Variables
std::string	hand1
	name of first Hand in Couple

std::string	hand2
	name of second Hand in Couple

real	stiffness
	stiffness of link between the two Hands while linking

real	length
	resting length of the link

real	diffusion
	diffusion coefficient while unattached

bool	fast_diffusion
	if true, an algorithm is used that assumes uniform concentration of diffusing Couple

bool	stiff
	prevent both Hands from binding at the same position on a Fiber (default=true)

Confinement	confine
	Confinement can be none, inside (default) or surface.

real	confine_stiff
	Unused Parameter: confinement stiffness (this is specified as `confine`[1])

std::string	confine_space
	name of space for confinement (this is specified as `confine`[2])

std::string	activity
	specialization More...

Detailed Description

Variable Documentation

std::string activity

The plain Couple may crosslink two Fiber irrespective of their configuration. Derived classes implement specificity, angular stiffness, etc.

List of classes accessible by specifying couple:activity.

`activity`	Clas	Parameters
`diffuse`	Couple	Parameters of Couple (default)
`fork`	Fork	Parameters of Fork
`crosslink`	Crosslink	Parameters of Crosslink
`bridge`	Bridge	Parameters of Bridge
`slide`	Shackle	Parameters of Shackle

Example:

set couple complex
{
  hand1 = kinesin
  hand2 = kinesin
  stiffness = 100
  diffusion = 10
  activity = crosslink
  length = 0.02
}

You can attach the hands of a Couple:

new couple protein
{
   attach1 = INTEGER, REAL
   attach2 = INTEGER, REAL
}

where:

INTEGER designates the fiber:
- 1 for the first fiber
- 2 for the second, etc.
- 0 designates the last fiber,
- -1 is the penultimate one, etc.
REAL is the abscissa of the attachment point