A set of classes and functions for manipulating bonds. More...

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. More...

Bond	IMP::atom::create_bond (Bonded a, Bonded b, Bond o)
	Connect the two wrapped particles by a custom bond. More...

Bond	IMP::atom::create_custom_bond (Bonded a, Bonded b, Float length, Float stiffness=-1)
	Connect the two wrapped particles by a custom bond. More...

void	IMP::atom::destroy_bond (Bond b)
	Destroy the bond connecting two particles. More...

Bond	IMP::atom::get_bond (Bonded a, Bonded b)
	Get the bond between two particles. More...

Function Documentation

Connect the two wrapped particles by a bond.

Parameters

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

Connect the two wrapped particles by a custom bond.

Create a bond by copying the information from the other bond

Definition at line 256 of file bond_decorators.h.

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Bond IMP::atom::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 kernel::Particle as a Bonded
[in]	b	The second kernel::Particle as a Bonded
[in]	length	The length of the bond.
[in]	stiffness	The stiffness of the bond.

Definition at line 237 of file bond_decorators.h.

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void IMP::atom::destroy_bond ( Bond b )

Destroy the bond connecting two particles.

Parameters

[in] b The bond.

Get the bond between two particles.

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