IMP  2.0.0
The Integrative Modeling Platform
Creating and restraining 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 create_bond (Bonded a, Bonded b, Int t)
 Connect the two wrapped particles by a bond. More...
 
Bond create_bond (Bonded a, Bonded b, Bond o)
 Connect the two wrapped particles by a custom 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...
 
Bond 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 to particles. More...
 
void destroy_bond (Bond b)
 Destroy the bond connecting to particles. More...
 
Bond get_bond (Bonded a, Bonded b)
 Get the bond between two particles. More...
 
Bond IMP::atom::get_bond (Bonded a, Bonded b)
 Get the bond between two particles. More...
 

Detailed Description

A set of classes and functions for manipulating bonds.

Function Documentation

Bond create_bond ( Bonded  a,
Bonded  b,
Int  t 
)
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.
Bond create_bond ( Bonded  a,
Bonded  b,
Int  t 
)
related
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.
Bond create_bond ( Bonded  a,
Bonded  b,
Bond  o 
)
related

Create a bond by copying the information from the othr bond

Definition at line 274 of file bond_decorators.h.

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

Create a bond by copying the information from the othr bond

Definition at line 274 of file bond_decorators.h.

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

Definition at line 253 of file bond_decorators.h.

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

Definition at line 253 of file bond_decorators.h.

void destroy_bond ( Bond  b)
Parameters
[in]bThe bond.
void destroy_bond ( Bond  b)
related
Parameters
[in]bThe bond.
Bond get_bond ( Bonded  a,
Bonded  b 
)
related

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

Bond get_bond ( Bonded  a,
Bonded  b 
)

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