 0.9204 -0.8662, 0.5683 0.9211 -0.863, 0.4702 0.922 -0.8598, 0.3721 0.9231 -0.8566, 0.2739 0.9243 -0.8534, 0.1758 0.9255 -0.8502, 0.0777 0.9266 -0.8472, -0.0204 0.9276 -0.8443, -0.1186 0.9285 -0.8417, -0.2167 0.9292 -0.8395, -0.3149 0.9297 -0.8377, -0.4131 0.93 -0.8363, -0.5113 0.9302 -0.8352, -0.6094 0.9302 -0.8343, -0.7076 0.9299 -0.8331, -0.8058 0.9293 -0.8317, -0.9039 0.9285 -0.8299, -1.0021 0.9273 -0.8277, -1.1002 0.926 -0.8252, -1.1984 0.9242 -0.8224, -1.2965 0.9222 -0.8196, -1.3946 0.9198 -0.8168, -1.4927 0.9173 -0.814 } new actin { mark = 13 - shape = -1.5322 6.5935 -3.9862, -1.4549 6.6459 -4.0164, -1.3775 6.6982 -4.0466, -1.3001 6.7505 -4.0768, -1.2226 6.8027 -4.107, -1.145 6.8548 -4.1371, -1.0674 6.9069 -4.1672, -0.9898 6.959 -4.1973, -0.9123 7.0112 -4.2273, -0.8348 7.0635 -4.2573, -0.7572 7.1158 -4.2872, -0.6796 7.168 -4.3171, -0.602 7.22 -4.3471, -0.5241999999999999 7.272 -4.3769, -0.4463 7.3238 -4.4067, -0.3684 7.3756 -4.4363, -0.2904 7.4273 -4.466, -0.2123 7.479 -4.4957, -0.1343 7.5306 -4.5255, -0.0564 7.5822 -4.5556, 0.0215 7.6339 -4.5857, 0.0993 7.6855 -4.6159, 0.177 7.7373 -4.6463 + shape = 0.2698 0.9512 -0.3819, 0.1756 0.941 -0.4079, 0.0815 0.931 -0.434, -0.0126 0.9212 -0.46, -0.1068 0.9115 -0.4861, -0.201 0.9021 -0.512, -0.2953 0.8928 -0.5378999999999999, -0.38959999999999995 0.8836 -0.5637, -0.4839 0.8744 -0.5892, -0.5784 0.8653 -0.6144, -0.673 0.8562 -0.6391, -0.7676 0.8471 -0.6635, -0.8624 0.838 -0.6876, -0.9572 0.8289999999999998 -0.7115, -1.052 0.8201 -0.7352, -1.1469 0.8111 -0.759, -1.2417 0.8021 -0.7828, -1.3365 0.7927 -0.8066000000000001, -1.4312 0.7831 -0.8304, -1.526 0.7731 -0.8543, -1.6206 0.7633 -0.8784, -1.7152 0.7534 -0.9027, -1.8098 0.7435 -0.9271 } new actin { mark = 14 - shape = -1.3163 -0.766 1.6564, -1.2609 -0.8471 1.656, -1.2054 -0.9281 1.6556, -1.1500000000000001 -1.0091 1.6549, -1.0944 -1.0901 1.6539, -1.0387 -1.1709 1.6527, -0.9827 -1.2515 1.651, -0.9266 -1.332 1.6491, -0.8703 -1.4125 1.6468, -0.814 -1.4929 1.6444, -0.758 -1.5734 1.6418, -0.7019999999999998 -1.6541 1.6394, -0.6462 -1.7348 1.6374, -0.5906 -1.8157 1.6357, -0.5352 -1.8968 1.6344, -0.4801 -1.978 1.6332, -0.425 -2.0593 1.6321, -0.3702 -2.1408 1.631, -0.3159 -2.2225 1.6296, -0.2619 -2.3045 1.628, -0.2082 -2.3867 1.6265, -0.1548 -2.4691 1.625, -0.1015 -2.5515 1.6236 + shape = -0.759 0.1184 -0.954, -0.6651 0.147 -0.9521, -0.5712 0.1758 -0.9502, -0.4774 0.2046 -0.9482, -0.3836 0.2335 -0.9464, -0.2898 0.2623 -0.9446, -0.1959 0.291 -0.9431, -0.1019 0.3195 -0.942, -0.008 0.3481 -0.9412, 0.086 0.3766 -0.941, 0.1798 0.4053 -0.9413, 0.2736 0.4343 -0.942, 0.3673 0.4637 -0.9429, 0.4609 0.4935 -0.9439, 0.5543 0.5236 -0.9448, 0.6476 0.5542 -0.9456, 0.7408 0.5851 -0.9462999999999999, 0.8338 0.6165 -0.947, 0.9267 0.6484 -0.9476, 1.0194 0.6807 -0.9482, 1.1119 0.7135 -0.9488, 1.2044 0.7465 -0.9494, 1.2969 0.7794 -0.9499 } new actin { mark = 15 - shape = -0.41 2.4346 1.2215, -0.4048 2.4206 1.3186, -0.3996 2.4067 1.4156, -0.3946 2.3929 1.5127, -0.3898 2.3791 1.6098, -0.3853 2.3654 1.7069, -0.381 2.3517 1.804, -0.3768 2.3377 1.9011, -0.3728 2.3233999999999995 1.9981, -0.3691 2.3086 2.0951, -0.3654 2.2934 2.192, -0.3618 2.2779 2.2889, -0.3581 2.2625 2.3858, -0.3543 2.2471 2.4827, -0.3504 2.2319 2.5796, -0.3466 2.2166 2.6765, -0.3427 2.2011 2.7733, -0.3389 2.1855 2.8702, -0.335 2.1697 2.967, -0.3309 2.1537 3.0638, -0.3267 2.1378 3.1606, -0.3224 2.122 3.2574, -0.318 2.1061 3.3541 + shape = -1.5433 0.0226 -0.9494, -1.5583999999999998 -0.0219 -0.8632, -1.5736 -0.0665 -0.777, -1.589 -0.1111 -0.6909, -1.6046 -0.1557 -0.6048, -1.6205 -0.2001 -0.5188, -1.6365999999999998 -0.2445 -0.4326, -1.6529 -0.2886 -0.3465, -1.6694 -0.3323 -0.2601, -1.6858 -0.3755 -0.1735, -1.7023 -0.4184 -0.0868, -1.7188000000000003 -0.4611 0.0001, -1.7352 -0.5037 0.0871, -1.7513 -0.5463 0.174, -1.7671 -0.5892 0.2609, -1.7825 -0.6325 0.3477, -1.7975 -0.6763 0.4343, -1.812 -0.7206 0.5207, -1.826 -0.7654 0.6069, -1.8394 -0.8106 0.693, -1.8523 -0.8562 0.779, -1.8649 -0.9021 0.8649, -1.8774 -0.948 0.9508 } new actin { mark = 16 - shape = 0.6501 -2.3733 7.478, 0.6587 -2.466 7.5093, 0.6673 -2.5586 7.5407, 0.6761 -2.6512 7.572, 0.685 -2.7439 7.6033, 0.6941 -2.8366 7.6342, 0.7034 -2.9294 7.6647, 0.7131 -3.0224 7.6949, 0.7229 -3.1154 7.7247, 0.7327 -3.2086 7.754, 0.7424 -3.302 7.7825, 0.7521 -3.3956 7.8105, 0.7619 -3.4894 7.838, 0.7719 -3.5832 7.8651, 0.7818 -3.6771 7.892, 0.7917 -3.771 7.9188, 0.8016 -3.8649 7.9456999999999995, 0.8115 -3.9589 7.9724, 0.8215 -4.0528 7.9991, 0.8317 -4.146800000000001 8.0256, 0.8421 -4.2408 8.0519, 0.8526 -4.3349 8.078, 0.8633 -4.4289 8.1042 + shape = 0.8614 -0.9609 -0.8832, 0.9081 -0.8745 -0.8813, 0.9546 -0.7881 -0.8794, 1.001 -0.7016 -0.8778, 1.0474 -0.6151 -0.8764, 1.0938 -0.5285 -0.8752, 1.1401 -0.44190000000000007 -0.8744, 1.1862 -0.3553 -0.8739, 1.2323 -0.2686 -0.8737, 1.2784 -0.1819 -0.874, 1.3245 -0.0952 -0.8746, 1.3705 -0.0085 -0.8754, 1.4164 0.0783 -0.8762, 1.462 0.1652 -0.8772, 1.5072 0.2524 -0.8781, 1.552 0.3398 -0.8787, 1.5964 0.4273 -0.8792, 1.6404 0.5151 -0.8798, 1.6844 0.6029 -0.8805, 1.7284 0.6906 -0.8815, 1.7724 0.7784 -0.8827999999999999, 1.8162 0.8662 -0.8844, 1.8601 0.9541 -0.8861 } new actin { mark = 17 - shape = -0.273 -7.8349 -2.3894, -0.3015 -7.7444 -2.4148, -0.33 -7.654 -2.4401, -0.3586 -7.5635 -2.4654, -0.3872 -7.473 -2.4907, -0.4156 -7.3825 -2.5159, -0.4438 -7.2918 -2.5409, -0.4719 -7.201 -2.5655, -0.4998 -7.11 -2.5898, -0.5277 -7.019 -2.6139, -0.5553 -6.9279 -2.638, -0.5827 -6.8368 -2.6623, -0.6101 -6.7457 -2.6865, -0.6376 -6.6546 -2.7108, -0.6654 -6.5636 -2.7351, -0.6934 -6.4727 -2.7595, -0.7216 -6.381999999999999 -2.7842, -0.75 -6.2913 -2.8091, -0.7785 -6.2008 -2.8341, -0.8073 -6.1103 -2.8593, -0.8364 -6.02 -2.8844, -0.8659 -5.9297 -2.9095, -0.8955000000000001 -5.8395 -2.9344 + shape = -0.8535 -0.9301 0.9245, -0.7553 -0.929 0.9262, -0.6572 -0.928 0.9279, -0.559 -0.9269 0.9295, -0.4608 -0.926 0.9308, -0.3627 -0.9252 0.9319, -0.2645 -0.9244 0.9328, -0.1663 -0.9236 0.9334, -0.0682 -0.9225 0.9339, 0.03 -0.9212 0.9342, 0.1282 -0.9198 0.9343, 0.2264 -0.9181 0.9343, 0.3245 -0.9166 0.9342, 0.4227 -0.9151 0.9341, 0.5209 -0.9138 0.9342, 0.6191 -0.9127 0.9344, 0.7172 -0.9119 0.9348, 0.8154 -0.9115 0.9353, 0.9136 -0.9115 0.9363, 1.0118 -0.9117 0.9378, 1.1099 -0.9119 0.9398, 1.2081 -0.912 0.9419, 1.3062 -0.912 0.9442 } new actin { mark = 18 - shape = 0.0227 2.6446 1.0163, 0.0479 2.5554 1.0485, 0.073 2.4661 1.0808, 0.098 2.3768 1.1131, 0.1229 2.2875 1.1455, 0.1478 2.1982 1.1778, 0.1726 2.1088 1.2099, 0.1975 2.0193 1.2417, 0.2225 1.9296999999999997 1.2732, 0.2476 1.84 1.3043, 0.2729 1.7503 1.3353, 0.2983 1.6606 1.3661, 0.3238 1.571 1.397, 0.3492 1.4814 1.4281, 0.3749 1.3919 1.4594, 0.4007 1.3026 1.4909, 0.4268 1.2134 1.5225, 0.4532 1.1242 1.5542, 0.4796 1.0351 1.5859, 0.5059 0.9461 1.6177, 0.5322 0.857 1.6496, 0.5585 0.7679 1.6815, 0.5848 0.6789 1.7135 + shape = -0.0604 0.09 0.9497, 0.0246 0.041 0.9476, 0.1097 -0.0081 0.9455, 0.19479999999999997 -0.057 0.9435, 0.2799 -0.1058 0.9416, 0.3651 -0.1546 0.9397, 0.4503 -0.2033 0.938, 0.5356 -0.2519 0.9362, 0.6211 -0.3002 0.9344, 0.7067 -0.3482 0.9328, 0.7925 -0.3959 0.9312, 0.8786 -0.4432 0.9296, 0.9649 -0.4899 0.928, 1.0515 -0.5361 0.9261, 1.1384 -0.5817 0.9239000000000002, 1.2256 -0.6267999999999999 0.9217, 1.313 -0.6714 0.9193, 1.4007 -0.7155 0.9168, 1.4886 -0.7592 0.9143, 1.5768 -0.8024 0.9118, 1.6651 -0.8451 0.9091, 1.7535 -0.8877 0.9065, 1.8419 -0.9303 0.9037 } new actin { mark = 19 - shape = 3.0219 -2.4329 -1.9935, 3.0538 -2.3921 -2.0769, 3.0858 -2.3513 -2.1603, 3.1179 -2.3105 -2.2436, 3.1504 -2.2697 -2.3268, 3.183 -2.2288 -2.4099, 3.2157 -2.1878 -2.4929, 3.2483 -2.1466 -2.5758, 3.2808999999999995 -2.1052 -2.6587, 3.3134 -2.0635 -2.7414, 3.3456 -2.0212 -2.824, 3.3776 -1.9787 -2.9065, 3.4096 -1.9357 -2.9888, 3.4412999999999996 -1.8924 -3.071, 3.4728 -1.8488 -3.1531, 3.504 -1.805 -3.2353, 3.5349 -1.761 -3.3174, 3.5657 -1.7166 -3.3994, 3.5965 -1.6722 -3.4813, 3.6273 -1.6278 -3.5633, 3.6582 -1.5834 -3.6453, 3.689 -1.5392 -3.7274, 3.7199 -1.4951 -3.8094 + shape = 0.2645 0.8106 0.9458, 0.1664 0.8092 0.9448, 0.0682 0.8078 0.9439, -0.03 0.8068 0.9431, -0.1281 0.8062 0.9423, -0.2263 0.8063 0.9417, -0.3245 0.8068 0.9411, -0.4227 0.8075 0.9406, -0.5208 0.8082 0.9402, -0.619 0.8091 0.9396, -0.7172 0.8099 0.9389, -0.8154 0.8106 0.938, -0.9136 0.8112 0.9369, -1.0117 0.8117 0.9357, -1.1099 0.8121 0.9344, -1.2081 0.8124 0.9327, -1.3062 0.8128 0.9308, -1.4044 0.813 0.9286, -1.5025 0.8132 0.9264, -1.6007 0.8133 0.9244, -1.6989 0.8133 0.9225, -1.797 0.8135 0.9208, -1.8952 0.8139 0.919 } new actin { mark = 20 - shape = -1.1575 -1.9759 1.7751, -1.1877 -2.0256 1.696, -1.2179 -2.0753 1.6169, -1.248 -2.1252 1.5379, -1.2781 -2.1752 1.4589, -1.3081 -2.2255 1.3801, -1.338 -2.2761 1.3014, -1.3678 -2.327 1.223, -1.3975 -2.3783 1.1447, -1.4272 -2.4299 1.0666, -1.4568 -2.4819 0.9887, -1.4864 -2.5341 0.911, -1.5163 -2.5862 0.8334, -1.5464 -2.6381 0.7557, -1.5766 -2.6899 0.6779, -1.607 -2.7414999999999994 0.6001, -1.6373 -2.793 0.5222, -1.6678 -2.8445 0.4444, -1.6984 -2.8961 0.3666, -1.7291 -2.9478 0.289, -1.7598 -2.9996 0.2115, -1.7904 -3.0515 0.1339, -1.821 -3.1033 0.0563 + shape = -0.813 -0.8694 0.9014, -0.7151 -0.8705 0.8943, -0.6172 -0.8716 0.8873, -0.5192 -0.8727 0.8803, -0.4213 -0.8738 0.8733, -0.3234 -0.8749 0.8665, -0.2254 -0.8759 0.8599, -0.1274 -0.8769 0.8536, -0.0295 -0.8779 0.8475, 0.0685 -0.8789 0.8416, 0.1666 -0.8799 0.8358, 0.2646 -0.8806 0.8305, 0.3626 -0.8813 0.8254, 0.4607 -0.8819 0.8207, 0.5588 -0.8822 0.8164, 0.6569 -0.8824 0.8123, 0.755 -0.8824 0.8084, 0.8531 -0.8822 0.8048, 0.9512 -0.882 0.8016, 1.0494 -0.8817 0.7987, 1.1475 -0.8813 0.796, 1.2457 -0.8811 0.7933, 1.3438 -0.8809 0.7907 } new actin { mark = 21 - shape = -2.0529 6.1986 2.4972, -2.0605 6.2651 2.569, -2.0681 6.3317 2.6408, -2.0759 6.3984 2.7124, -2.084 6.4653 2.7838, -2.0921 6.5323 2.8550999999999997, -2.1003 6.5996 2.9261, -2.1084 6.667 2.997, -2.1166 6.7346 3.0678, -2.1245 6.802 3.1387, -2.1323 6.8693 3.2098, -2.1397 6.9364 3.2811, -2.1468 7.0033 3.3527, -2.1536 7.07 3.4244, -2.1605 7.1365 3.4962, -2.1672 7.202799999999999 3.5683, -2.174 7.2689 3.6406, -2.181 7.3349 3.713, -2.1882 7.4008 3.7854, -2.1954 7.4668 3.8577, -2.2028 7.5329 3.93, -2.2104 7.599 4.0022, -2.2179 7.6651 4.0743 + shape = 1.734 -0.11 0.9363, 1.7414 -0.0637 0.85, 1.7487 -0.0173 0.7638, 1.7559000000000002 0.0292 0.6777, 1.7628 0.0759 0.5916, 1.7693 0.1228 0.5056, 1.7755 0.17 0.4197, 1.7813000000000003 0.2177 0.3341, 1.7868 0.2658 0.2487, 1.7922 0.3142 0.1634, 1.7974 0.3628 0.0783, 1.8025 0.4116 -0.0068, 1.8074 0.4603 -0.0919, 1.8122 0.509 -0.177, 1.8168 0.5574 -0.2623, 1.8212 0.6058 -0.3476, 1.8252 0.6541 -0.433, 1.8289 0.7024 -0.5184, 1.8322 0.7507 -0.6038, 1.8353 0.7991 -0.6892, 1.8383 0.8476 -0.7745, 1.8413 0.8962 -0.8598, 1.8442 0.9447 -0.9451 } new actin { mark = 22 - shape = 3.8268 0.5343 -0.4572, 3.7836 0.5983 -0.5179, 3.7403 0.6623 -0.5785, 3.697 0.7265 -0.6388, 3.6534 0.7909 -0.6988, 3.6095 0.8554 -0.7584, 3.5653 0.92 -0.8178, 3.5209 0.9844 -0.8771, 3.4761 1.0485 -0.9364, 3.4311 1.1123 -0.996, 3.3859 1.1757 -1.0558, 3.3406 1.2388 -1.116, 3.2954 1.3016 -1.1764, 3.2503 1.3644 -1.237, 3.2056 1.4273 -1.2977, 3.1609 1.4902 -1.3584, 3.1162 1.553 -1.4192, 3.0714 1.6157 -1.48, 3.0265 1.6784 -1.5408, 2.9813 1.7409 -1.6016, 2.9359 1.8033 -1.6624, 2.8903 1.8655 -1.7231, 2.8446 1.9277 -1.7839 + shape = 1.7907 -0.9353 -0.1143, 1.795 -0.8509 -0.0643, 1.7994 -0.7664 -0.0144, 1.8036 -0.6818 0.0353, 1.8075 -0.5972 0.0848, 1.811 -0.5124 0.1342, 1.814 -0.4275 0.1834, 1.8163999999999998 -0.3424 0.2324, 1.8182 -0.2573 0.2812, 1.8196 -0.172 0.3299, 1.8207 -0.0868 0.3787, 1.8214 -0.0015 0.4274, 1.8215 0.0838 0.476, 1.8211 0.1692 0.5243, 1.8203 0.2549 0.5723, 1.8194 0.3406 0.6201, 1.8187 0.4265 0.6677, 1.8185 0.5124 0.7151, 1.8186 0.5985 0.7624, 1.8188 0.6847 0.8095, 1.819 0.771 0.8563, 1.819 0.8573 0.903, 1.819 0.9437 0.9497 } new actin { mark = 23 - shape = 2.258 -0.0397 1.1931000000000003, 2.2533 -0.0258 1.096, 2.2485 -0.0118 0.9989, 2.2436 0.0022 0.9019, 2.2384 0.0164 0.8049, 2.2328 0.0307 0.7079, 2.2265 0.0451 0.611, 2.2197 0.0596 0.5141, 2.2124 0.0742 0.4173, 2.2047 0.0891 0.3205, 2.1968 0.1042 0.2239, 2.1887 0.1196 0.1272, 2.1805 0.1351 0.0306, 2.1723 0.151 -0.0659, 2.1639 0.1673 -0.1624, 2.1555 0.1838 -0.2588, 2.1471 0.2005 -0.3552, 2.1387 0.2174 -0.4515, 2.1302 0.2346 -0.5478, 2.1218 0.252 -0.6441, 2.1134 0.2697 -0.7403, 2.1052 0.2876 -0.8365, 2.097 0.3057 -0.9327 + shape = 1.1902 0.0368 0.8905, 1.0992000000000002 0.0736 0.8946, 1.0083 0.1104 0.8986, 0.9175 0.1475 0.9024, 0.8267 0.1847 0.9059, 0.7359 0.2221 0.9089, 0.6453 0.2597 0.9114, 0.5545 0.2971 0.9135, 0.4637 0.3343 0.9153, 0.3726 0.371 0.9168, 0.2815 0.4075 0.918, 0.1902 0.4435 0.9192, 0.0988 0.4793 0.9203, 0.0072 0.5147 0.9216, -0.0845 0.5498 0.9232, -0.1763 0.5847 0.925, -0.2681 0.6194 0.9271, -0.3599 0.6542 0.9291, -0.4516 0.6891 0.9313, -0.5434 0.724 0.9335, -0.6351 0.759 0.9356, -0.7267 0.7942 0.9376, -0.8182999999999999 0.8294 0.9396 } new actin { mark = 24 - shape = -4.0133 -4.3726 -5.1549, -4.1006 -4.4077 -5.183, -4.1878 -4.4428 -5.2112, -4.2751 -4.4778 -5.2394, -4.3624 -4.5126 -5.2677, -4.4499 -4.5472 -5.296, -4.5373 -4.5816 -5.3243, -4.6248 -4.6159 -5.3527, -4.7123 -4.65 -5.3813, -4.7998 -4.684 -5.4102, -4.8873 -4.7177 -5.4392, -4.9748 -4.7515 -5.4684, -5.0621 -4.7852 -5.4979, -5.1494 -4.8188 -5.5276, -5.2368 -4.8522 -5.5576, -5.3242 -4.8854 -5.5875, -5.4117 -4.9185 -5.6174, -5.4992 -4.9515 -5.6471, -5.5867 -4.9846 -5.6769, -5.6742 -5.0178 -5.7065, -5.7618 -5.0509 -5.7361, -5.8494 -5.0838 -5.7657, -5.9371 -5.1167 -5.7953 + shape = 0.8196 0.9455 0.9089, 0.7669 0.8628 0.9074, 0.714 0.78 0.9059, 0.6612 0.6973 0.9046, 0.6086 0.6144 0.9036, 0.5562 0.5314 0.9026, 0.504 0.4482 0.9019, 0.4521 0.3649 0.9011, 0.4004 0.2814 0.9003, 0.3488 0.1979 0.8994, 0.2973 0.1143 0.8986, 0.2459 0.0307 0.8978, 0.1943 -0.0529 0.8972, 0.1427 -0.1364 0.8965, 0.091 -0.2199 0.8958, 0.0394 -0.3034 0.8949, -0.012 -0.3871 0.8936, -0.0629 -0.471 0.892, -0.1135 -0.5551 0.8902, -0.1636 -0.6395000000000001 0.8884, -0.2135 -0.724 0.8867, -0.2633 -0.8087 0.8851, -0.313 -0.8933 0.8834 } new actin { mark = 25 - shape = 3.1119 3.7659 -3.8977, 3.1515 3.8267 -3.9638, 3.1911 3.8875 -4.0299, 3.2307 3.9484 -4.096, 3.2704 4.0093 -4.1619, 3.3103 4.0702 -4.2278, 3.3504 4.131099999999999 -4.2936, 3.3908 4.192 -4.3591, 3.4313 4.253 -4.4245, 3.4719 4.3141 -4.4897, 3.5127 4.3754 -4.5546, 3.5537 4.4368 -4.6194, 3.5945 4.4983 -4.6841, 3.6354 4.5598 -4.7488, 3.6765 4.6212 -4.8135, 3.7176 4.6826 -4.8781, 3.759 4.744 -4.9426, 3.8004 4.8055 -5.0069, 3.8419 4.8671 -5.0712, 3.8837 4.9285 -5.1354, 3.9258 4.9897 -5.1995, 3.9683 5.0506 -5.2637, 4.0109 5.1115 -5.3279 + shape = 1.9119 0.0153 0.1164, 1.8206 0.0108 0.1523, 1.7293 0.0064 0.1881, 1.6379 0.0019 0.2238, 1.5466 -0.0027 0.2594, 1.4553 -0.0073 0.2953, 1.3641 -0.0119 0.3315, 1.2731 -0.0166 0.368, 1.1823 -0.0213 0.4049, 1.0915 -0.0261 0.4421, 1.0009 -0.0308 0.4797, 0.9105 -0.0357 0.5175, 0.8201 -0.0406 0.5556, 0.7297 -0.0456 0.5937, 0.6394 -0.0507 0.6319, 0.5491 -0.0559 0.6701, 0.4588 -0.061 0.7082, 0.3685 -0.066 0.7464, 0.2782 -0.0709 0.7846, 0.1879 -0.0758 0.8227, 0.0975 -0.0807 0.8609, 0.0072 -0.0854 0.8991, -0.0832 -0.0899 0.9372 } new actin { mark = 26 - shape = 1.0013 -0.0049 3.3805, 1.0087 -0.0886 3.4313, 1.0162 -0.1724 3.482, 1.0238 -0.2563 3.5324, 1.0315 -0.3404 3.5824, 1.0394 -0.4246 3.6323, 1.0474 -0.5089 3.682, 1.0554 -0.5931 3.7318, 1.0636 -0.6775 3.7814, 1.0722 -0.7619 3.8308, 1.0812 -0.8465 3.8798, 1.0905 -0.9312 3.9285, 1.1001 -1.0163 3.9766, 1.1098 -1.1015 4.0244, 1.1193 -1.1869 4.0719, 1.1286000000000003 -1.2723 4.1193, 1.1375 -1.3577 4.167, 1.1461 -1.4429 4.2151, 1.1542 -1.5279 4.2636, 1.162 -1.6127 4.3124, 1.1696 -1.6975 4.3613, 1.1769 -1.7823 4.4103, 1.184 -1.867 4.459299999999999 + shape = 0.5559 0.9278 0.8407, 0.4578 0.9301 0.841, 0.3596 0.9324 0.8415, 0.2615 0.9346000000000001 0.842, 0.16330000000000003 0.9368 0.8429, 0.0652 0.9388 0.844, -0.033 0.9407 0.8452, -0.1312 0.9424 0.8465, -0.2293 0.9438 0.848, -0.3275 0.9448 0.8499, -0.4256 0.9454 0.852, -0.5238 0.9456 0.8545, -0.6219 0.9454 0.8573, -0.7201 0.9449 0.8602, -0.8182 0.9442 0.8632, -0.9163 0.943 0.8664, -1.0144 0.9416 0.8698, -1.1125 0.94 0.8734, -1.2106 0.9384 0.8773, -1.3087 0.937 0.8815, -1.4068 0.9358 0.8859, -1.5049 0.935 0.8903, -1.6029 0.9342 0.8947 } new actin { mark = 27 - shape = 2.522 -0.7896 -6.4796, 2.5691 -0.7332 -6.5447, 2.6163 -0.677 -6.6099, 2.6637 -0.6209 -6.6751, 2.7113 -0.5654 -6.7406, 2.7594 -0.5105 -6.8063, 2.8081 -0.4563 -6.8722, 2.8575 -0.403 -6.9381, 2.9076 -0.3502 -7.004, 2.9584 -0.2979 -7.0698, 3.01 -0.2459 -7.1352, 3.0623000000000005 -0.1941 -7.2002, 3.1151 -0.1422 -7.2646, 3.1685 -0.09 -7.328400000000001, 3.2221 -0.0375 -7.3917, 3.2759 0.0152 -7.4547, 3.3294 0.0682 -7.5177, 3.3828000000000005 0.1213 -7.5807, 3.4358 0.1745 -7.6439, 3.4885 0.2278 -7.7073, 3.541 0.2811 -7.771, 3.5933 0.3344 -7.8348, 3.6455 0.3877 -7.898599999999999 + shape = 1.2226 0.9541 -0.1577, 1.2514 0.8674 -0.1937, 1.2802 0.7807 -0.2297, 1.3089 0.694 -0.2655, 1.3376 0.6072 -0.3013, 1.3662 0.5204 -0.3372, 1.3947 0.4336 -0.3732, 1.4231 0.3468 -0.4092, 1.4512 0.2599 -0.4453, 1.4794 0.1731 -0.4815, 1.5076 0.0864 -0.5179, 1.5361 -0.0 -0.5548, 1.5648 -0.0862 -0.592, 1.5935 -0.1724 -0.6293, 1.6221 -0.2586 -0.6666, 1.6504 -0.3449 -0.7038, 1.6784 -0.4315 -0.7406, 1.7061 -0.5183 -0.7772, 1.7335 -0.6052 -0.8138, 1.7606 -0.6922 -0.8503, 1.7876 -0.7793 -0.8868, 1.8146 -0.8664 -0.9233, 1.8415 -0.9534 -0.9598 } new actin { mark = 28 - shape = -4.5368 -0.6703 -2.0015, -4.4787 -0.6006 -2.0388, -4.4205 -0.5309 -2.0761, -4.3621 -0.4612 -2.1132, -4.3036 -0.3915 -2.15, -4.2451 -0.3216 -2.1866, -4.1866 -0.2517 -2.2231, -4.1283 -0.1815 -2.2594, -4.0703 -0.1112 -2.2958, -4.0126 -0.04069999999999999 -2.3324, -3.9552 0.03 -2.3692, -3.8981 0.1008 -2.4061, -3.8412 0.1718 -2.443, -3.7847 0.2431 -2.48, -3.7286 0.3146 -2.5169, -3.6727 0.3864 -2.5539, -3.6172 0.4584 -2.5909, -3.5617 0.5305 -2.6279, -3.5064 0.6027 -2.6648, -3.4511 0.675 -2.7016, -3.3958 0.7474 -2.7384, -3.3405 0.8196 -2.7751, -3.2851 0.8919 -2.8119 + shape = -0.0766 0.8587 0.8862, 0.0069 0.8072 0.8895, 0.0904 0.7556 0.8927, 0.1739 0.7041 0.8957, 0.2574 0.6525 0.8985, 0.3409 0.6009 0.9011, 0.4245 0.5494 0.9033, 0.5081 0.498 0.9053, 0.5918 0.4468 0.907, 0.6757 0.3958 0.9089, 0.7597 0.3449 0.911, 0.8436999999999999 0.2942 0.9133, 0.9279 0.2438 0.9157, 1.0122 0.1934 0.918, 1.0965 0.1432 0.9203, 1.1809 0.0931 0.9225, 1.2654 0.0431 0.9243, 1.35 -0.0067 0.9258, 1.4347 -0.0563 0.927, 1.5194 -0.1059 0.928, 1.6042 -0.1555 0.9287, 1.6889 -0.2051 0.9293, 1.7735 -0.2549 0.93 } new actin { mark = 29 - shape = 0.8895 -0.4791 1.0636, 0.8479 -0.4199 0.9970999999999999, 0.8064 -0.3608 0.9307, 0.7649 -0.3017000000000001 0.8641, 0.7234 -0.2429 0.7974, 0.6818 -0.1843 0.7305, 0.6402 -0.126 0.6633, 0.5988 -0.0679 0.5959, 0.5576 -0.0102 0.528, 0.5165 0.047 0.4596, 0.4755 0.1038 0.3908, 0.4343 0.1602 0.3218, 0.393 0.2163 0.2526, 0.35150000000000003 0.2721 0.1833, 0.3098 0.3279 0.1141, 0.2681 0.3837 0.0449, 0.2264 0.4397 -0.0241, 0.1848 0.496 -0.0929, 0.1433 0.5525 -0.1617, 0.1019 0.609 -0.2304, 0.0604 0.6656 -0.2991, 0.0189 0.7222 -0.3678, -0.0227 0.7788 -0.4364 + shape = 0.4718 -0.8443 0.9276, 0.398 -0.8484 0.8629, 0.3243 -0.8525 0.7982, 0.2507 -0.8564 0.7334, 0.1772 -0.8605 0.6684, 0.1038 -0.8645 0.6033, 0.0306 -0.8685 0.538, -0.0428 -0.8724 0.4729, -0.1163 -0.8763 0.4079, -0.1899 -0.8803 0.3431, -0.2637 -0.8843 0.2785, -0.3377 -0.8884 0.2141, -0.4119 -0.8925 0.1499, -0.4863 -0.8965 0.0859, -0.5608 -0.9002 0.0221, -0.6353 -0.9038 -0.0417, -0.7099 -0.907 -0.1055, -0.7846 -0.9098 -0.1692, -0.8593 -0.9126 -0.2328, -0.9342 -0.9154 -0.2962, -1.0093 -0.9181 -0.3594, -1.0845 -0.9208 -0.4224, -1.1599 -0.9233 -0.4854 } new actin { mark = 30 - shape = 10.77 -0.4473 -0.2271, 10.7229 -0.5254 -0.2634, 10.6759 -0.6037 -0.2996, 10.6292 -0.6821 -0.3357, 10.5828 -0.7608 -0.3717, 10.5369 -0.8398 -0.4077, 10.4917 -0.9191 -0.4438, 10.4471 -0.9987 -0.48, 10.4031 -1.0786 -0.5164, 10.3596 -1.1587 -0.5529, 10.3166 -1.2391 -0.5895, 10.2741 -1.3196 -0.6261, 10.2319 -1.4004 -0.6627, 10.19 -1.4813 -0.6993, 10.1484 -1.5623 -0.736, 10.1068 -1.6433 -0.7728, 10.0651 -1.7242 -0.8095, 10.0231 -1.805 -0.8463, 9.9809 -1.8856 -0.883, 9.9383 -1.9661 -0.9198, 9.8955 -2.0465 -0.9566, 9.8524 -2.1267 -0.9933, 9.8091 -2.2069 -1.0298 + shape = 0.8844 0.9567 0.7844, 0.9319 0.871 0.7902, 0.9795 0.7853 0.796, 1.027 0.6997 0.8022, 1.0745 0.614 0.8086, 1.1219 0.5283 0.8153, 1.1692 0.44240000000000007 0.8219, 1.2163 0.3566 0.8285, 1.2632 0.2705 0.835, 1.3099 0.1844 0.8413, 1.3564 0.0982 0.8476, 1.4027 0.0118 0.8538, 1.4489 -0.0746 0.8602, 1.4949 -0.1611 0.8668, 1.5409 -0.2475 0.8737, 1.5869 -0.334 0.8808, 1.6329 -0.4204 0.8883, 1.6788 -0.5068 0.8959, 1.7247 -0.5933 0.9034, 1.7704 -0.6799 0.9109, 1.8162 -0.7664 0.918, 1.862 -0.853 0.9251, 1.9079 -0.9395 0.9321 } -run 100 system +run 1000 system { nb_frames = 1 } diff --git a/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/filaments.txt b/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/filaments.txt index c9f2923..fd37018 100644 --- a/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/filaments.txt +++ b/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/filaments.txt @@ -1,23 +1,30 @@ -FILAMENT Actin-Polymer 2750.946642304728 766.6536887792527 997.9461479874915 2885.5900256571913 752.6129662665528 998.2442453822055 -FILAMENT Actin-Polymer 2750.3454962849846 1029.7559662736094 922.0105312144175 3181.0046890272797 1046.4728247258436 923.4426217272126 -FILAMENT Actin-Polymer 2750.075946195886 913.7747134617484 1008.3400833666508 3160.9423973709354 898.6222820350051 1007.5022616265372 -FILAMENT Actin-Polymer 2750.0919688576746 824.290231986306 1004.1454054882732 3162.4041837047407 800.7353076835237 1002.2192374114034 -FILAMENT Actin-Polymer 2750.3986436333935 856.3063598442845 992.2323622260703 3167.127628944413 895.6470577562579 978.1758014954269 -FILAMENT Actin-Polymer 2750.807568887789 1016.9043068683256 964.0398397368548 3172.2856187444995 1031.5700739145168 983.5997206697348 -FILAMENT Actin-Polymer 2750.4609960367598 1098.376956224426 899.1053831160183 3145.8900214459927 1132.5366275315157 892.7439702758893 -FILAMENT Actin-Polymer 2751.0169525784404 1010.2399154689526 1091.0661894121072 3165.363722701667 1017.5807950011873 1128.1302281144035 -FILAMENT Actin-Polymer 2750.2990625391258 895.3292715224086 1099.1689267617307 3158.5482759524466 879.2741004131207 1114.576189757649 -FILAMENT Actin-Polymer 2750.1295689116105 970.3658597274489 801.5275694805064 3158.1645694762574 944.0519894402751 788.4047832867373 -FILAMENT Actin-Polymer 2750.5430678061043 1143.1864695754657 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603.2 1519.4 245.20000000000005 557.9000000000001 1605.0 229.9000000000001 512.1 1690.5 214.9000000000001 466.1 1776.0 200.0999999999999 420.1 1861.4 185.29999999999995 374.0 1946.8 +FILAMENT Actin-Polymer 354.79999999999995 1915.2 1112.8 343.39999999999986 1829.8 1065.7 332.10000000000014 1744.4 1018.5 320.9000000000001 1659.1 971.2 309.70000000000005 1573.8 923.8 298.5999999999999 1488.5 876.5 287.70000000000005 1403.2 829.1 276.79999999999995 1317.9 781.8 266.10000000000014 1232.6 734.3 255.5 1147.4 686.7 245.30000000000018 1062.2 639.0 235.30000000000018 977.1 591.1 225.5 892.1 543.0 215.79999999999995 807.1 494.70000000000005 206.0999999999999 722.2 446.5 196.39999999999986 637.3 398.1 186.80000000000018 552.4000000000001 349.6 177.10000000000014 467.70000000000005 301.0000000000001 167.29999999999995 383.0 252.29999999999995 157.29999999999995 298.30000000000007 203.60000000000002 147.10000000000014 213.70000000000005 154.80000000000007 136.70000000000005 129.20000000000005 106.0 126.20000000000005 44.60000000000002 57.30000000000007 +FILAMENT Actin-Polymer 2676.5 1405.9 1746.5 2659.6 1348.0 1669.1 2642.8 1290.0 1591.6 2626.1 1232.1 1514.1 2609.5 1174.1 1436.6 2592.8 1115.9 1359.3 2576.2 1057.5 1282.2 2559.2 998.7 1205.4 2541.8 939.7 1128.9 2523.8 880.5 1052.7 2505.5 821.4 976.4 2487.1 762.6 900.0 2468.7 704.0 823.3 2450.6 645.7 746.5 2432.6 587.5 669.5 2414.8 529.6 592.2 2397.2 472.0 514.7 2379.8 414.5 437.0000000000001 2362.5 357.19999999999993 359.19999999999993 2345.4 299.9000000000001 281.29999999999995 2328.3 242.5000000000001 203.60000000000002 2311.2 184.89999999999998 125.89999999999998 2293.9 127.29999999999995 48.30000000000007 +FILAMENT Actin-Polymer 1875.4 1936.8 64.5 1844.1 1898.6 149.29999999999995 1812.9 1860.3 234.19999999999993 1781.7 1822.0 319.0 1750.5 1784.0 404.0 1719.1 1746.1 488.90000000000003 1687.5 1708.4 573.9000000000001 1655.8 1670.6999999999998 658.8 1624.1 1632.8000000000002 743.7 1592.6 1594.7 828.5 1561.4 1556.5 913.4 1530.4 1518.1999999999998 998.3 1499.5 1480.1 1083.4 1468.7 1442.2 1168.6 1437.8 1404.7 1253.8 1406.8000000000002 1367.3 1339.2 1375.6 1330.1 1424.5 1344.1999999999998 1293.3 1509.9 1312.8 1256.7 1595.5 1281.2 1220.1 1680.9 1249.6 1183.3 1766.3 1217.8 1146.4 1851.5 1185.9 1109.5 1936.6999999999998 +FILAMENT Actin-Polymer 3872.1000000000004 1917.6999999999998 1132.9 3874.0 1833.0 1083.2 3875.8 1748.4 1033.5 3877.3999999999996 1663.9 983.6 3878.7 1579.3000000000002 933.7 3879.8 1494.6 884.1 3880.7 1409.7 834.8 3881.6 1324.5 785.9 3882.5 1239.2 737.4 3883.5 1153.7 689.1 3884.7 1068.0 641.2 3886.1000000000004 982.2 593.5 3887.3999999999996 896.3 546.0 3888.8 810.3 498.6000000000001 3890.2 724.3 451.30000000000007 3891.6 638.2 404.0 3893.2 552.3 356.6 3894.9 466.4000000000001 309.0000000000001 3896.8 380.6 261.29999999999995 3899.0 294.9000000000001 213.4000000000001 3901.3 209.30000000000007 165.39999999999998 3903.7 123.80000000000007 117.29999999999995 3905.8999999999996 38.200000000000045 69.20000000000005 +FILAMENT Actin-Polymer 1375.7 860.4 44.69999999999993 1406.2 822.9 130.20000000000005 1436.6 785.4 215.60000000000002 1467.0 747.9 301.1 1497.1 710.5 386.80000000000007 1526.8 673.2 472.6 1556.0 636.1 558.7 1584.7 599.4 645.1 1613.2 563.1 731.8 1641.4 527.2 818.7 1669.3 491.4 905.7 1696.8 455.70000000000005 993.0 1723.9 420.0 1080.3 1750.9 384.29999999999995 1167.7 1777.8 348.5 1255.1 1804.6 312.9 1342.5 1831.2 277.29999999999995 1430.1 1857.7 241.89999999999998 1517.8000000000002 1883.9 206.4000000000001 1605.5 1909.8 170.69999999999993 1693.2 1935.5 134.60000000000002 1780.8000000000002 1961.0 98.19999999999993 1868.3 1986.4 61.60000000000002 1955.8 +FILAMENT Actin-Polymer 89.69999999999982 1913.9 373.4 185.70000000000005 1896.1 363.1 281.70000000000005 1878.3 352.80000000000007 377.70000000000005 1860.6 342.5 473.79999999999995 1843.1999999999998 332.20000000000005 569.9000000000001 1826.0 321.9 666.0 1809.1 311.5 762.2 1792.3 301.1 858.4000000000001 1775.6 290.5 954.5 1759.1 279.69999999999993 1050.6999999999998 1742.5 268.70000000000005 1146.8000000000002 1726.1 257.6 1243.0 1709.6 246.39999999999998 1339.1 1693.0 235.29999999999995 1435.3000000000002 1676.4 224.4000000000001 1531.4 1659.5 214.0 1627.6 1642.3 204.0999999999999 1723.7 1625.0 194.5 1819.9 1607.9 185.10000000000002 1916.2 1590.9 175.69999999999993 2012.4 1574.1 166.20000000000005 2108.7 1557.2 156.5 2204.9 1540.4 146.70000000000005 +FILAMENT Actin-Polymer 1569.6 1267.0 176.69999999999993 1653.5 1216.1 179.0000000000001 1737.5 1165.3 181.30000000000007 1821.5 1114.6 183.70000000000005 1905.6 1064.0 186.30000000000007 1989.8 1013.6 189.30000000000007 2074.2 963.5 192.5 2158.8 913.7 196.0 2243.6 864.4 199.60000000000002 2328.5 815.3 203.4000000000001 2413.5 766.2 207.4000000000001 2498.3 717.0 211.60000000000002 2583.0 667.5 216.0 2667.7 618.0 220.60000000000002 2752.3 568.5 225.5 2837.2 519.4 230.60000000000002 2922.2 470.6 235.89999999999998 3007.5 422.30000000000007 241.70000000000005 3093.0 374.5000000000001 247.89999999999998 3178.6000000000004 326.79999999999995 254.60000000000002 3264.1 279.20000000000005 261.80000000000007 3349.7 231.60000000000002 269.20000000000005 3435.2 183.89999999999998 276.9000000000001 +FILAMENT Actin-Polymer 3714.3 1940.3 160.20000000000005 3650.4 1865.7 157.5 3586.5 1791.2 154.69999999999993 3522.6 1716.7 151.60000000000002 3458.7 1642.3 148.29999999999995 3394.6000000000004 1568.0 144.70000000000005 3330.3 1493.9 141.20000000000005 3265.8 1420.0 137.70000000000005 3201.0 1346.2 134.29999999999995 3136.0 1272.7 130.9000000000001 3070.7 1199.5 127.5 3005.2 1126.4 123.89999999999998 2939.6 1053.5 120.10000000000002 2873.7 980.8 116.10000000000002 2807.7 908.3 111.60000000000002 2741.4 836.0 106.70000000000005 2675.1 763.8 101.5 2608.7 691.7 96.0 2542.3 619.5999999999999 90.40000000000009 2475.9 547.4000000000001 84.60000000000002 2409.7 475.19999999999993 78.5 2343.5 403.0 72.30000000000007 2277.3 330.79999999999995 65.79999999999995 +FILAMENT Actin-Polymer 2367.8 341.6 1922.6999999999998 2277.8 327.5 1886.0 2187.9 313.30000000000007 1849.1999999999998 2098.0 299.0000000000001 1812.4 2008.2 284.5 1775.4 1918.6 269.9000000000001 1738.1999999999998 1829.1 255.29999999999995 1700.5 1739.7 240.89999999999998 1662.4 1650.5 226.89999999999998 1624.0 1561.3 213.30000000000007 1585.2 1472.1999999999998 200.0999999999999 1546.1 1383.3 187.39999999999998 1506.5 1294.4 175.10000000000002 1466.7 1205.5 163.20000000000005 1426.9 1116.4 151.5 1387.2 1027.2 140.10000000000002 1347.9 937.8 129.0 1308.7 848.4000000000001 118.10000000000002 1269.7 758.8999999999999 107.60000000000002 1230.7 669.4000000000001 97.19999999999993 1191.8 579.8000000000002 87.0 1152.9 490.0999999999999 76.89999999999998 1114.2 400.5 66.70000000000005 1075.5 \ No newline at end of file diff --git a/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675.txt b/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675.txt index 6c72689..6256d2e 100644 --- a/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675.txt +++ b/in/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675.txt @@ -66,7 +66,7 @@ CHEMISTRYFILE: chemistryinput.txt CALGORITHM: NRM NUMTOTALSTEPS: -RUNTIME: 4.999999900000001 +RUNTIME: 1.0 NUMSTEPSPERS: SNAPSHOTTIME: 1.0 diff --git a/vivarium_models/composites/filament_alternatives.py b/vivarium_models/composites/filament_alternatives.py index 383e0ab..fbab8ee 100644 --- a/vivarium_models/composites/filament_alternatives.py +++ b/vivarium_models/composites/filament_alternatives.py @@ -8,13 +8,21 @@ from vivarium_models.processes.medyan import MedyanProcess from vivarium_models.processes.cytosim import CytosimProcess -ALTERNATOR_PERIODS = [5.0, 5.0] +ALTERNATOR_PERIODS = [2.0, 2.0] class FilamentAlternatives(Composer): defaults = { "periodic_event": {"periods": ALTERNATOR_PERIODS}, - "medyan": {"time_step": 5.0, "_condition": ("choices", "medyan_active")}, - "cytosim": {"time_step": 5.0, "_condition": ("choices", "cytosim_active")}, + "medyan": { + "time_step": 1.0, + "_condition": ("choices", "medyan_active")}, + "cytosim": { + "time_step": 1.0, + "_condition": ("choices", "cytosim_active"), + 'confine': { + 'side': 'inside', + 'force': 100, + 'space': 'cell'}}, "alternator": {"choices": ["medyan_active", "cytosim_active"]}, } @@ -282,7 +290,7 @@ def test_filament_alternatives(): medyan_config = { "medyan_executable": args.medyan_executable_path, # "...../medyan/build/medyan" - "transform_points": [0, 0, 0], + "transform_points": [2000, 1000, 1000], } filament_alternatives_config = {'medyan': medyan_config} @@ -301,7 +309,7 @@ def test_filament_alternatives(): import ipdb; ipdb.set_trace() - engine.update(30) + engine.update(10) engine.emitter.get_data() diff --git a/vivarium_models/processes/cytosim.py b/vivarium_models/processes/cytosim.py index aecc837..025d31d 100644 --- a/vivarium_models/processes/cytosim.py +++ b/vivarium_models/processes/cytosim.py @@ -29,6 +29,7 @@ NAME = "CYTOSIM" RELATIVE_MICRON = 0.001 +BOUNDARY_BUFFER = 0.95 def fiber_section(id, fiber): points = fiber['points'] @@ -103,18 +104,10 @@ def __init__(self, parameters=None): def ports_schema(self): ports = fibers_schema() - ports['choices'] = { - 'medyan_active': { - '_default': True, - '_emit': True}, - 'readdy_active': { - '_default': False, - '_emit': True}} - return ports - def calculate_timestep(self, state): - return 0.1 + # def calculate_timestep(self, state): + # return 0.1 def initial_state(self, config): return {} @@ -125,7 +118,7 @@ def next_update(self, timestep, state): fiber_sections = [fiber_section(id, fiber) for id, fiber in initial_fibers.items()] - box_extent = state['fibers_box_extent'] * RELATIVE_MICRON + box_extent = state['fibers_box_extent'] * RELATIVE_MICRON * BOUNDARY_BUFFER template = env.get_template(self.parameters['cytosim_template']) cytosim_config = template.render( diff --git a/vivarium_models/processes/medyan.py b/vivarium_models/processes/medyan.py index e3f0de9..f25530b 100644 --- a/vivarium_models/processes/medyan.py +++ b/vivarium_models/processes/medyan.py @@ -44,7 +44,7 @@ class MedyanProcess(Process): def __init__(self, parameters=None): super().__init__(parameters) - assert self.parameters["time_step"] > self.parameters["snapshot"] + assert self.parameters["time_step"] >= self.parameters["snapshot"] def ports_schema(self): return fibers_schema()