SMS_BP
Single Molecule Simulations -BP
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SMS_BP.condensate_movement.Condensate Class Reference

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)
 

Public Attributes

 initial_position
 
 initial_time
 
 diffusion_coefficient
 
 hurst_exponent
 
 units_time
 
 units_position
 
 condensate_id
 
 initial_scale
 
 dim
 
 cell_space
 
 cell_axial_range
 
 times
 
 condensate_positions
 
 scale
 

Protected Member Functions

None _generate_condensate_positions (self, int time)
 

Protected Attributes

 _times
 
 _condensate_positions
 
 _scale
 

Detailed Description

 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.

Constructor & Destructor Documentation

◆ __init__()

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 )

Member Function Documentation

◆ __call__()

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.

◆ _generate_condensate_positions()

None SMS_BP.condensate_movement.Condensate._generate_condensate_positions ( self,
int time )
protected
 Generates the condensate positions up to a given time.

Parameters:
-----------
time: int
    Time up to which to generate the condensate positions.

◆ add_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.

◆ calculate_scale()

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.

◆ condensate_positions() [1/2]

np.ndarray SMS_BP.condensate_movement.Condensate.condensate_positions ( self)
 Returns the positions of the condensate.

◆ condensate_positions() [2/2]

None SMS_BP.condensate_movement.Condensate.condensate_positions ( self,
value )

◆ generate_condensate_positions()

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.

◆ plot_condensate()

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.

◆ scale() [1/2]

np.ndarray SMS_BP.condensate_movement.Condensate.scale ( self)
 Returns the scale of the condensate.

◆ scale() [2/2]

None SMS_BP.condensate_movement.Condensate.scale ( self,
value )

◆ times() [1/2]

np.ndarray SMS_BP.condensate_movement.Condensate.times ( self)
 Returns the times of the condensate.

◆ times() [2/2]

None SMS_BP.condensate_movement.Condensate.times ( self,
value )

Member Data Documentation

◆ _condensate_positions

SMS_BP.condensate_movement.Condensate._condensate_positions
protected

◆ _scale

SMS_BP.condensate_movement.Condensate._scale
protected

◆ _times

SMS_BP.condensate_movement.Condensate._times
protected

◆ cell_axial_range

SMS_BP.condensate_movement.Condensate.cell_axial_range

◆ cell_space

SMS_BP.condensate_movement.Condensate.cell_space

◆ condensate_id

SMS_BP.condensate_movement.Condensate.condensate_id

◆ condensate_positions

SMS_BP.condensate_movement.Condensate.condensate_positions

◆ diffusion_coefficient

SMS_BP.condensate_movement.Condensate.diffusion_coefficient

◆ dim

SMS_BP.condensate_movement.Condensate.dim

◆ hurst_exponent

SMS_BP.condensate_movement.Condensate.hurst_exponent

◆ initial_position

SMS_BP.condensate_movement.Condensate.initial_position

◆ initial_scale

SMS_BP.condensate_movement.Condensate.initial_scale

◆ initial_time

SMS_BP.condensate_movement.Condensate.initial_time

◆ scale

SMS_BP.condensate_movement.Condensate.scale

◆ times

SMS_BP.condensate_movement.Condensate.times

◆ units_position

SMS_BP.condensate_movement.Condensate.units_position

◆ units_time

SMS_BP.condensate_movement.Condensate.units_time

The documentation for this class was generated from the following file: