Creating and restraining bonds

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Detailed Description

A set of classes and functions for manipulating bonds.

Classes
class	IMP::atom::Bond
	A decorator for wrapping a particle representing a molecular bond. More...
class	IMP::atom::Bonded
	A decorator for a particle which has bonds. More...
class	IMP::atom::BondedPairFilter
	A filter for bonds. More...
class	IMP::atom::BondEndpointsRefiner
	Return the endpoints of a bond. More...
class	IMP::atom::BondPairContainer
	A container that returns pairs of the endpoints of the bonds. More...
class	IMP::atom::BondSingletonScore
	Score the bond based on a UnaryFunction,. More...

Functions
Bond	IMP::atom::create_bond (Bonded a, Bonded b, Int t)
	Connect the two wrapped particles by a bond.
Bond	create_bond (Bonded a, Bonded b, Int t)
	Connect the two wrapped particles by a bond.
Bond	create_bond (Bonded a, Bonded b, Bond o)
	Connect the two wrapped particles by a custom bond.
Bond	IMP::atom::create_bond (Bonded a, Bonded b, Bond o)
	Connect the two wrapped particles by a custom bond.
Bond	IMP::atom::create_custom_bond (Bonded a, Bonded b, Float length, Float stiffness=-1)
	Connect the two wrapped particles by a custom bond.
Bond	create_custom_bond (Bonded a, Bonded b, Float length, Float stiffness=-1)
	Connect the two wrapped particles by a custom bond.
void	IMP::atom::destroy_bond (Bond b)
	Destroy the bond connecting to particles.
void	destroy_bond (Bond b)
	Destroy the bond connecting to particles.
Bond	get_bond (Bonded a, Bonded b)
	Get the bond between two particles.
Bond	IMP::atom::get_bond (Bonded a, Bonded b)
	Get the bond between two particles.

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Function Documentation

Bond create_bond	(	Bonded	a,
		Bonded	b,
		Int	t
	)

Connect the two wrapped particles by a bond.

Parameters:

[in]	a	The first Particle as a Bonded
[in]	b	The second Particle as a Bonded
[in]	t	The type to use for the bond

Returns:

Bond of the bond Particle.

Bond create_bond ( Bonded  a, Bonded  b, Int  t  )

related

Connect the two wrapped particles by a bond.

Parameters:

[in]	a	The first Particle as a Bonded
[in]	b	The second Particle as a Bonded
[in]	t	The type to use for the bond

Returns:

Bond of the bond Particle.

Bond create_bond ( Bonded  a, Bonded  b, Bond  o  )

related

Connect the two wrapped particles by a custom bond.

Create a bond by copying the information from the othr bond

Bond create_bond	(	Bonded	a,
		Bonded	b,
		Bond	o
	)

Connect the two wrapped particles by a custom bond.

Create a bond by copying the information from the othr bond

Bond create_custom_bond	(	Bonded	a,
		Bonded	b,
		Float	length,
		Float	stiffness = -1
	)

Connect the two wrapped particles by a custom bond.

Parameters:

[in]	a	The first Particle as a Bonded
[in]	b	The second Particle as a Bonded
[in]	length	The length of the bond.
[in]	stiffness	The stiffness of the bond.

Returns:

Bond of the bond Particle.

Bond create_custom_bond ( Bonded  a, Bonded  b, Float  length, Float  stiffness = -1  )

related

Connect the two wrapped particles by a custom bond.

Parameters:

[in]	a	The first Particle as a Bonded
[in]	b	The second Particle as a Bonded
[in]	length	The length of the bond.
[in]	stiffness	The stiffness of the bond.

Returns:

Bond of the bond Particle.

void destroy_bond

(

Bond

b

)

Destroy the bond connecting to particles.

Parameters:

[in]

b

The bond.

void destroy_bond ( Bond  b )

related

Destroy the bond connecting to particles.

Parameters:

[in]

b

The bond.

Bond get_bond ( Bonded  a, Bonded  b  )

related

Get the bond between two particles.

Bond() is returned if the particles are not bonded.

Bond get_bond	(	Bonded	a,
		Bonded	b
	)

Get the bond between two particles.

Bond() is returned if the particles are not bonded.