IMP Reference Guide
2.8.0
The Integrative Modeling Platform
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Classes, functions and executables for modeling of the Spindle Pole Body. More...
Classes, functions and executables for modeling of the Spindle Pole Body.
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.
MPI must be used to compile the IMP code so that replica exchange can be used.
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.
This is the main executable for running sampling using Well-Tempered Ensemble Replica Exchange, based on FRET, yeast two-hybrid and other restraints.
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.
Models are clustered taking their weight into account. Distance threshold-based clustering is performed with a 1.5 nm threshold.
Localization density is calculated per protein for models of a given cluster.
To better localize the protein termini, localization density is calculated per bead per protein for a given cluster.
Code to output the restraint values of a model. Takes 2 RMFs as input: one containing structural coordinations and another containing ISD values.
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:
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 | |
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... | |
typedef IMP::Vector<IMP::Pointer< AttributeDistancePairScore > > IMP::spb::AttributeDistancePairScores |
A vector of reference-counting object pointers.
Definition at line 49 of file AttributeDistancePairScore.h.
typedef IMP::Vector<IMP::WeakPointer< AttributeDistancePairScore > > IMP::spb::AttributeDistancePairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 49 of file AttributeDistancePairScore.h.
typedef IMP::Vector< HelixDecorator > IMP::spb::HelixDecorators |
Pass or store a set of HelixDecorator .
Definition at line 60 of file HelixDecorator.h.
typedef IMP::Vector<IMP::Pointer< KinkPairScore > > IMP::spb::KinkPairScores |
A vector of reference-counting object pointers.
Definition at line 40 of file KinkPairScore.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 40 of file KinkPairScore.h.
A vector of reference-counting object pointers.
Definition at line 41 of file RigidBodyPackingScore.h.
typedef IMP::Vector<IMP::WeakPointer< RigidBodyPackingScore > > IMP::spb::RigidBodyPackingScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 41 of file RigidBodyPackingScore.h.
std::string IMP::spb::get_data_path | ( | std::string | file_name | ) |
Return the full path to one of this module's data files.
To read the data file "data_library" that was placed in the data
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.
std::string IMP::spb::get_example_path | ( | std::string | file_name | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples
directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh
script.