Cytosim PI Cytoskeleton Simulator

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Variables
Parameters of Couple
All object parameters

## 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