Classes, functions and executables for modeling of the Spindle Pole Body. More...

Detailed Description

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

Integrative Modeling of the Spindle Pole Body Core

Here we determine the molecular architecture of the yeast spindle pole body (SPB), the structural and functional equivalent of the metazoan centrosome. Data from in vivo FRET and yeast two-hybrid, along with SAXS, X-ray crystallography, and electron microscopy were integrated by a Bayesian structure modeling approach.

This module provides classes, functions and executables for running the sampling, analysis, clustering and density calculation for this project.

Prerequisites:

MPI must be used to compile the IMP code so that replica exchange can be used.

Note:

For detailed information on inputs, outputs and how to run each executable, refer to the README and files in the SPB biosystems page.

Here's a brief description of the command line executables.

spb

This is the main executable for running sampling using Well-Tempered Ensemble Replica Exchange, based on FRET, yeast two-hybrid and other restraints.

spb_analysis

After running sampling, we need to rescore the final ensemble (all models at 1 K) based on the EM2D score. This step performs the rescoring and attaches a weight to each model (higher the better) based on the Well-tempered ensemble Replica Exchange method.

spb_cluster

Models are clustered taking their weight into account. Distance threshold-based clustering is performed with a 1.5 nm threshold.

spb_density

Localization density is calculated per protein for models of a given cluster.

spb_density_perbead

To better localize the protein termini, localization density is calculated per bead per protein for a given cluster.

spb_test_score

Code to output the restraint values of a model. Takes 2 RMFs as input: one containing structural coordinations and another containing ISD values.

Info

Author(s): Massimiliano Bonomi, Shruthi Viswanath

Maintainer: shruthivis

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

S. Viswanath*, M. Bonomi*, S.J. Kim, V.A. Klenchin, K.C. Taylor, K.C. Yabut, N.T. Umbreit, H.A. Van Epps, J. Meehl, M.H. Jones, D. Russel, J.A. Velazquez-Muriel, M. Winey, I. Rayment, T.N. Davis, A. Sali, and E.G. Muller. The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling. Mol Biol Cell 28, 3298-3314, 2017.
See main IMP papers list.

Classes
class	AttributeDistancePairScore
	Apply a function to an attribute. More...

class	BoxedMover
	Move a particle and keep it in a box. More...

class	CellMover
	Apply a mover that moves particles inside the unit cell. More...

class	ChiSquareMetric

class	ContactMapMetric

class	DiameterRgyrRestraint
	Diameter and radius of gyration Restraint. More...

class	DistanceRMSDMetric

class	DistanceTerminiRestraint
	A distance restraint between protein termini. More...

class	EM2DRestraint

class	Gaussian
	Gaussian function (symmetric about the mean) More...

class	HelixDecorator
	Add helix parameters to a particle. More...

class	ISDRestraint
	Apply an NOE distance restraint between two particles. More...

class	KinkPairScore
	Score on the crossing angles between two helices. More...

class	MolecularDynamicsWithWte
	Simple molecular dynamics optimizer. More...

class	MonteCarloWithWte
	MonteCarlo in the Well-Tempered Ensemble. More...

class	NuisanceRangeModifier
	Ensure that a Nuisance stays within its set range. More...

class	PbcBoxedMover
	Move a particle and keep it in a box. More...

class	PbcBoxedRigidBodyMover
	Modify the transformation of a rigid body. More...

class	RigidBodyNewMover
	Modify the transformation of a rigid body. More...

class	RigidBodyPackingScore
	Score on the crossing angles between two helices. More...

class	RMSDMetric

class	SameParticlePairFilter

class	SameRigidBodyPairFilter

class	TiltSingletonScore
	Apply a function to the distance to a fixed point. More...

class	TransformationSymmetry
	Set the coordinates of a particle to be a transformed version of a reference. More...

class	TwoStateGoModelRestraint
	Two-state Go-Model Restraint. More...

class	UniformBoundedRestraint

Typedefs
typedef IMP::Vector < IMP::Pointer < AttributeDistancePairScore > >	AttributeDistancePairScores

typedef IMP::Vector < IMP::WeakPointer < AttributeDistancePairScore > >	AttributeDistancePairScoresTemp

typedef IMP::Vector < HelixDecorator >	HelixDecorators

typedef IMP::Vector < IMP::Pointer< KinkPairScore > >	KinkPairScores

typedef IMP::Vector < IMP::WeakPointer < KinkPairScore > >	KinkPairScoresTemp

typedef IMP::Vector < IMP::Pointer < RigidBodyPackingScore > >	RigidBodyPackingScores

typedef IMP::Vector < IMP::WeakPointer < RigidBodyPackingScore > >	RigidBodyPackingScoresTemp

Functions
void	add_BallMover (Particles ps, double dx, core::MonteCarloMovers &mvs)

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

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

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

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

std::map< std::string, IMP::Pointer< Particle > >	add_ISD_particles (Model m, RestraintSet allrs, spb::SPBParameters mydata, core::MonteCarloMovers &mvs)

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

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

void	add_NuisanceMover (Particle *p, double dp, core::MonteCarloMovers &mvs)

void	add_PbcBoxedMover (Particles ps, double dx, algebra::Vector3Ds centers, algebra::Transformation3Ds trs, core::MonteCarloMovers &mvs, Particle SideXY, Particle SideZ)

void	add_PbcBoxedRigidBodyMover (Particles ps, double dx, double dang, algebra::Vector3Ds centers, algebra::Transformation3Ds trs, core::MonteCarloMovers &mvs, Particle SideXY, Particle SideZ)

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

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

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

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

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

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

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

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

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

atom::Molecules	create_coiled_coil (Model *m, std::string name, std::string filename_A, std::string filename_B, int nbeads, display::Color colore, int copy, algebra::Vector3D x0, int offset=0)

atom::Molecule	create_GFP (Model m, std::string name, int copy, container::ListSingletonContainer lsc, algebra::Vector3D x0, core::MonteCarloMovers &mvs, spb::SPBParameters mydata, Particle SideXY, Particle SideZ)

statistics::PartitionalClustering *	create_gromos_clustering (statistics::Metric *d, double cutoff)

int *	create_indexes (int nrep)

atom::Molecule	create_merged_protein (Model m, RestraintSet allrs, std::string name, atom::Molecules proteins, int copy, double kappa, double dist=-1.0)

atom::Molecule	create_protein (Model m, RestraintSet allrs, std::string name, double mass, int nbeads, display::Color color, int copy, double kappa, algebra::Vector3D x0, bool use_connectivity, int start_residue=1, int length=-1)

atom::Molecule	create_protein (Model *m, std::string name, std::string filename, int nbeads, display::Color colore, int copy, algebra::Vector3D x0, int offset=0, bool makerigid=true)

atom::Hierarchies	create_representation (Model m, RestraintSet allrs, spb::SPBParameters mydata, container::ListSingletonContainer CP_ps, container::ListSingletonContainer IL2_ps, core::MonteCarloMovers &mvs, Particle SideXY, Particle SideZ, int iseed)

double *	create_temperatures (double tmin, double tmax, int nrep)

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

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

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

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

IMP::Pointer< isd::FretRestraint >	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 >	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 >	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)

bool	get_acceptance (double score0, double score1, double delta_wte, double T0, double T1)

int	get_friend (int *index, int myrank, int step, int nrep)

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

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

SPBParameters	get_SPBParameters (IMP::TextInput in, std::string suffix)

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

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

void	load_restart (atom::Hierarchies &all_mol, spb::SPBParameters mydata)

double	radians (double d)

void	recenter_rb (core::RigidBody &rb, core::XYZRs &rbps, algebra::Vector3D x0, bool coiledcoil=false)

IMP::Pointer< core::MonteCarlo >	setup_SPBMonteCarlo (Model *m, core::MonteCarloMovers &mvs, double temp, spb::SPBParameters myparam)

std::map< std::string, IMP::Pointer< RestraintSet > >	spb_assemble_restraints (Model m, RestraintSet allrs, spb::SPBParameters &myparam, atom::Hierarchies &all_mol, container::ListSingletonContainer CP_ps, container::ListSingletonContainer IL2_ps, std::map< std::string, IMP::Pointer< Particle > > ISD_ps)

IMP::Pointer < container::MinimumPairRestraint >	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 >	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 >	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 >	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)

Standard module functions
All `IMP` modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()

std::string	get_module_name ()

std::string	get_data_path (std::string file_name)
	Return the full path to one of this module's data files. More...

std::string	get_example_path (std::string file_name)
	Return the full path to one of this module's example files. More...