From a472d0463c19c12f4802474945e119fc12121f8b Mon Sep 17 00:00:00 2001 From: Ryan Spangler Date: Thu, 24 Feb 2022 00:28:17 -0800 Subject: [PATCH] doing more of the cym file generation in the template --- in/cytosim-buckling.cym | 99 +++++++------------ vivarium_models/processes/cytosim.py | 48 ++++----- .../templates/cytosim-buckling.cym | 12 ++- 3 files changed, 75 insertions(+), 84 deletions(-) diff --git a/in/cytosim-buckling.cym b/in/cytosim-buckling.cym index 090e66b..62063e7 100644 --- a/in/cytosim-buckling.cym +++ b/in/cytosim-buckling.cym @@ -23,6 +23,9 @@ set fiber actin rigidity = 10 segmentation = 0.1 display = ( point=6,1; line=10,2; ) + + confine = inside, 100, cell + } set hand binder @@ -41,218 +44,192 @@ set single link stiffness = 1000 } + new actin { mark = 1 - shape = 1.2321 -0.8285 -0.5043, 1.2148 -0.9209 -0.5324, 1.1976 -1.0134 -0.5605, 1.1804 -1.1059 -0.5886, 1.1631 -1.1984 -0.6167, 1.1459 -1.2909 -0.6447, 1.1285 -1.3834 -0.6728, 1.1112 -1.4758 -0.7008, 1.0937 -1.5683 -0.7289, 1.0762 -1.6607 -0.757, 1.0586 -1.7531 -0.7851, 1.041 -1.8455 -0.8132, 1.0232 -1.9379 -0.8414, 1.0054 -2.0302 -0.8696, 0.9875 -2.1226 -0.8978, 0.9695 -2.2149 -0.926, 0.9515 -2.3071 -0.9542, 0.9334 -2.3994 -0.9825, 0.9153 -2.4917 -1.0108, 0.8972 -2.5839 -1.0391, 0.879 -2.6762 -1.0674, 0.8609 -2.7684 -1.0958, 0.8427 -2.8606 -1.1241 + shape = 0.002 0.9626 1.0018, -0.0888 0.9255 0.9984, -0.1796 0.8883 0.995, -0.2704 0.8511 0.9915, -0.3612 0.814 0.988, -0.452 0.7768 0.9844, -0.5429 0.7397 0.9808, -0.6337 0.7026 0.9771, -0.7245 0.6655 0.9733, -0.8154 0.6285 0.9695, -0.9062 0.5915 0.9657, -0.9970999999999999 0.5544 0.9619, -1.0879 0.5174 0.9579999999999999, -1.1788 0.4804 0.9542, -1.2696 0.4434 0.9504, -1.3605 0.4064 0.9466, -1.4514 0.3695 0.9428, -1.5423 0.3325 0.939, -1.6332 0.2956 0.9353, -1.7241 0.2586 0.9317, -1.815 0.2217 0.928, -1.9059 0.1848 0.9243, -1.9968 0.1479 0.9207 } - new actin { mark = 2 - shape = 1.1404 2.5627 -1.3346, 1.2014 2.5452 -1.2596, 1.2624 2.5277 -1.1847, 1.3234 2.5102 -1.1098, 1.3844 2.4927 -1.0349, 1.4455 2.4753 -0.96, 1.5065 2.4579 -0.8851, 1.5676 2.4406 -0.8102, 1.6287 2.4233 -0.7353, 1.6899 2.4061 -0.6604, 1.751 2.3889 -0.5855, 1.8121 2.3718 -0.5106, 1.8732 2.3547 -0.4357, 1.9343 2.3376 -0.3607, 1.9954 2.3206 -0.2858, 2.0564 2.3035 -0.2108, 2.1174 2.2865 -0.1358, 2.1784 2.2694 -0.0607, 2.2394 2.2524 0.0143, 2.3004 2.2354 0.0894, 2.3613 2.2183 0.1644, 2.4223 2.2013 0.23949999999999996, 2.4833 2.1843 0.3145 + shape = 1.9703 0.9813 -0.064, 1.9698 0.8913 -0.1032, 1.9693 0.8013 -0.1424, 1.9688 0.7113 -0.1816, 1.9682 0.6213 -0.2209, 1.9677 0.5313 -0.2601, 1.9671 0.4413 -0.2993, 1.9665 0.3513 -0.3385, 1.9658 0.2613 -0.3778, 1.9651 0.1713 -0.4171, 1.9644 0.0813 -0.4564, 1.9636 -0.0086 -0.4957, 1.9628 -0.0985 -0.5351, 1.9619 -0.1884 -0.5746, 1.961 -0.2783 -0.614, 1.9601 -0.3682 -0.6536, 1.9591000000000003 -0.4581 -0.6931, 1.958 -0.5479 -0.7328, 1.9569 -0.6377 -0.7724, 1.9558 -0.7275 -0.8121, 1.9547 -0.8173 -0.8517, 1.9535 -0.9071 -0.8914, 1.9524 -0.9969 -0.9311 } - new actin { mark = 3 - shape = 1.5896 3.6613 1.3877, 1.5981 3.7343 1.3226, 1.6067 3.8073 1.2575, 1.6153 3.8803 1.1924, 1.6239 3.9532999999999996 1.1272, 1.6326 4.0262 1.0620999999999998, 1.6412 4.0991 0.9969, 1.6498 4.172 0.9317, 1.6584 4.2449 0.8664, 1.667 4.3177 0.8011, 1.6755 4.3905 0.7358, 1.684 4.4632 0.6704, 1.6925 4.5359 0.6049, 1.701 4.6086 0.5395, 1.7094 4.6812 0.474, 1.7177 4.7538 0.4084, 1.7261 4.8264 0.3428, 1.7344 4.899 0.2772, 1.7426 4.9716 0.2116, 1.7508 5.0442 0.146, 1.759 5.1167 0.0803, 1.7671 5.1892 0.0147, 1.7753 5.2618 -0.051 + shape = -0.8583999999999999 -0.8338 0.6145, -0.7614 -0.8415 0.6279, -0.6645 -0.8491 0.6414, -0.5675 -0.8568 0.6548, -0.4706 -0.8645 0.6683, -0.3736 -0.8721 0.6818, -0.2767 -0.8797 0.6953, -0.1797 -0.8874 0.7089, -0.0828 -0.8949 0.7225, 0.0142 -0.9025 0.7361, 0.1111 -0.91 0.7498, 0.20800000000000002 -0.9176 0.7636, 0.3049 -0.9251 0.7773, 0.4018 -0.9325 0.7911, 0.4988 -0.94 0.805, 0.5957 -0.9475 0.8188, 0.6926 -0.955 0.8327, 0.7895 -0.9624 0.8466, 0.8864 -0.9699 0.8604, 0.9833 -0.9774 0.8743, 1.0802 -0.9849 0.8881, 1.1771 -0.9923 0.902, 1.274 -0.9998 0.9159 } - new actin { mark = 4 - shape = 0.1391 -0.305 -0.5466, 0.0599 -0.266 -0.5895, -0.0193 -0.2269 -0.6324, -0.0985 -0.1878 -0.6753, -0.1778 -0.1488 -0.7181, -0.257 -0.1097 -0.761, -0.3363 -0.0707 -0.8038, -0.4156 -0.0317 -0.8466, -0.4949 0.0073 -0.8893, -0.5743 0.0463 -0.9319, -0.6537 0.0854 -0.9745, -0.7331 0.1244 -1.017, -0.8125 0.1635 -1.0595, -0.892 0.2026 -1.102, -0.9714 0.2416 -1.1444, -1.0509 0.2807 -1.1869, -1.1303 0.3197 -1.2293, -1.2097 0.3588 -1.2718, -1.2892 0.3978 -1.3143, -1.3686 0.4368 -1.3568, -1.448 0.4758 -1.3994, -1.5275 0.5148 -1.4419, -1.6069 0.5538 -1.4845 + shape = -0.065 1.0008 -0.2088, 0.0283 1.0007 -0.2394, 0.1216 1.0006 -0.27, 0.2149 1.0004 -0.3006, 0.3081 1.0003 -0.3312, 0.4014 1.0001 -0.3617, 0.4948 0.9998 -0.3923, 0.5881 0.9995 -0.4228, 0.6814 0.9991 -0.4533, 0.7748 0.9986 -0.4837, 0.8680999999999999 0.998 -0.514, 0.9615 0.9973 -0.5442, 1.055 0.9964 -0.5744, 1.1484 0.9955 -0.6045, 1.2419000000000002 0.9945 -0.6346, 1.3354 0.9934 -0.6646, 1.4289 0.9923 -0.6945, 1.5224 0.9911 -0.7245, 1.6159 0.9898 -0.7544, 1.7094 0.9885 -0.7843, 1.8029 0.9872 -0.8142, 1.8964 0.9858 -0.8441, 1.9899 0.9845 -0.874 } - new actin { mark = 5 - shape = 2.3944 0.6301 -1.3852, 2.4106 0.5865 -1.4716, 2.4268 0.5428 -1.5581, 2.443 0.4992 -1.6445, 2.4592 0.4555 -1.731, 2.4754 0.4119 -1.8174, 2.4916 0.3682 -1.9039, 2.5077 0.3246 -1.9903, 2.5238 0.2809 -2.0768, 2.5398 0.2372 -2.1632, 2.5558 0.1935 -2.2497, 2.5718 0.1498 -2.3361, 2.5877 0.1061 -2.4226, 2.6035 0.0624 -2.5091, 2.6193 0.0187 -2.5956, 2.6351 -0.025 -2.6821, 2.6508 -0.06870000000000001 -2.7686, 2.6665 -0.1124 -2.8550999999999997, 2.6822 -0.156 -2.9416, 2.6978 -0.1998 -3.0282, 2.7135 -0.2435 -3.1147, 2.7291 -0.2872 -3.2012, 2.7447 -0.3309 -3.2877 + shape = -1.614 -1.003 -0.2647, -1.6279 -0.9121 -0.2992, -1.6418 -0.8212 -0.3336, -1.6556 -0.7303 -0.368, -1.6695 -0.6394 -0.40229999999999994, -1.6834 -0.5484 -0.4367, -1.6972 -0.4575 -0.4709, -1.7111 -0.3665 -0.5051, -1.7251 -0.2755 -0.5392, -1.739 -0.1844 -0.5733, -1.753 -0.0934 -0.6072, -1.767 -0.0023 -0.641, -1.781 0.0889 -0.6746, -1.7951 0.1801 -0.7081, -1.8092 0.2714 -0.7415, -1.8233 0.3627 -0.7747, -1.8374 0.454 -0.8078, -1.8516 0.5454 -0.8407, -1.8658 0.6369 -0.8736, -1.8799 0.7283 -0.9063, -1.8942 0.8198 -0.939, -1.9084 0.9113 -0.9716999999999999, -1.9226 1.0028 -1.0043 } - new actin { mark = 6 - shape = -1.3389 -2.4441 -1.6673, -1.408 -2.4564000000000004 -1.5986, -1.4771 -2.4687 -1.5299, -1.5462 -2.481 -1.4612, -1.6153 -2.4932 -1.3926, -1.6843 -2.5055 -1.3239, -1.7534 -2.5178 -1.2551, -1.8224 -2.5301 -1.1864, -1.8914 -2.5424 -1.1176, -1.9603 -2.5547 -1.0488, -2.0293 -2.5669 -0.98, -2.0981 -2.5791 -0.9111, -2.1669999999999994 -2.5913 -0.8421, -2.2358 -2.6035 -0.7732, -2.3046 -2.6156 -0.7042, -2.3734 -2.6276 -0.6351, -2.4422 -2.6397 -0.5661, -2.5109 -2.6517 -0.4971, -2.5797 -2.6637 -0.428, -2.6485 -2.6757 -0.359, -2.7173 -2.6877 -0.29, -2.7861 -2.6997 -0.221, -2.8549 -2.7117 -0.152 + shape = 0.0385 -0.999 0.7968, 0.078 -0.9096 0.8065, 0.1175 -0.8203000000000001 0.8161, 0.157 -0.7309 0.8257, 0.1965 -0.6415 0.8354, 0.236 -0.5521 0.845, 0.2755 -0.4628 0.8546, 0.315 -0.3734 0.8642, 0.3545 -0.284 0.8739, 0.394 -0.1947 0.8835, 0.4335 -0.1053 0.8932, 0.4731 -0.016 0.9029, 0.5126 0.0734 0.9125, 0.5522 0.1627 0.9221, 0.5917 0.2521 0.9317, 0.6313 0.3414 0.9412, 0.6708 0.4308 0.9506, 0.7103 0.5202 0.96, 0.7497 0.6096 0.9692, 0.7892 0.6991 0.9784, 0.8286 0.7885 0.9874000000000002, 0.868 0.878 0.9964, 0.9075 0.9675 1.0054 } - new actin { mark = 7 - shape = 0.0059 0.9613 0.0926, -0.0111 0.969 -0.0038, -0.0281 0.9766 -0.1001, -0.0452 0.9843 -0.1965, -0.0622 0.992 -0.2929, -0.0792 0.9997 -0.3893, -0.0963 1.0074 -0.4857, -0.1133 1.0152 -0.5821, -0.1304 1.0229 -0.6784, -0.1474 1.0306 -0.7748, -0.1645 1.0383 -0.8712, -0.1815 1.046 -0.9676, -0.1986 1.0536 -1.064, -0.2157 1.0612 -1.1604, -0.2328 1.0688 -1.2567, -0.2499 1.0763 -1.3531, -0.267 1.0838 -1.4495, -0.2841 1.0913 -1.5459, -0.3013 1.0987 -1.6423, -0.3184 1.1061 -1.7387, -0.3355 1.1135 -1.8351, -0.3527 1.1209 -1.9315, -0.3698 1.1282 -2.0279 + shape = 0.2284 -0.8846 -0.7554, 0.1344 -0.8893 -0.7277, 0.0403 -0.894 -0.7, -0.0538 -0.8987 -0.6723, -0.1478 -0.9034 -0.6446, -0.2419 -0.9081 -0.6169, -0.336 -0.9128 -0.5892, -0.4301 -0.9176 -0.5616, -0.5241999999999999 -0.9223 -0.534, -0.6183 -0.9271 -0.5064, -0.7124 -0.9319 -0.4789, -0.8066000000000001 -0.9367 -0.4515, -0.9007 -0.9416 -0.4241, -0.9949 -0.9464 -0.3967, -1.089 -0.9513 -0.3693, -1.1832 -0.9562 -0.3419, -1.2774 -0.9611 -0.3145, -1.3715 -0.966 -0.2871, -1.4657 -0.971 -0.2598, -1.5598 -0.976 -0.2324, -1.654 -0.9811 -0.205, -1.7481 -0.9861 -0.1776, -1.8423 -0.9912 -0.1503 } - new actin { mark = 8 - shape = 0.0006 1.2829 2.8986, 0.0623 1.3555 2.875, 0.1241 1.4281 2.8514, 0.1858 1.5007 2.8278, 0.2476 1.5733 2.8042, 0.3094 1.6459 2.7806, 0.3711 1.7185 2.7571, 0.4329 1.7911 2.7336, 0.4946 1.8637 2.7101, 0.5564 1.9363 2.6866, 0.6182 2.0089 2.6631, 0.6799 2.0816 2.6396, 0.7417 2.1542 2.616, 0.8034 2.2268 2.5925, 0.8652 2.2994 2.5689, 0.927 2.3719 2.5453, 0.9888 2.4445 2.5217, 1.0506 2.517 2.4981, 1.1124 2.5895 2.4745, 1.1743 2.6621 2.4508, 1.2361 2.7345 2.4271, 1.298 2.807 2.4035, 1.3598 2.8795 2.3798 + shape = 1.9719 0.4999 -0.7054, 1.9676 0.4398 -0.6278000000000001, 1.9632 0.3798 -0.5503, 1.9588 0.3197 -0.4727, 1.9544 0.2597 -0.3952, 1.9501 0.1997 -0.3176, 1.9456 0.1396 -0.2401, 1.9412 0.0796 -0.1625, 1.9367 0.0196 -0.0849, 1.9322 -0.0404 -0.0074, 1.9277 -0.1004 0.0702, 1.9231 -0.1604 0.1479, 1.9185 -0.2203 0.2255, 1.9139 -0.2802 0.3031, 1.9093 -0.3401 0.3808, 1.9047 -0.4 0.4584, 1.9 -0.46 0.5361, 1.8953 -0.5199 0.6137, 1.8907 -0.5798 0.6912999999999999, 1.886 -0.6398 0.7689, 1.8814 -0.6998 0.8465, 1.8767 -0.7598 0.9241, 1.8721 -0.8198 1.0017 } - new actin { mark = 9 - shape = -4.2649 -1.5026 0.5193, -4.2453 -1.4143 0.5575, -4.2257 -1.3259 0.5956, -4.2061 -1.2376 0.6338, -4.1865 -1.1493 0.672, -4.1669 -1.061 0.7101, -4.1472 -0.9727000000000001 0.7482, -4.1276 -0.8843 0.7864, -4.108 -0.796 0.8245, -4.0884 -0.7077 0.8626, -4.0688 -0.6194 0.9008, -4.0493 -0.531 0.939, -4.0298 -0.4427 0.9772, -4.0104 -0.3544 1.0155, -3.991 -0.2661 1.0538, -3.9717 -0.1778 1.0921, -3.9525 -0.0895 1.1305, -3.9333 -0.0012 1.1689, -3.9141 0.0871 1.2073, -3.8949 0.1754 1.2457, -3.8758 0.2637 1.2841, -3.8567 0.352 1.3225, -3.8376 0.4404 1.3609 + shape = -0.0354 0.0129 0.5667, -0.122 0.0568 0.5817, -0.2085 0.10070000000000001 0.5967, -0.295 0.1446 0.6116, -0.3816 0.1885 0.6266, -0.4681 0.2324 0.6416, -0.5546 0.2763 0.6566, -0.6412 0.3201 0.6716, -0.7278 0.364 0.6866, -0.8143 0.4078 0.7017, -0.9009 0.4516 0.7167000000000001, -0.9875 0.4953 0.7318, -1.0741 0.539 0.7469, -1.1608 0.5826 0.7619, -1.2474 0.6263 0.777, -1.3341 0.6698 0.7921, -1.4208 0.7134 0.8072, -1.5075 0.7569 0.8222, -1.5942 0.8004 0.8373, -1.681 0.8438 0.8525, -1.7677 0.8873 0.8676, -1.8545 0.9307 0.8827, -1.9412 0.9741 0.8978 } - new actin { mark = 10 - shape = -1.2257 1.1565 1.7855, -1.1643 1.1067 1.7272, -1.103 1.057 1.6689, -1.0416 1.0073 1.6106, -0.9803 0.9575 1.5522, -0.919 0.9078 1.4939, -0.8577 0.858 1.4355, -0.7964 0.8082 1.3772, -0.7351 0.7584 1.3188, -0.6739 0.7086 1.2605, -0.6126 0.6587 1.2021, -0.5514 0.6088 1.1438, -0.4902 0.5589 1.0854, -0.429 0.509 1.0271, -0.3677 0.459 0.9689, -0.3065 0.409 0.9106, -0.2452 0.359 0.8525, -0.1839 0.309 0.7943, -0.1226 0.2589 0.7362, -0.0612 0.2089 0.6782, 0.0001 0.1588 0.6201, 0.0614 0.1087 0.5621, 0.1228 0.0586 0.5041 + shape = -1.5023 -0.9664 0.9715, -1.4041 -0.967 0.9724, -1.306 -0.9676 0.9734, -1.2078 -0.9683 0.9743, -1.1096 -0.9689 0.9752, -1.0114 -0.9694 0.9762, -0.9133 -0.9699 0.9771, -0.8151 -0.9704 0.9782, -0.7169 -0.9709 0.9792, -0.6187 -0.9713 0.9803, -0.5206 -0.9718 0.9814, -0.4224 -0.9722 0.9827, -0.3242 -0.9726 0.9839, -0.2261 -0.973 0.9853, -0.1279 -0.9733 0.9868, -0.0297 -0.9737000000000001 0.9883, 0.0685 -0.974 0.9899, 0.1666 -0.9744 0.9915, 0.2648 -0.9747 0.9932, 0.363 -0.975 0.9949, 0.4611 -0.9753 0.9966, 0.5593 -0.9756 0.9984, 0.6575 -0.9759 1.0001 } - new actin { mark = 11 - shape = 4.4802 0.3967 -0.6477, 4.539 0.3334 -0.6943, 4.5979 0.27 -0.7408, 4.6567 0.2067 -0.7873, 4.7156 0.1434 -0.8338, 4.7744 0.08 -0.8803, 4.8332 0.0166 -0.9268, 4.892 -0.0469 -0.9733, 4.9507 -0.1104 -1.0197, 5.0094 -0.1739 -1.0662, 5.0681 -0.2375 -1.1126, 5.1267 -0.30119999999999997 -1.159, 5.1853 -0.3648 -1.2054, 5.2439 -0.4285 -1.2518, 5.3025 -0.4922 -1.2982, 5.3611 -0.5559 -1.3446, 5.4196 -0.6196 -1.391, 5.4781 -0.6833 -1.4374, 5.5366 -0.7471 -1.4838, 5.5951 -0.8108 -1.5303, 5.6536 -0.8746 -1.5767, 5.712 -0.9383 -1.6231, 5.7705 -1.0021 -1.6696 + shape = -0.211 0.0825 0.6727, -0.1143 0.0925 0.6865, -0.0176 0.1025 0.7004, 0.079 0.1125 0.7142, 0.1757 0.1225 0.728, 0.2724 0.1325 0.7418, 0.3691 0.1425 0.7555, 0.4658 0.1525 0.7693, 0.5625 0.1626 0.7829, 0.6592 0.1726 0.7966, 0.756 0.18259999999999998 0.8102, 0.8527 0.1926 0.8237, 0.9494 0.2025 0.8372, 1.0462 0.2125 0.8508, 1.1429 0.2225 0.8643, 1.2396 0.2325 0.8777, 1.3364 0.2425 0.8912, 1.4331 0.2525 0.9046, 1.5299 0.2625 0.918, 1.6266 0.2726 0.9314, 1.7234 0.2826 0.9447, 1.8201 0.2926 0.9579999999999999, 1.9169 0.3027 0.9713 } - 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new actin { mark = 22 - shape = -2.2038 -0.0474 0.8497, -2.2449 0.0193 0.9089, -2.286 0.086 0.9681, -2.327 0.1526 1.0274, -2.3681 0.2193 1.0866, -2.4092 0.2859 1.1459, -2.4503 0.3525 1.2052, -2.4914 0.4191 1.2645, -2.5325 0.4856 1.3239, -2.5736 0.5521 1.3833, -2.6147 0.6185 1.4428, -2.6558 0.6849 1.5023, -2.697 0.7512 1.5619, -2.7381 0.8175 1.6215, -2.7793 0.8837 1.6812, -2.8205 0.9499 1.7408, -2.8616 1.0161 1.8005, -2.9028 1.0824 1.8602, -2.9439 1.1486 1.92, -2.9849 1.2148 1.9797, -3.026 1.281 2.0395, -3.067 1.3473 2.0992, -3.108 1.4135 2.1589 + shape = 1.3923 -0.922 0.9937, 1.3331 -0.8436999999999999 0.9909, 1.274 -0.7653 0.988, 1.2148 -0.687 0.9852, 1.1557 -0.6087 0.9824, 1.0966 -0.5303 0.9796, 1.0376 -0.452 0.9768, 0.9785 -0.3736 0.974, 0.9195 -0.2951 0.9712, 0.8605 -0.2167 0.9685, 0.8015 -0.1383 0.9657, 0.7426 -0.0598 0.9629, 0.6836 0.0187 0.9601, 0.6247 0.0972 0.9574, 0.5658 0.1757 0.9547, 0.5069 0.2542 0.9519, 0.4481 0.3327 0.9492, 0.3892 0.4113 0.9465, 0.3304 0.4898 0.9438, 0.2716 0.5684 0.9411, 0.2128 0.647 0.9384, 0.154 0.7255 0.9356, 0.0952 0.8041 0.9329 } - new actin { mark = 23 - shape = 1.2002 2.9736 0.0401, 1.296 2.9795 0.0607, 1.3918 2.9853 0.08139999999999999, 1.4876 2.9912 0.1021, 1.5834 2.997 0.1227, 1.6793 3.0029 0.1433, 1.7751 3.0087 0.1639, 1.8709 3.0146 0.1845, 1.9667 3.0204 0.205, 2.0626 3.0263 0.2255, 2.1584 3.0321 0.2459, 2.2543 3.0379 0.2663, 2.3502 3.0438 0.2867, 2.446 3.0496 0.307, 2.5419 3.0554 0.3273, 2.6378 3.0612 0.3476, 2.7337 3.067 0.3679, 2.8296 3.0728 0.3882, 2.9255 3.0786 0.4084, 3.0214 3.0845 0.4286, 3.1173 3.0903 0.4489, 3.2132 3.0961 0.4691, 3.3091 3.1019 0.4893 + shape = -0.2765 -0.8728 0.9998, -0.1784 -0.877 0.9998, -0.0804 -0.8813 0.9999, 0.0177 -0.8855 1.0, 0.1158 -0.8898 1.0, 0.2139 -0.894 1.0, 0.312 -0.8983 1.0001, 0.4101 -0.9026 1.0001, 0.5082 -0.9069 1.0001, 0.6063 -0.9112 1.0001, 0.7044 -0.9155 1.0001, 0.8024 -0.9199 1.0001, 0.9005 -0.9242 1.0, 0.9986 -0.9285 1.0001, 1.0967 -0.9329 1.0001, 1.1948 -0.9372 1.0001, 1.2929 -0.9416 1.0001, 1.391 -0.9459 1.0002, 1.489 -0.9503 1.0002, 1.5871 -0.9547 1.0002, 1.6852 -0.9590000000000001 1.0002, 1.7833000000000003 -0.9634 1.0003, 1.8814 -0.9677 1.0003 } - new actin { mark = 24 - shape = -0.9014 -1.1197 3.3365, -0.8223 -1.0649 3.3561, -0.7432 -1.0102 3.3757, -0.6641 -0.9555 3.3953, -0.5849 -0.9008 3.415, -0.5058 -0.8461 3.4346, -0.4266 -0.7915 3.4543, -0.3475 -0.7369 3.474, -0.2683 -0.6823 3.4937, -0.189 -0.6277 3.5134, -0.1098 -0.5732 3.5331, -0.0305 -0.5187 3.5529, 0.04869999999999999 -0.4643 3.5726, 0.128 -0.4098 3.5924, 0.2072 -0.3553 3.6122, 0.2864999999999999 -0.3009 3.6321, 0.3657000000000001 -0.2464 3.6519, 0.4449 -0.1919 3.6717, 0.5241 -0.13740000000000002 3.6916000000000007, 0.6033 -0.0829 3.7114, 0.6825 -0.0283 3.7313, 0.7617 0.0262 3.7511, 0.8409 0.0807 3.771 + shape = 1.1582 0.9796 0.9919, 1.1964 0.9806 0.9015, 1.2346 0.9816 0.811, 1.2727 0.9826 0.7206, 1.3109 0.9836 0.6301, 1.349 0.9846 0.5396, 1.3871 0.9856 0.4492, 1.4251 0.9867 0.3587, 1.4631 0.9877 0.2681, 1.5011 0.9887 0.1776, 1.5391 0.9896 0.0871, 1.5771 0.9905 -0.0035, 1.615 0.9914 -0.094, 1.6529 0.9923 -0.1846, 1.6907 0.9932 -0.2752, 1.7285 0.994 -0.3658, 1.7663 0.9949 -0.4564, 1.8041 0.9957 -0.547, 1.8419 0.9966 -0.6376, 1.8797 0.9974 -0.7283, 1.9174 0.9982 -0.8189, 1.9552 0.9991 -0.9095, 1.9929 0.9999 -1.0001 } - new actin { mark = 25 - shape = -2.8035 -1.6508 -2.2037, -2.8786 -1.6891 -2.2541, -2.9537 -1.7273 -2.3044, -3.0289 -1.7655 -2.3547, -3.104 -1.8038 -2.405, -3.1791 -1.842 -2.4554, -3.2542 -1.8803 -2.5057, -3.3293 -1.9185 -2.5561, -3.4043 -1.9567 -2.6066, -3.4794 -1.9949 -2.6571, -3.5545 -2.033 -2.7076, -3.6295 -2.0711 -2.7581, -3.7046 -2.1091 -2.8087, -3.7796 -2.1472 -2.8593, -3.8547 -2.1851 -2.91, -3.9297 -2.2231 -2.9607000000000006, -4.0047 -2.2611 -3.0114, -4.0797 -2.299 -3.0621, -4.1548 -2.3369 -3.1128, -4.2298 -2.3749 -3.1635, -4.3048 -2.4128 -3.2142, -4.3799 -2.4508 -3.2649, -4.4549 -2.4887 -3.3155 + shape = -1.3517 0.9061 -0.9993, -1.3815 0.8734 -0.9117, -1.4112 0.8406 -0.824, -1.4409 0.8079 -0.7363, -1.4706 0.7752 -0.6486, -1.5003 0.7424 -0.561, -1.5299 0.7096 -0.4733, -1.5596 0.6767 -0.3857, -1.5892 0.6438 -0.2981, -1.6189 0.6109 -0.2104, -1.6485 0.5779 -0.1228, -1.6781 0.5449 -0.0352, -1.7076 0.5119 0.0524, -1.737 0.4788 0.14, -1.7664 0.4456 0.2276, -1.7958 0.4123 0.3152, -1.8251 0.379 0.40280000000000005, -1.8544 0.3456 0.4903, -1.8836 0.3122 0.5779, -1.9128 0.2787 0.6655, -1.942 0.2453 0.753, -1.9712 0.2118 0.8406, -2.0004 0.1783 0.9281 } - new actin { mark = 26 - shape = -0.3441 -1.32 -1.8093, -0.432 -1.3634 -1.8139, -0.52 -1.4068 -1.8184000000000002, -0.6079 -1.4503 -1.8229, -0.6958 -1.4937 -1.8275, -0.7838 -1.5372 -1.832, -0.8717 -1.5806 -1.8365, -0.9596 -1.6241 -1.841, -1.0475 -1.6676 -1.8456, -1.1354 -1.7111 -1.8501, -1.2233 -1.7547 -1.8547, -1.3112 -1.7982 -1.8593, -1.3991 -1.8416 -1.864, -1.487 -1.8851 -1.8687, -1.575 -1.9285 -1.8734, -1.6629 -1.9719 -1.8782, -1.7509 -2.0153 -1.8831, -1.8389 -2.0586 -1.888, -1.9269 -2.1018 -1.8929, -2.0149 -2.1451 -1.8978, -2.1029 -2.1883 -1.9027, -2.1909 -2.2316 -1.9076, -2.2789 -2.2748 -1.9125 + shape = -1.0941 0.9981000000000001 0.9487, -1.135 0.9877 0.8601, -1.176 0.9772 0.7714, -1.2169 0.9668 0.6828, -1.2578 0.9564 0.5942, -1.2988 0.9459 0.5056, -1.3398 0.9355 0.417, -1.3808 0.925 0.3284, -1.4218 0.9146 0.2398, -1.4629 0.9041 0.1512, -1.504 0.8936 0.0627, -1.5452 0.8831 -0.0258, -1.5864 0.8725 -0.1143, -1.6276 0.862 -0.2028, -1.6688 0.8514 -0.2913, -1.7101 0.8408 -0.3797, -1.7514 0.8302 -0.4682, -1.7926 0.8196 -0.5566, -1.8339 0.809 -0.6451, -1.8752 0.7983 -0.7335, -1.9165 0.7875 -0.8219, -1.9578 0.7768 -0.9103, -1.9991 0.7661 -0.9988 } - new actin { mark = 27 - shape = -2.569 0.0629 -0.1015, -2.4906 0.119 -0.0828, -2.4122 0.175 -0.064, -2.3338 0.2311 -0.0453, -2.2554 0.2871 -0.0265, -2.177 0.3431 -0.0078, -2.0986 0.3992 0.011, -2.0202 0.4552 0.0297, -1.9418 0.5113 0.0485, -1.8635 0.5675 0.0673, -1.7852 0.6236 0.0861, -1.7069 0.6798 0.1049, -1.6286 0.736 0.1238, -1.5504 0.7923 0.1426, -1.4722 0.8486 0.1615, -1.3941 0.9049 0.1805, -1.316 0.9613 0.1995, -1.238 1.0177 0.2185, -1.1599 1.0742 0.2375, -1.0819 1.1306 0.2566, -1.0039 1.1871 0.2757, -0.9259 1.2436 0.2948, -0.8479 1.3 0.31390000000000007 + shape = -0.5424 0.7955 -1.0005, -0.4486 0.7665000000000001 -1.0004, -0.3548 0.7375 -1.0004, -0.261 0.7085 -1.0003, -0.1672 0.6795 -1.0003, -0.0734 0.6506 -1.0002, 0.0204 0.6217 -1.0002, 0.1142 0.5928 -1.0001, 0.2081 0.5639 -1.0001, 0.3019 0.5351 -1.0, 0.3958 0.5063 -1.0, 0.4897 0.4775 -1.0, 0.5836 0.4487 -1.0, 0.6774 0.42 -1.0, 0.7713 0.3912 -1.0, 0.8652 0.3625 -0.9999, 0.9591 0.3337 -0.9999, 1.0529 0.305 -0.9999, 1.1468 0.2762 -0.9999, 1.2407 0.2475 -0.9999, 1.3346 0.2187 -0.9999, 1.4284 0.19 -0.9999, 1.5223 0.1612 -0.9999 } - new actin { mark = 28 - shape = 0.4029 -1.7313 -0.9874000000000002, 0.364 -1.8104 -0.9441, 0.3252 -1.8895 -0.9008, 0.2863 -1.9685 -0.8573999999999999, 0.2474 -2.0476 -0.8141, 0.2085 -2.1266 -0.7707, 0.1696 -2.2057 -0.7273, 0.1307 -2.2846000000000006 -0.6839, 0.0917 -2.3636 -0.6405, 0.0527 -2.4425 -0.597, 0.0135 -2.5213 -0.5535, -0.0256 -2.6001 -0.51, -0.0649 -2.6789 -0.4664, -0.1042 -2.7576 -0.4229, -0.1436 -2.8363 -0.3793, -0.183 -2.915 -0.3358, -0.2224 -2.9937 -0.2922, -0.2619 -3.0723 -0.2486, -0.3013 -3.1509 -0.205, -0.3408 -3.2296 -0.1615, -0.3803 -3.3082 -0.1179, -0.4198 -3.3869 -0.0743, -0.4592 -3.4655 -0.0308 + shape = -1.2995 -0.9506 0.2107, -1.2143 -0.9505 0.1618, -1.1292 -0.9503 0.113, -1.044 -0.9502 0.0642, -0.9588 -0.9501 0.0154, -0.8736 -0.95 -0.0334, -0.7884 -0.9499 -0.0822, -0.7032 -0.9497 -0.131, -0.618 -0.9496 -0.1798, -0.5328 -0.9494 -0.2285, -0.4475 -0.9493 -0.2773, -0.3623 -0.9491 -0.326, -0.2771 -0.949 -0.3747, -0.1918 -0.9489 -0.4234, -0.1066 -0.9488 -0.4722, -0.0213 -0.9488 -0.5209, 0.0639 -0.9487 -0.5696, 0.1491 -0.9488 -0.6184, 0.2343 -0.9488 -0.6672, 0.3195 -0.9489 -0.716, 0.4047 -0.949 -0.7648, 0.4899 -0.9491 -0.8136, 0.5751 -0.9492 -0.8624 } - new actin { mark = 29 - shape = 0.0191 2.9285 -1.479, 0.0768 2.9368 -1.4, 0.1345 2.945 -1.321, 0.1921 2.9532 -1.2419000000000002, 0.2498 2.9614 -1.1629, 0.3074 2.9696 -1.0838, 0.365 2.9778 -1.0047, 0.4226 2.9858 -0.9256, 0.4802 2.9938 -0.8465, 0.5377 3.0018 -0.7673, 0.5952 3.0096 -0.6881, 0.6527 3.0174 -0.6089, 0.7101 3.0251 -0.5296, 0.7675000000000001 3.0327 -0.4504, 0.8249 3.0402 -0.3711, 0.8822 3.0477 -0.2917, 0.9395 3.0552 -0.2123, 0.9967 3.0627 -0.1329, 1.0539 3.0701 -0.0534, 1.1111 3.0776 0.0261, 1.1682 3.085 0.1056, 1.2254 3.0924 0.1851, 1.2825 3.0998 0.2646 + shape = -1.2902 -0.9998 -0.4911, -1.2177 -0.9998 -0.425, -1.1452 -0.9998 -0.3588, -1.0726 -0.9998 -0.2926, -1.0001 -0.9998 -0.2265, -0.9275 -0.9998 -0.1604, -0.8549 -0.9998 -0.0942, -0.7823 -0.9998 -0.0281, -0.7097 -0.9998 0.0379, -0.6371 -0.9998 0.10400000000000001, -0.5644 -0.9998 0.17, -0.4917 -0.9998 0.2361, -0.419 -0.9998 0.3021, -0.3463 -0.9997 0.368, -0.2736 -0.9996 0.434, -0.2009 -0.9994 0.5, -0.1282 -0.9991 0.5659, -0.0554 -0.9988 0.6318, 0.0173 -0.9985 0.6978, 0.0901 -0.9981000000000001 0.7637, 0.16279999999999997 -0.9977 0.8297, 0.2355 -0.9973 0.8957, 0.3082 -0.9969 0.9616 } - new actin { mark = 30 - shape = 3.2825 -1.722 0.3052, 3.2155 -1.7435 0.2367, 3.1485 -1.7649 0.1683, 3.0815 -1.7864 0.0998, 3.0145 -1.808 0.0313, 2.9476 -1.8295 -0.0371, 2.8806 -1.8511 -0.1056, 2.8136 -1.8727 -0.1741, 2.7466 -1.8943 -0.2425, 2.6796 -1.9159 -0.3109, 2.6124999999999994 -1.9375 -0.3793, 2.5454 -1.9591000000000003 -0.4476, 2.4783 -1.9807 -0.516, 2.4112 -2.0024 -0.5843, 2.3441 -2.024 -0.6526, 2.2769 -2.0455 -0.7209, 2.2098 -2.0671 -0.7892, 2.1427 -2.0887 -0.8575, 2.0755 -2.1102 -0.9258, 2.0084 -2.1318 -0.9941, 1.9412 -2.1533 -1.0624, 1.874 -2.1748 -1.1307, 1.8068 -2.1963 -1.199 + shape = -1.6126 0.8567 0.9886, -1.6276 0.7728 0.9398, -1.6427 0.6889 0.891, -1.6578 0.6051 0.8422, -1.6728 0.5212 0.7934, -1.6878 0.4373 0.7446, -1.7028 0.3534 0.6959, -1.7178 0.2695 0.6472, -1.7328 0.1856 0.5985, -1.7477 0.1016 0.5499, -1.7626 0.0175 0.5014, -1.7774 -0.0665 0.4529, -1.7923 -0.1507 0.4046, -1.8071 -0.2349 0.3563, -1.8218 -0.3192 0.3081, -1.8366 -0.4035 0.26, -1.8513 -0.4878 0.212, -1.866 -0.5722 0.164, -1.8806 -0.6566 0.116, -1.8953 -0.741 0.0681, -1.9099 -0.8255 0.0201, -1.9246 -0.9099 -0.0278, -1.9392 -0.9943 -0.0757 } -run 1000 system + + +run 100 system { - nb_frames = 10 + nb_frames = 1 } % report single:force force.txt { verbose=0; } diff --git a/vivarium_models/processes/cytosim.py b/vivarium_models/processes/cytosim.py index 32be9fc..1de4900 100644 --- a/vivarium_models/processes/cytosim.py +++ b/vivarium_models/processes/cytosim.py @@ -34,17 +34,22 @@ def fiber_section(id, fiber): points = fiber['points'] # convert to microns point_strs = [" ".join([str(element * RELATIVE_MICRON) for element in point]) for point in points] - point_line = ', '.join(point_strs) + return { + 'id': id, + 'points': point_strs} + + + # point_line = ', '.join(point_strs) - lines = [ - f'new actin', - '{', - f' mark = {id}', - f' shape = {point_line}', - '}', - ] + # lines = [ + # f'new actin', + # '{', + # f' mark = {id}', + # f' shape = {point_line}', + # '}', + # ] - return '\n'.join(lines) + # return '\n'.join(lines) def load_report(output): @@ -74,6 +79,7 @@ class CytosimProcess(Process): 'internal_timestep': 0.001, 'cytosim_template': "cytosim-buckling.cym", 'cell_radius': 5, + 'confine': None, "input_directory": "in/", "output_directory": "out/", 'cytosim_sim': "../cytosim/bin/sim", @@ -97,6 +103,9 @@ def ports_schema(self): return ports + def calculate_timestep(self, state): + return 0.1 + def initial_state(self, config): return {} @@ -112,10 +121,12 @@ def next_update(self, timestep, state): cytosim_config = template.render( internal_timestep=self.parameters['internal_timestep'], # radius=self.parameters['cell_radius'], + confine=self.parameters['confine'], bounds_x=box_extent[0], bounds_y=box_extent[1], bounds_z=box_extent[2], - filament_section='\n\n\n'.join(fiber_sections), + filaments=fiber_sections, + # filament_section='\n\n\n'.join(fiber_sections), simulation_time=int(timestep/self.parameters['internal_timestep']), ) @@ -155,7 +166,11 @@ def next_update(self, timestep, state): def main(): - cytosim = CytosimProcess({}) + cytosim = CytosimProcess({ + 'confine': { + 'side': 'inside', + 'force': 100, + 'space': 'cell'}}) engine = Engine( processes={'cytosim': cytosim}, @@ -170,17 +185,6 @@ def main(): engine.update(10.0) output = engine.emitter.get_data() - # output = simulate_process( - # cytosim, { - # 'initial_state': initial_fibers, - # 'total_time': 5, - # 'return_raw_data': True, - # 'settings': { - # 'emitter': 'simularium' - # }, - # } - # ) - import ipdb; ipdb.set_trace() if __name__ == '__main__': diff --git a/vivarium_models/templates/cytosim-buckling.cym b/vivarium_models/templates/cytosim-buckling.cym index 222c7e5..88e5c18 100644 --- a/vivarium_models/templates/cytosim-buckling.cym +++ b/vivarium_models/templates/cytosim-buckling.cym @@ -23,6 +23,9 @@ set fiber actin rigidity = 10 segmentation = 0.1 display = ( point=6,1; line=10,2; ) + {% if confine %} + confine = {{confine.side}}, {{confine.force}}, {{confine.space}} + {% endif %} } set hand binder @@ -41,11 +44,18 @@ set single link stiffness = 1000 } +{% for filament in filaments %} +new actin +{ + mark = {{filament.id}} + shape = {{filament.points|join(', ')}} +} +{% endfor %} {{filament_section}} run {{simulation_time}} system { - nb_frames = 10 + nb_frames = 1 } % report single:force force.txt { verbose=0; }