SPB Restraints. More...

#include <IMP.h>
#include <IMP/atom.h>
#include <IMP/core.h>
#include <IMP/em2d.h>
#include <IMP/isd.h>
#include "spb_config.h"

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Namespaces
	IMP
	Base functionality and abstract base classes for representation, scoring and sampling.

	IMP::spb
	Classes, functions and executables for modeling of the Spindle Pole Body.

Functions
void	IMP::spb::add_bayesian_layer_restraint (RestraintSet allrs, container::ListSingletonContainer lsc, Particle a, Particle b)

void	IMP::spb::add_diameter_rgyr_restraint (RestraintSet *allrs, const atom::Hierarchy &h, std::string protein, double diameter, double rgyr, double kappa)

void	IMP::spb::add_GFP_restraint (Model m, RestraintSet allrs, const atom::Hierarchy &h, double kappa)

void	IMP::spb::add_internal_restraint (Model m, RestraintSet allrs, std::string name, atom::Molecule protein_a, atom::Molecule protein_b, double kappa, double dist)

void	IMP::spb::add_layer_restraint (RestraintSet allrs, container::ListSingletonContainer lsc, FloatRange range, double kappa)

void	IMP::spb::add_link (Model m, RestraintSet allrs, const atom::Hierarchy &h, std::string protein_a, std::string residues_a, atom::Hierarchies &hs, std::string protein_b, IntRange residues_b, double kappa)

void	IMP::spb::add_link (Model m, RestraintSet allrs, const atom::Hierarchy &h, std::string protein_a, std::string residues_a, atom::Hierarchies &hs, std::string protein_b, std::string residues_b, double kappa)

void	IMP::spb::add_my_connectivity (Model m, RestraintSet allrs, std::string name, atom::Molecule protein, double kappa)

void	IMP::spb::add_restrain_coiledcoil_to_cterm (Model m, RestraintSet allrs, const atom::Hierarchy &hs, std::string protein_a, Particle *dist, double sigma0_dist)

void	IMP::spb::add_restrain_protein_length (RestraintSet allrs, const atom::Hierarchy &hs, std::string protein_a, Particle dist, double sigma0_dist)

void	IMP::spb::add_SPBexcluded_volume (Model m, RestraintSet allrs, atom::Hierarchies &hs, bool GFP_exc_volume, double kappa)

void	IMP::spb::add_stay_close_restraint (Model m, RestraintSet allrs, const atom::Hierarchy &h, std::string protein, double kappa)

void	IMP::spb::add_stay_close_restraint (Model m, RestraintSet allrs, const atom::Hierarchy &h, std::string protein, int residue, double kappa)

void	IMP::spb::add_stay_on_plane_restraint (Model m, RestraintSet allrs, const atom::Hierarchy &h, std::string protein, int residue, double kappa)

void	IMP::spb::add_symmetry_restraint (Model m, atom::Hierarchies &hs, algebra::Transformation3Ds transformations, Particle SideXY, Particle *SideZ)

void	IMP::spb::add_tilt (Model m, RestraintSet allrs, const atom::Hierarchy &h, std::string name, IntRange range, double tilt, double kappa)

void	IMP::spb::add_tilt_restraint (Model m, RestraintSet allrs, Particle *p, FloatRange trange, double kappa)

IMP::Pointer < container::MinimumPairRestraint >	IMP::spb::do_bipartite_mindist (Model *m, Particles p1, Particles p2, IMP::Pointer< core::SphereDistancePairScore > sps, bool filter=true)

IMP::Pointer < container::MinimumPairRestraint >	IMP::spb::do_bipartite_mindist (Model *m, Particles p1, Particles p2, IMP::Pointer< core::DistancePairScore > sps, bool filter=true)

IMP::Pointer< spb::EM2DRestraint >	IMP::spb::em2d_restraint (atom::Hierarchies &hs, std::string protein, EM2DParameters EM2D, Particle *Sigma)

IMP::Pointer< spb::EM2DRestraint >	IMP::spb::em2d_restraint (atom::Hierarchies &hs, std::string protein, EM2DParameters EM2D, Floats sigma_grid, Floats fmod_grid)

IMP::Pointer< isd::FretRestraint >	IMP::spb::fret_restraint (atom::Hierarchies &hs, std::string protein_a, std::string residues_a, std::string protein_b, std::string residues_b, double fexp, FretParameters Fret, std::string cell_type, bool use_GFP, Particle Kda, Particle Ida, Particle R0, Particle Sigma0, Particle *pBl)

IMP::Pointer< isd::FretRestraint >	IMP::spb::fret_restraint (atom::Hierarchies &hs, std::string protein_a, std::string residues_a, std::string protein_b, int residues_b, double fexp, FretParameters Fret, std::string cell_type, bool use_GFP, Particle Kda, Particle Ida, Particle R0, Particle Sigma0, Particle *pBl)

IMP::Pointer< isd::FretRestraint >	IMP::spb::fret_restraint (atom::Hierarchies &hs, std::string protein_a, int residues_a, std::string protein_b, std::string residues_b, double fexp, FretParameters Fret, std::string cell_type, bool use_GFP, Particle Kda, Particle Ida, Particle R0, Particle Sigma0, Particle *pBl)

IMP::Pointer < core::DistancePairScore >	IMP::spb::get_pair_score (FloatRange dist, double kappa)

std::vector< core::RigidBody >	IMP::spb::get_rigid_bodies (Particles ps)

IMP::Pointer < core::SphereDistancePairScore >	IMP::spb::get_sphere_pair_score (FloatRange dist, double kappa)

IMP::Pointer < core::SphereDistancePairScore >	IMP::spb::get_sphere_pair_score (double dist, double kappa)

IMP::Pointer < container::MinimumPairRestraint >	IMP::spb::y2h_restraint (Model *m, const atom::Hierarchy &ha, std::string protein_a, IntRange residues_a, atom::Hierarchies &hb, std::string protein_b, IntRange residues_b, double kappa)

IMP::Pointer < container::MinimumPairRestraint >	IMP::spb::y2h_restraint (Model *m, const atom::Hierarchy &ha, std::string protein_a, std::string residues_a, atom::Hierarchies &hb, std::string protein_b, std::string residues_b, double kappa)

IMP::Pointer < container::MinimumPairRestraint >	IMP::spb::y2h_restraint (Model *m, const atom::Hierarchy &ha, std::string protein_a, IntRange residues_a, atom::Hierarchies &hb, std::string protein_b, std::string residues_b, double kappa)

IMP::Pointer < container::MinimumPairRestraint >	IMP::spb::y2h_restraint (Model *m, const atom::Hierarchy &ha, std::string protein_a, std::string residues_a, atom::Hierarchies &hb, std::string protein_b, IntRange residues_b, double kappa)

Detailed Description

SPB Restraints.

Definition in file spb_restraint.h.

Namespaces

Functions

Detailed Description