SingleSet Class Reference

Detailed Description

A Single is stored in one of 2 NodeList, depending on its state:

• fList = free,
• aList = attached.

Each list is accessible via its head firstF() and firstA(). This way, the state of the Single are known when accessing them.

A Single is automatically transfered to the appropriate list, if its Hand binds or unbind. This is one role of HandMonitor: HandMonitor::afterAttachment() and HandMonitor::afterDetachment() are called by the Hand, and calls SingleSet::relink().

Inheritance diagram for SingleSet:

Public Member Functions
	SingleSet (Simul &s)
	creator
virtual	~SingleSet ()
	destructor
std::string	kind () const
	identifies the class
Property *	newProperty (const std::string &kind, const std::string &name, Glossary &) const
	create a new property for class kind with given name More...
Object *	newObject (const std::string &kind, const std::string &prop, Glossary &opt)
	create a new object from the corresponding property
Object *	newObjectT (const Tag tag, int prop_index)
	construct object
ObjectList	newObjects (const std::string &kind, const std::string &prop, Glossary &)
	create a new object directly from a glossary
void	removeWrists (Object *obj)
	remove all Wrists anchored on Object 'obj'
Single *	firstF () const
	returns the first free Single
Single *	firstA () const
	returns the first bound Single
Single *	find (Number n) const
	return pointer to the Object of given Number, or zero if not found
ObjectList	collect (bool(*func)(Object const *, void *), void *) const
	collect Object for which func(obj, val) == true
void	erase ()
	erase all Object and all Property
unsigned int	size () const
	number of elements
void	mix ()
	mix order of elements
void	freeze ()
	transfer all object to ice
void	thaw (bool erase)
	delete objects, or put them back in normal list
void	step (FiberSet const &, FiberGrid const &)
	Monte-Carlo step.
void	write (OutputWrapper &) const
	write
void	foldPosition (const Modulo *) const
	modulo the position (periodic boundary conditions)
int	bad () const
	check internal consistency, returns 0 if everything is OK
Public Member Functions inherited from ObjectSet
	ObjectSet (Simul &s)
	creator
virtual	~ObjectSet ()
	destructor
virtual ObjectList	newPlacedObjects (const std::string &kind, const std::string &name, Glossary &opt)
	create new objects, translate and rotate them according to specifications in opt More...
virtual void	add (Object *)
	register Object, and add it at the end of the list
void	add (ObjectList &)
	remove Object in ObjectList
virtual void	remove (Object *)
	remove Object
void	remove (ObjectList &)
	remove Object in ObjectList
virtual void	relink (Object *)
	unlink and relink object. This places it last in the list More...
void	erase (Object *)
	remove Object, and delete it
Object *	first () const
	first Object in the list
Object *	first (const Property *) const
	return an Object which has this property More...
Object *	last () const
	last Object
Object *	find (const Number n) const
	find Object of given serial-number (see Inventoried)
Object *	findObject (long n) const
	return Object with serial-number if ( n > 0 ) or object from the end of the list if ( n <= 0 ) More...
void	readObject (InputWrapper &, Tag, char pretag)
	read one Object from file More...

Additional Inherited Members
Static Public Member Functions inherited from ObjectSet
static void	translateObjects (ObjectList const &, Vector const &)
	apply translation to all Objects in ObjectList More...
static void	rotateObjects (ObjectList const &, Rotation const &)
	apply rotation to all Objects in ObjectList More...
Public Attributes inherited from ObjectSet
Inventory	inventory
	holds pointers to the Objects in a array of Numbers
NodeList	nodes
	holds pointers to the Objects in a doubly linked list
Simul &	simul
	the Simul containing this ObjectSet
Protected Member Functions inherited from ObjectSet
void	forget (NodeList &)
	remove all nodes in the list from the inventory
Static Protected Member Functions inherited from ObjectSet
static ObjectList	collect (const NodeList &, bool(*func)(Object const *, void *), void *)
	collect Object from NodeList for which func(obj, val) == true
static void	write (const NodeList &, OutputWrapper &)
	write Object in NodeList to file More...
static Vector	placeObjects (ObjectList const &, Glossary &opt, const Space *)
	place all Objects in ObjectList using the same combinations of translation/rotation More...
Protected Attributes inherited from ObjectSet
NodeList	ice
	a list used to store the objects temporarily while a state is imported

Member Function Documentation

Property * newProperty ( const std::string &  kd, const std::string &  nm, Glossary &  opt  ) const

virtual

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)

Implements ObjectSet.