IMP::npctransport::FGChain Class Reference

#include <IMP/npctransport/FGChain.h>

Inheritance diagram for IMP::npctransport::FGChain:

Detailed Description

a chain with a root

root - root of hierarchy beads - fine chain particles

Definition at line 37 of file FGChain.h.

Public Member Functions
	FGChain (IMP::Particle *root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name="chain %1%")
double	get_backbone_k () const
	get the force constant between consecutive chain beads More...
IMP::Particle *	get_bead (unsigned int i) const
	get the i'th bead in the chain (assume valid root) More...
IMP::ParticleIndex	get_bead_index (unsigned int i) const
	get the i'th bead index in the chain (assume valid root) More...
IMP::ParticlesTemp	get_beads () const
	get the beads of the chain (assume valid root) More...
virtual Restraints	get_chain_restraints (Scoring const *scoring_manager)
unsigned int	get_number_of_beads () const
	get the number of beads in the chain (assume valid root) More...
double	get_rest_length_factor () const
atom::Hierarchy	get_root () const
virtual std::string	get_type_name () const override
virtual ::IMP::VersionInfo	get_version_info () const override
	Get information about the module and version of the object. More...
void	set_backbone_k (double k)
void	set_rest_length_factor (double rlf)
Public Member Functions inherited from IMP::Object
virtual void	clear_caches ()
CheckLevel	get_check_level () const
LogLevel	get_log_level () const
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...
void	set_was_used (bool tf) const
void	show (std::ostream &out=std::cout) const
const std::string &	get_name () const
void	set_name (std::string name)

Protected Member Functions
void	set_root (Particle *p)
void	set_root (atom::Hierarchy root)
Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...
virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::npctransport::FGChain::FGChain	(	IMP::Particle *	root,
		double	backbone_k = 0.0,
		double	rest_length_factor = 1.0,
		std::string	name = "chain %1%"
	)

initialized an FG chain with given backbone k and rest length factor, and a specified root whose leaves are the beads of the chain.

Parameters

root	root of the chain (leaves are assumed beads). can be null = to be added later
backbone_k	force constant between consecutive chain beads
rest_length_factor	equilibrium distance factor between consecutive beads relative to the sum of their radii
name	chain object name

See Also

LinearWellPairScore

Definition at line 82 of file FGChain.h.

Member Function Documentation

double IMP::npctransport::FGChain::get_backbone_k

(

)

const

get the force constant between consecutive chain beads

Definition at line 182 of file FGChain.h.

IMP::Particle* IMP::npctransport::FGChain::get_bead

(

unsigned int

i

)

const

get the i'th bead in the chain (assume valid root)

Definition at line 128 of file FGChain.h.

IMP::ParticleIndex IMP::npctransport::FGChain::get_bead_index

(

unsigned int

i

)

const

get the i'th bead index in the chain (assume valid root)

Definition at line 132 of file FGChain.h.

IMP::ParticlesTemp IMP::npctransport::FGChain::get_beads

(

)

const

get the beads of the chain (assume valid root)

Definition at line 124 of file FGChain.h.

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virtual Restraints IMP::npctransport::FGChain::get_chain_restraints ( Scoring const *  scoring_manager )

virtual

Returns a restraint associated with internal interactions by this chain. Once this method has been called once, it is assumed that the chain topology remains static (the behavior of the restraint if the chain topology changes is undefined, e.g. if beads are added)

Note

this restraint is affected by future calls to set_rest_length_factor() and set_backbone_k(). However, it applies only to the topology of the chain at the time of call, if the chain topology changes, this methods should be called again.

assumes that the chain has a valid root whose leaves are beads

unsigned int IMP::npctransport::FGChain::get_number_of_beads

(

)

const

get the number of beads in the chain (assume valid root)

Definition at line 136 of file FGChain.h.

double IMP::npctransport::FGChain::get_rest_length_factor

(

)

const

get the equilibrium distance factor between consecutive beads relative to the sum of their radii

Definition at line 177 of file FGChain.h.

virtual ::IMP::VersionInfo IMP::npctransport::FGChain::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 186 of file FGChain.h.

void IMP::npctransport::FGChain::set_backbone_k

(

double

k

)

set the force constant between consecutive chain beads

Note

This affects also restraints previously returned by get_chain_restraints()

See Also

LinearWellPairScore

void IMP::npctransport::FGChain::set_rest_length_factor

(

double

rlf

)

set the equilibrium distance factor between consecutive beads relative to the sum of their radii

Note

This affects also restraints previously returned by get_chain_restraints()

See Also

LinearWellPairScore

HarmonicSpringSingletonScore

RelaxingSpring

void IMP::npctransport::FGChain::set_root ( Particle *  p )

protected

set the root of the chain to this particle with the beads being the leaves of Hierarchy(p)

Note

it is assumed that p is decorated as atom::Hiererachy

Definition at line 106 of file FGChain.h.

void IMP::npctransport::FGChain::set_root ( atom::Hierarchy  root )

protected

set the root of the chain to this particle with the beads being the leaves of Hierarchy(p)

Definition at line 115 of file FGChain.h.

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The documentation for this class was generated from the following file:

• FGChain.h