SMS_BP
Single Molecule Simulations -BP
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Public Member Functions | |
__init__ (self, np.ndarray inital_position=np.array([0, 0, 0]), int initial_time=0, float diffusion_coefficient=0, float hurst_exponent=0, str units_time='ms', str units_position='um', int condensate_id=0, float initial_scale=0, np.ndarray cell_space=np.array([[0, 0], [0, 0], [0, 0]]), float|int cell_axial_range=0) | |
np.ndarray | times (self) |
None | times (self, value) |
np.ndarray | condensate_positions (self) |
None | condensate_positions (self, value) |
np.ndarray | scale (self) |
None | scale (self, value) |
None | add_positions (self, np.ndarray time, np.ndarray position, np.ndarray scale) |
list | __call__ (self, int time, str time_unit) |
None | generate_condensate_positions (self, int time) |
np.ndarray | calculate_scale (self, np.ndarray time, np.ndarray position) |
plt.Axes | plot_condensate (self, plt.Axes ax, **kwargs) |
Protected Member Functions | |
None | _generate_condensate_positions (self, int time) |
Protected Attributes | |
_times | |
_condensate_positions | |
_scale | |
Condensate class for storing condensate data. Parameters: ----------- inital_position: np.ndarray = np.array([0, 0, 0]) Initial position of the condensate. initial_time: float = 0 Initial time of the condensates. diffusion_coefficient: float = 0 Diffusion coefficient of the condensate. hurst_exponent: float = 0 Hurst exponent of the condensate. units_time: str = 's' Units of time. Units work as follows: in the class reference frame, start from 0 and iterate by 1 each time. For a units_time of "ms", 1 represents 1ms. For a units_time of "s", 1 represents 1s. For a units_time of "20ms", 1 represents 20ms. units_position: str = 'um' Units of position. condensate_id: int = 0 ID of the condensate. initial_scale: float = 0 Initial scale of the condensate. cell_space: np.ndarray = np.array([[0,0],[0,0],[0,0]]) Space of the cell. cell_axial_range: float|int = 0 Axial range of the cell.
SMS_BP.condensate_movement.Condensate.__init__ | ( | self, | |
np.ndarray | inital_position = np.array([0, 0, 0]), | ||
int | initial_time = 0, | ||
float | diffusion_coefficient = 0, | ||
float | hurst_exponent = 0, | ||
str | units_time = 'ms', | ||
str | units_position = 'um', | ||
int | condensate_id = 0, | ||
float | initial_scale = 0, | ||
np.ndarray | cell_space = np.array([[0, 0], [0, 0], [0, 0]]), | ||
float | int | cell_axial_range = 0 ) |
list SMS_BP.condensate_movement.Condensate.__call__ | ( | self, | |
int | time, | ||
str | time_unit ) |
Returns the position and scale of the condensate at a given time. Parameters: ----------- time: float Time at which to return the position of the condensate. User needs to convert to the reference frame of the condensate class. time_unit: str Units of time. Just to make sure the user is aware of the conversion they need to do to get into the reference frame of the condensate class. Returns: -------- Dict of the position and scale of the condensate at the given time. Keys: Position: np.ndarray Position of the condensate at the given time. Scale: float Scale of the condensate at the given time.
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Generates the condensate positions up to a given time. Parameters: ----------- time: int Time up to which to generate the condensate positions.
None SMS_BP.condensate_movement.Condensate.add_positions | ( | self, | |
np.ndarray | time, | ||
np.ndarray | position, | ||
np.ndarray | scale ) |
Adds positions to the condensate. Parameters: ----------- time: np.ndarray Times at which to add positions. position: np.ndarray Positions to add to the condensate. scale: np.ndarray Scale to add to the condensate.
np.ndarray SMS_BP.condensate_movement.Condensate.calculate_scale | ( | self, | |
np.ndarray | time, | ||
np.ndarray | position ) |
Calculates the scale of the condensate at a given time. Parameters: ----------- time: np.ndarray Times at which to calculate the scale. position: np.ndarray Positions at which to calculate the scale.
np.ndarray SMS_BP.condensate_movement.Condensate.condensate_positions | ( | self | ) |
Returns the positions of the condensate.
None SMS_BP.condensate_movement.Condensate.condensate_positions | ( | self, | |
value ) |
None SMS_BP.condensate_movement.Condensate.generate_condensate_positions | ( | self, | |
int | time ) |
Generates the condensate positions up to a given time. Parameters: ----------- time: int Time up to which to generate the condensate positions.
plt.Axes SMS_BP.condensate_movement.Condensate.plot_condensate | ( | self, | |
plt.Axes | ax, | ||
** | kwargs ) |
Plots the condensate Parameters: ----------- ax: plt.Axes Axes to plot the condensate on. **kwargs: Keyword arguments to pass to the plot function.
np.ndarray SMS_BP.condensate_movement.Condensate.scale | ( | self | ) |
Returns the scale of the condensate.
None SMS_BP.condensate_movement.Condensate.scale | ( | self, | |
value ) |
np.ndarray SMS_BP.condensate_movement.Condensate.times | ( | self | ) |
Returns the times of the condensate.
None SMS_BP.condensate_movement.Condensate.times | ( | self, | |
value ) |
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SMS_BP.condensate_movement.Condensate.cell_axial_range |
SMS_BP.condensate_movement.Condensate.cell_space |
SMS_BP.condensate_movement.Condensate.condensate_id |
SMS_BP.condensate_movement.Condensate.condensate_positions |
SMS_BP.condensate_movement.Condensate.diffusion_coefficient |
SMS_BP.condensate_movement.Condensate.dim |
SMS_BP.condensate_movement.Condensate.hurst_exponent |
SMS_BP.condensate_movement.Condensate.initial_position |
SMS_BP.condensate_movement.Condensate.initial_scale |
SMS_BP.condensate_movement.Condensate.initial_time |
SMS_BP.condensate_movement.Condensate.scale |
SMS_BP.condensate_movement.Condensate.times |
SMS_BP.condensate_movement.Condensate.units_position |
SMS_BP.condensate_movement.Condensate.units_time |