Parameters of Single

Variables
std::string	hand
	name of Hand
real	stiffness
	stiffness of link
real	length
	resting length of link
real	diffusion
	diffusion coefficient
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

List of classes accessible by specifying single:activity:

activity	Class	Description
diffuse	Single	a single Hand that is mobile (default)
fixed	Picket	a single Hand anchored at a fixed position

Another class Wrist is used automatically to anchor a Single to a Mecable.

Example:

set single grafted
{
  hand = kinesin
  stiffness = 100
  activity = fixed
} 

A newly created Single can be anchored to a Mecable:

new single NAME {
  base = CLASS_NAME, INTEGER_REF, INTEGER_INDEX
}

where:

• CLASS_NAME is the name of the object class (eg. solid)
• INTEGER_REF designates the object:
  • 1 for first object
  • 2 for second...
  • 0 designates the last object,
  • -1 is the penultimate one, etc.
• INTEGER_INDEX designates a point on this object:
  • 0 = first point
  • 1 = second point...

if INTERGER1 is negative, the last object is used.

You can attach a Single to a fiber:

new single protein
{
   attach = INTEGER, REAL
}

where:

• INTEGER designates the fiber:
  • 1 for the first fiber
  • 2 for the second, etc
  • a negative number indicates the last fiber created
• REAL is the abscissa of the attachment point (0=MINUS_END)