Cytosim Buckling

setup.py

@@ -81,7 +81,7 @@
     name="vivarium_models",
     packages=find_packages(exclude=["tests", "*.tests", "*.tests.*"]),
     package_data={
-        '': ['templates/*']},
+        '': ['templates/*', 'templates/medyan_Chandrasekaran_2019_no_tread_2mUNI_alphaA_0.1_MA_0.675/*']},
     python_requires=">=3.8",
     setup_requires=setup_requirements,
     test_suite="vivarium_models/tests",

vivarium_models/composites/moving_anchor.py

@@ -0,0 +1,163 @@
+from vivarium.core.composer import Composer
+from vivarium.core.engine import Engine
+from vivarium.processes.alternator import PeriodicEvent
+
+from vivarium_cytosim import CytosimProcess
+from vivarium_models.data.fibers import single_fiber
+
+from vivarium.core.process import Step
+
+import numpy as np
+import copy
+
+READDY_TIMESTEP = 0.0000001
+ALTERNATOR_PERIODS = [2.0, READDY_TIMESTEP]
+
+
+class AnchorMover(Step):
+    defaults = {
+        "fiber_id": 0,
+        "point_index": 0,
+        "movement_vector": [0, 0, 0],
+    }
+
+    def __init__(self, config=None):
+        super().__init__(config)
+
+    def ports_schema(self):
+        return {
+            "fibers": {
+                "*": {
+                    "type_name": {
+                        "_default": "",
+                        "_updater": "set",
+                        "_emit": True,
+                    },
+                    "points": {
+                        "_default": [],
+                        "_updater": "set",
+                        "_emit": True,
+                    },
+                }
+            }
+        }
+
+    def next_update(self, timestep, state):
+        points = state["fibers"][self.parameters["fiber_id"]]["points"]
+        anchor = points[self.parameters["point_index"]]
+        anchor_moved = anchor + np.array(self.parameters["movement_vector"])
+        points[self.parameters["point_index"]] = anchor_moved
+
+        return {
+            "fibers": {
+                self.parameters["fiber_id"]: {
+                    "points": points
+                }
+            }
+        }
+
+class AnchorMoverCytosim(CytosimProcess):
+    new_defaults = {
+        "fiber_id": 0,
+        "point_index": 0,
+        "movement_vector": [0, 0, 0],
+    }
+
+    def __init__(self, config=None):
+        parameters = copy.deepcopy(self.new_defaults)
+        parameters.update(config)
+        super().__init__(parameters)
+
+    def next_update(self, timestep, state):
+        points = state["fibers"][self.parameters["fiber_id"]]["points"]
+        anchor = points[self.parameters["point_index"]]
+        anchor_moved = anchor + np.array(self.parameters["movement_vector"])
+        points[self.parameters["point_index"]] = anchor_moved
+        update = super().next_update(timestep, state)
+        return update
+
+class BucklingSqueeze(Composer):
+    defaults = {
+        "periodic_event": {
+            "periods": [1.0]
+        },
+        "cytosim_anchor_mover_squeeze": {
+            'model_name': 'buckling_squeeze',
+            "movement_vector": [5, 0, 0],
+            "fiber_id": "1",
+        },
+        # "cytosim_squeeze": {
+        #     'model_name': 'buckling_squeeze'
+        # },
+        # "anchor_mover": {
+        #     "movement_vector": [0, 5, 0],
+        #     "fiber_id": "1",
+        # }
+    }
+
+    def __init__(self, config=None):
+        super().__init__(config)
+
+    def generate_processes(self, config):
+        periodic_event = PeriodicEvent(config["periodic_event"])
+        # cytosim_squeeze = CytosimProcess(config['cytosim_squeeze'])
+        # anchor_mover = AnchorMover(config["anchor_mover"])
+        cytosim_anchor_mover_squeeze = AnchorMoverCytosim(config["cytosim_anchor_mover_squeeze"])
+
+        return {
+            "periodic_event": periodic_event,
+            # 'cytosim_squeeze': cytosim_squeeze,
+            # "anchor_mover": anchor_mover,
+            "cytosim_anchor_mover_squeeze": cytosim_anchor_mover_squeeze
+        }
+
+    def generate_topology(self, config):
+        return {
+            "periodic_event": {
+                "event_trigger": ("alternate_trigger",),
+                "period_index": ("period_index",),
+            },
+            # "cytosim_squeeze": {
+            #     "fibers": ("fibers",),
+            #     "fibers_box_extent": ("fibers_box_extent",),
+            # },
+            # "anchor_mover": {
+            #     "fibers": ("fibers",),
+            # }
+            "cytosim_anchor_mover_squeeze": {
+                "fibers": ("fibers",),
+                "fibers_box_extent": ("fibers_box_extent",),
+            },
+        }
+
+
+def test_buckling_squeeze():
+    initial_state = single_fiber()
+    initial_state['choices'] = 'N/A'
+    cytosim_config = {
+        'actin_segmentation': 0.005,
+        "timestep": 5,
+        "template_directory": "vivarium_models/templates/"}
+    buckling_squeeze_config = {
+        # "cytosim_squeeze": cytosim_config
+         "cytosim_anchor_mover_squeeze": cytosim_config
+    }
+    buckling_squeeze = BucklingSqueeze(buckling_squeeze_config)
+    composite = buckling_squeeze.generate()
+    composite["initial_state"] = initial_state
+    engine = Engine(
+        processes=composite["processes"],
+        topology=composite["topology"],
+        initial_state=composite["initial_state"],
+        emitter="simularium",
+        emit_processes=True,
+    )
+    engine.update(100)
+
+    output = engine.emitter.get_data()
+    # import ipdb; ipdb.set_trace()
+
+
+
+if __name__ == "__main__":
+    test_buckling_squeeze()

vivarium_models/data/fibers.py

@@ -1,4 +1,5 @@
 import numpy as np
+import copy
 
 initial_fibers = {
     "fibers_box_extent": np.array([4000.0, 2000.0, 2000.0]),
@@ -226,3 +227,84 @@ def centered_initial_fibers():
                 fiber_points[point_index] - 0.5 * initial_fibers["fibers_box_extent"]
             )
     return result
+
+def map_fibers(f, initial_fibers):
+    result = copy.deepcopy(initial_fibers)
+    for fiber_id in initial_fibers["fibers"]:
+        fiber_points = initial_fibers["fibers"][fiber_id]["points"]
+        for point_index in range(len(fiber_points)):
+            result["fibers"][fiber_id]["points"][point_index] = (
+                f(fiber_points[point_index], initial_fibers["fibers_box_extent"])
+            )
+    return result
+
+
+def single_fiber():
+    fiber = {
+        "fibers_box_extent": np.array([4000.0, 2000.0, 2000.0]),
+        "fibers": {
+            '1': {
+                "type_name": "Actin-Polymer",
+                "points": [
+                    np.array([-0.250, 0.000, 0.000]),
+                    np.array([-0.240, 0.000, 0.000]),
+                    np.array([-0.230, 0.000, 0.000]),
+                    np.array([-0.220, 0.000, 0.000]),
+                    np.array([-0.210, 0.000, 0.000]),
+                    np.array([-0.200, 0.000, 0.000]),
+                    np.array([-0.190, 0.000, 0.000]),
+                    np.array([-0.180, 0.000, 0.000]),
+                    np.array([-0.170, 0.000, 0.000]),
+                    np.array([-0.160, 0.000, 0.000]),
+                    np.array([-0.150, 0.000, 0.000]),
+                    np.array([-0.140, 0.000, 0.000]),
+                    np.array([-0.130, 0.000, 0.000]),
+                    np.array([-0.120, 0.000, 0.000]),
+                    np.array([-0.110, 0.000, 0.000]),
+                    np.array([-0.100, 0.000, 0.000]),
+                    np.array([-0.090, 0.000, 0.000]),
+                    np.array([-0.080, 0.000, 0.000]),
+                    np.array([-0.070, 0.000, 0.000]),
+                    np.array([-0.060, 0.000, 0.000]),
+                    np.array([-0.050, 0.000, 0.000]),
+                    np.array([-0.040, 0.000, 0.000]),
+                    np.array([-0.030, 0.000, 0.000]),
+                    np.array([-0.020, 0.000, 0.000]),
+                    np.array([-0.010, 0.000, 0.000]),
+                    np.array([0.000, 0.000, 0.000]),
+                    np.array([0.010, 0.000, 0.000]),
+                    np.array([0.020, 0.000, 0.000]),
+                    np.array([0.030, 0.000, 0.000]),
+                    np.array([0.040, 0.000, 0.000]),
+                    np.array([0.050, 0.000, 0.000]),
+                    np.array([0.060, 0.000, 0.000]),
+                    np.array([0.070, 0.000, 0.000]),
+                    np.array([0.080, 0.000, 0.000]),
+                    np.array([0.090, 0.000, 0.000]),
+                    np.array([0.100, 0.000, 0.000]),
+                    np.array([0.110, 0.000, 0.000]),
+                    np.array([0.120, 0.000, 0.000]),
+                    np.array([0.130, 0.000, 0.000]),
+                    np.array([0.140, 0.000, 0.000]),
+                    np.array([0.150, 0.000, 0.000]),
+                    np.array([0.160, 0.000, 0.000]),
+                    np.array([0.170, 0.000, 0.000]),
+                    np.array([0.180, 0.000, 0.000]),
+                    np.array([0.190, 0.000, 0.000]),
+                    np.array([0.200, 0.000, 0.000]),
+                    np.array([0.210, 0.000, 0.000]),
+                    np.array([0.220, 0.000, 0.000]),
+                    np.array([0.230, 0.000, 0.000]),
+                    np.array([0.240, 0.000, 0.000]),
+                    np.array([0.250, 0.000, 0.000]),
+                ]}}}
+
+    scaled = map_fibers(
+        lambda fiber_points, box_extent: fiber_points * 1000,
+        fiber)
+
+    return scaled
+
+if __name__ == '__main__':
+    fiber = single_fiber()
+    import ipdb; ipdb.set_trace()

vivarium_models/processes/simularium_emitter.py

@@ -309,4 +309,4 @@ def get_data(self) -> dict:
         simularium_converter = SimulariumEmitter.get_simularium_converter(
             trajectory, box_dimensions, 0.1
         )
-        simularium_converter.write_JSON("out/actin_test")
+        simularium_converter.save("out/actin_test")

vivarium_models/templates/buckling_squeeze.cym

@@ -0,0 +1,98 @@
+% Fiber under compression to measure buckling force
+% F. Nedelec, 23.05.2017, 21.02.2018
+
+
+set simul system
+{
+    time_step = {{internal_timestep}}
+    viscosity = {{viscosity}}
+    kT = {{kT}}
+}
+
+set space cell
+{
+    shape = sphere
+}
+
+new cell
+{
+    radius = 2
+}
+
+set fiber filament
+{
+    rigidity = 1
+    segmentation = {{actin_segmentation}}
+    display = ( point=6,1; line=10,2; )
+    {% if confine %}
+    confine = {{confine.side}}, {{confine.force}}, {{confine.space}}
+    {% endif %}
+}
+
+set hand binder
+{
+    % 10 events per second, 0.05 um binding radius
+
+    binding = 10, 0.05
+
+    % 0 events per second, infinite unbinding force
+
+    unbinding = 0, inf
+    bind_also_end = 1
+
+    display = ( width=3; size=12; color=green )
+}
+
+set single linker
+{
+    hand = binder
+    activity = fixed
+    stiffness = 1000
+}
+
+
+{% for filament in filaments %}
+new filament
+{
+    mark = {{filament.id}}
+    shape = {{filament.points|join(', ')}}
+    placement = off
+    attach1 = linker, 0, minus_end
+    attach2 = linker, 0, plus_end
+}
+{% endfor %}
+
+% but figure out how to set the location of individual segmentation points on an actin filament (fiber)
+
+% new linker
+% {
+%     position = -4.5 0 0 
+%     % attach = fiber1, 0
+% }
+
+% new linker
+% {
+%     position = +4.5 0 0 
+%     % attach = fiber1, 10
+% }
+
+run {{simulation_time}} system
+{
+    % this could be 1 if you want to just get the last state
+    nb_frames = 1
+}
+
+% change some properties
+% for example, see "event.cym"
+
+% continue running
+
+% retrieve the state:
+% positions of everything 
+
+
+%  you want to grab 
+% positions (fiber points) (single) etc
+
+% report single:force force.txt { verbose=0; }
+% report fiber:tension tension.txt { verbose=0; plane = 1 0 0, 0; }