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IMP Reference Guide  develop.29b24c6ad6,2021/05/15
The Integrative Modeling Platform
Creating and restraining bonds

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

Bond IMP::atom::create_bond ( Bonded  a,
Bonded  b,
Int  t 
)

Connect the two wrapped particles by a bond.

Parameters
[in]aThe first Particle as a Bonded
[in]bThe second Particle as a Bonded
[in]tThe type to use for the bond
Returns
Bond of the bond Particle.
See Also
Bond
Bonded
Bond IMP::atom::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 other bond

See Also
Bond
Bonded

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]aThe first Particle as a Bonded
[in]bThe second Particle as a Bonded
[in]lengthThe length of the bond.
[in]stiffnessThe stiffness of the bond.
Returns
Bond of the bond Particle.
See Also
Bond
Bonded

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]bThe bond.
See Also
Bond
Bonded
Bond IMP::atom::get_bond ( Bonded  a,
Bonded  b 
)

Get the bond between two particles.

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

See Also
Bond
Bonded