The default Fiber is of fixed length, but derived class can change length. More...

Classes
class	ClassicFiber
	A Fiber with a standard two-state model of dynamic instability at the PLUS_END. More...

class	DynamicFiber
	A Fiber with discrete growth and dynamic instability at the PLUS_END. More...

class	TreadmillingFiber
	A Fiber with assembly at both ends. More...

class	Tubule
	Adds dynamic instability (growth/shrinkage of the ends) to a Fiber. More...

Detailed Description

A fiber is a filament of constant length. Derived classes are available, where different models of how length may change have been implemented.

List of classes accessible by specifying fiber:activity.

`activity`	Class	Parameter
`none`	Fiber	Parameters of Fiber (default)
`classic`	ClassicFiber	Parameters of ClassicFiber
`dynamic`	DynamicFiber	Parameters of DynamicFiber
`treadmill`	TreadmillingFiber	Parameters of TreadmillingFiber
`tubule`	Tubule (deprecated)	Parameters of Tubule

When creating a new Fiber, you may specify:

the initial length,
the initial state of the PLUS_END and MINUS_END,
if the position refers to the center or to the tip of the fiber

Syntax:

new fiber ...
{
  length = REAL, LENGTH_MODIFIER
  end_state = PLUS_END_STATE, MINUS_END_STATE
  reference = REFERENCE
}

The optional LENGTH_MODIFIER can be:

exponential,
REAL

This introduces variability, without changing the mean length. The second form generates a flat distribution of width 2*LENGTH_MODIFIER.

The initial states PLUS_END_STATE and MINUS_END_STATE can be:

0 = white
1 = green
4 = red

Optional reference specificiation:

center [default]
plus_end
minus_end

Examples:

new fiber ...
{
  length = 1
  plus_end_state = 1
  minus_end_state = 0
}

which is equivalent to:

new fiber ...
{
  length = 1
  end_state = green, white
}

You may add a Picket to immobilize a Fiber to the ground:

new fiber microtubule
{
  single = NAME_OF_SINGLE, MODE
}

NAME should be the name of a defined single. Possible MODE:

minus_end
plus_end
minus_dir, [distance]
center

For MODE == minus_dir, 2 Singles are added, and their distance should be specified as the third argument:

new fiber actin
{
  single = NAME_OF_SINGLE, MODE, DISTANCE
}

Add Couple pre-attached to the Fiber:

new fiber microtubule
{
  couple = NAME_OF_SINGLE, NUMBER, LEN
}

Couples are attached via their first Hand, and they are distributed along Fiber, at distance LEN from the MINUS_END. If LEN is not specified, they are distributed all along the fiber.

Classes

Detailed Description