Detailed Description

The npctransport module is a module for simulating transport through the NPC.

Authors: Barak Raveh, Daniel Russel

License:

Publications: Timney*, Raveh* et al., JCB 2016

Building from source in a nutshell (see https://integrativemodeling.org/latest/doc/manual/installation.html for general IMP installation instruction):

Make sure IMP prerequisites are installed
Install the CGAL package
Install the protobuf package
Download IMP source code as explained in the installation manual
Build IMP according to online instructions
The npctransport installation can be tested using ctest, eg - "ctest -R npctransport"

Versions: 4.5

optimization of ball size used to define close pair range results in faster runs for larger particles

fg_simulation: run NPC transport simulations

The fg_simulation command line tool can be used to run simulations of NPC FG repeat domains using this module. For an example of its use, see our 2018 study in Nature.

Classes
class	AnchorToCylidnricalPorePairScore

class	BipartitePairsStatisticsOptimizerState

class	BodyStatisticsOptimizerState

class	BrownianDynamicsTAMDWithSlabSupport
	Simple Brownian dynamics simulator. More...

class	ChainStatisticsOptimizerState

class	ExcludeZRangeSingletonScore
	Exclude particles from the given range of z coordinates. More...

class	FGChain

class	FunctorLinearInteractionPairScore
	Score a pair of particles. More...

class	FunctorLinearSoftSpherePairScore
	Score a pair of particles. More...

class	GlobalStatisticsOptimizerState

class	HarmonicSpringSingletonScore

class	HarmonicWellPairScore

class	HierarchyWithSitesLoadLink
	Load sites data from an RMF file. More...

class	HierarchyWithSitesSaveLink
	Save sites data to an RMF file. More...

class	LinearInteraction

class	LinearInteractionPairScore

class	LinearSoftSpherePairScore

class	LinearWellPairScore

class	ParticleFactory
	Factory that produces diffusing particles with specified attributes. More...

class	ParticleTransportStatisticsOptimizerState

class	PoreRadiusSingletonScore

class	RelaxingSpring
	A decorator for a spring particle connecting two diffusing particles. More...

class	Scoring
	Scoring associated with a SimulationData object. More...

class	SimulationData
	Store all parameters for a simulation. More...

class	SitesGeometry

class	SitesPairScore
	Apply a function to the distance between two particles with a set of specific binding sites. More...

struct	SitesPairScoreParameters

class	SlabWithCylindricalPore

class	SlabWithCylindricalPorePairScore
	XXXX. More...

class	SlabWithCylindricalPoreWireGeometry
	XXXX. More...

class	SlabWithPore

class	SlabWithToroidalPore

class	SlabWithToroidalPorePairScore
	Score for a slab with a toroidal pore. More...

class	SlabWithToroidalPoreWireGeometry
	XXXX. More...

class	Statistics
	Statistics and order parameters about the simulations. More...

class	Transporting
	A decorator for a particle transporting through a barrier. More...

class	TypedSitesGeometry

class	ZBiasSingletonScore
	Score that biases particles to go down the Z axis. More...

Typedefs
typedef IMP::Vector < Avro2PBReader >	Avro2PBReaders

typedef IMP::Vector < IMP::Pointer < BipartitePairsStatisticsOptimizerState > >	BipartitePairsStatisticsOptimizerStates

typedef IMP::Vector < IMP::WeakPointer < BipartitePairsStatisticsOptimizerState > >	BipartitePairsStatisticsOptimizerStatesTemp

typedef IMP::Vector < IMP::Pointer < BodyStatisticsOptimizerState > >	BodyStatisticsOptimizerStates

typedef IMP::Vector < IMP::WeakPointer < BodyStatisticsOptimizerState > >	BodyStatisticsOptimizerStatesTemp

typedef IMP::Vector < IMP::Pointer < ChainStatisticsOptimizerState > >	ChainStatisticsOptimizerStates

typedef IMP::Vector < IMP::WeakPointer < ChainStatisticsOptimizerState > >	ChainStatisticsOptimizerStatesTemp

typedef IMP::Vector < IMP::Pointer< FGChain > >	FGChains

typedef IMP::Vector < IMP::WeakPointer< FGChain > >	FGChainsTemp

typedef IMP::Vector < IMP::Pointer < GlobalStatisticsOptimizerState > >	GlobalStatisticsOptimizerStates

typedef IMP::Vector < IMP::WeakPointer < GlobalStatisticsOptimizerState > >	GlobalStatisticsOptimizerStatesTemp

typedef IMP::Vector < IMP::Pointer < HarmonicSpringSingletonScore > >	HarmonicSpringSingletonScores

typedef IMP::Vector < IMP::WeakPointer < HarmonicSpringSingletonScore > >	HarmonicSpringSingletonScoresTemp

typedef IMP::Vector < IMP::Pointer < HarmonicWellPairScore > >	HarmonicWellPairScores

typedef IMP::Vector < IMP::WeakPointer < HarmonicWellPairScore > >	HarmonicWellPairScoresTemp

typedef std::pair < IMP::core::ParticleType, IMP::core::ParticleType >	InteractionType
	an interaction that involves particles of two types More...

typedef IMP::Vector < InteractionType >	InteractionTypes

typedef IMP::Vector < IMP::Pointer < LinearInteraction > >	LinearInteractions

typedef score_functor::SphereDistance < LinearInteraction >	LinearInteractionScore

typedef IMP::Vector < IMP::WeakPointer < LinearInteraction > >	LinearInteractionsTemp

typedef score_functor::SphereDistance < score_functor::LinearLowerBound >	LinearSoftSphereScore

typedef IMP::Vector < IMP::Pointer < LinearWellPairScore > >	LinearWellPairScores

typedef IMP::Vector < IMP::WeakPointer < LinearWellPairScore > >	LinearWellPairScoresTemp

typedef IMP::Vector < IMP::Pointer < ParticleTransportStatisticsOptimizerState > >	ParticleTransportStatisticsOptimizerStates

typedef IMP::Vector < IMP::WeakPointer < ParticleTransportStatisticsOptimizerState > >	ParticleTransportStatisticsOptimizerStatesTemp

typedef boost::unordered_set < core::ParticleType >	ParticleTypeSet

typedef IMP::Vector < RelaxingSpring >	RelaxingSprings

typedef IMP::Vector < SitesPairScoreParameters >	SitesPairScoreParametersList

typedef IMP::Vector < SlabWithCylindricalPore >	SlabsWithCylindricalPores

typedef IMP::Vector< SlabWithPore >	SlabsWithPores

typedef IMP::Vector < SlabWithToroidalPore >	SlabsWithToroidalPores

typedef IMP::Vector< Transporting >	Transportings

Functions
void	add_hierarchies_with_sites (RMF::FileHandle fh, const atom::Hierarchies &hs)

void	add_hierarchies_with_sites (RMF::NodeHandle fh, const atom::Hierarchies &hs)

void	add_hierarchy_with_sites (RMF::FileHandle fh, atom::Hierarchy hs)

void	add_test_sites (RMF::FileHandle fh, core::ParticleType t, double display_radius, algebra::Vector3Ds sites)

void	add_test_sites (RMF::FileHandle fh, core::ParticleType t, algebra::Sphere3Ds sites)

int	assign_ranges (std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed)

void	copy_FGs_coordinates (SimulationData const src_sd, SimulationData trg_sd)
	copy coordinates of src_sd to trg_sd for FG repeats only More...

void	copy_hierarchy_reference_frame_recursive (Particle src_p, Particle trg_p)

void	copy_particle_reference_frame_if_applicable (Particle src_p, Particle trg_p)

boost::timer	create_boost_timer ()

FGChain *	create_fg_chain (IMP::npctransport::SimulationData *sd, atom::Hierarchy parent, const ::npctransport_proto::Assignment_FGAssignment &fg_data, display::Color c)

atom::Hierarchies	create_hierarchies_with_sites (RMF::FileConstHandle fh, Model *m)

double	do_evaluate_index (algebra::Sphere3D &d_xyzr0, algebra::Sphere3D &d_xyzr1, DerivativeAccumulator *da, const algebra::Vector3D &delta, double delta_length, double x0, double k)

double	do_evaluate_index_harmonic (Model m, const ParticleIndexPair &pp, DerivativeAccumulator da, const algebra::Vector3D &delta, double delta_length, double x0, double k)

void	do_main_loop (SimulationData *sd, const RestraintsTemp &init_restraints)

unsigned int	find_or_add_fg_bead_of_type (::npctransport_proto::Statistics *s, IMP::core::ParticleType pt)

unsigned int	find_or_add_fg_chain_of_type (::npctransport_proto::Statistics *s, IMP::core::ParticleType pt)

unsigned int	find_or_add_floater_of_type (::npctransport_proto::Statistics *s, IMP::core::ParticleType pt)

unsigned int	find_or_add_interaction_of_type (::npctransport_proto::Statistics *s, IMP::npctransport::InteractionType it)

internal_avro::ValidSchema	get_avro_data_file_schema ()

double	get_close_pairs_range (double max_range, double max_range_factor)

double	get_close_pairs_range (const ::npctransport_proto::Assignment &config)

int	get_dump_interval_in_frames (const ::npctransport_proto::Assignment &config, double time_step)

FGChain *	get_fg_chain (atom::Hierarchy root)

FGChain *	get_fg_chain (Particle *p_root)

int	get_frames_from_ns (double ns, double time_step)

algebra::Vector3D	get_global_from_local_v3 (Particle *p, const algebra::Vector3D &local)

template<class t_ordered_set >
boost::tuple< unsigned int, unsigned int >	get_n_lost_and_gained (t_ordered_set old, t_ordered_set cur)

ParticlesTemp	get_non_optimizable_particles (ParticlesTemp const &particles)

int	get_number_of_frames (const ::npctransport_proto::Assignment &config, double time_step)

int	get_number_of_work_units (std::string configuration_file)

ParticlesTemp	get_optimizable_particles (ParticlesTemp const &particles)

int	get_output_statistics_interval_in_frames (const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=1.0)

ParticleIndexes	get_particle_indexes (ParticlesTemp const &particles)

void	get_protobuf_configuration_from_text (std::string config_txt, std::string config_pb)

WeakObjectKey	get_simulation_data_key ()

algebra::Vector3Ds	get_spheres_centers (algebra::Sphere3Ds const &spheres)

template<typename V3iter >
algebra::Sphere3Ds	get_spheres_from_vectors (V3iter first, V3iter last, double radius)
	convert vectors to spheres of passed radius More...

algebra::Sphere3Ds	get_spheres_from_vectors (algebra::Vector3Ds const &vs, double radius)
	convert vectors to spheres of passed radius More...

int	get_statistics_interval_in_frames (const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=0.1)

double	get_time_step (double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0)

double	get_time_step (const ::npctransport_proto::Assignment &config, double max_trans_relative_to_radius=0.1)

void	inflate_floater (SimulationData *sd, const std::string floater_name, const float new_radius)
	inflate floater of specified type to new_radius More...

void	initialize_positions (SimulationData *sd, const RestraintsTemp &extra_restraints=RestraintsTemp(), bool debug=false, double short_init_factor=1.0, bool is_disable_randomize=false, bool are_fgs_pre_initialized=false)

void	link_hierarchies_with_sites (RMF::FileConstHandle fh, const atom::Hierarchies &hs)

bool	load_output_protobuf (std::string output_fname,::npctransport_proto::Output &output)

void	load_pb_conformation (const ::npctransport_proto::Conformation &conformation, IMP::SingletonContainerAdaptor beads, boost::unordered_map< core::ParticleType, algebra::Sphere3Ds > &sites)

InteractionType	make_ordered_interaction_type (IMP::core::ParticleType t0, IMP::core::ParticleType t1)
	convenience method for creating and interaction type in swig More...

InteractionType	make_unordered_interaction_type (IMP::core::ParticleType t0, IMP::core::ParticleType t1)

template<class t_value >
std::pair< t_value, t_value >	make_unordered_pair (t_value v0, t_value v1)
	Canonize such that v0>=v1 so order doesn't matter. More...

IMP::ParticleIndexPair	make_unordered_particle_index_pair (IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)

ParticleIndexPair	make_unordered_particle_index_pair (ParticleIndexPair pip)

template<class ParticlesList , class BoundingVolume >
void	randomize_particles (const ParticlesList &ps, const BoundingVolume &bv)

template<class RigidBody , class BoundingVolume >
void	randomize_rigid_body (RigidBody rbi, const BoundingVolume &bv)

void	remove_Nup42 (SimulationData *sd)
	remove nup42 and its anchors (also from obstacles) More...

void	reset_box_size (SimulationData *sd, double box_size)
	change box size sd to specified box size and update output file More...

void	save_pb_conformation (IMP::SingletonContainerAdaptor beads, const boost::unordered_map< core::ParticleType, algebra::Sphere3Ds > &sites,::npctransport_proto::Conformation *conformation)

void	show_ranges (std::string fname)

IMP::npctransport::SimulationData *	startup (int argc, char *argv[])

void	write_geometry (const ParticlesTemp &kaps, const algebra::Sphere3Ds &kap_sites, const ParticlesTemp &chains, const algebra::Sphere3Ds &chain_sites, const RestraintsTemp &rs, display::Writer *out)

Variables
const double	FS_IN_NS = 1.0E+6

const double	HALF_SQRT_MAX_DOUBLE = 0.5 * std::sqrt( MAX_DOUBLE )

const double	MAX_DOUBLE = std::numeric_limits< double >::max()

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...

Typedef Documentation

typedef IMP::Vector< Avro2PBReader > IMP::npctransport::Avro2PBReaders

Pass or store a set of Avro2PBReader .

Definition at line 90 of file Avro2PBReader.h.

typedef IMP::Vector<IMP::Pointer< BipartitePairsStatisticsOptimizerState > > IMP::npctransport::BipartitePairsStatisticsOptimizerStates

A vector of reference-counting object pointers.

Definition at line 274 of file BipartitePairsStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::WeakPointer< BipartitePairsStatisticsOptimizerState > > IMP::npctransport::BipartitePairsStatisticsOptimizerStatesTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: BipartitePairsStatisticsOptimizerState

Definition at line 274 of file BipartitePairsStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::Pointer< BodyStatisticsOptimizerState > > IMP::npctransport::BodyStatisticsOptimizerStates

A vector of reference-counting object pointers.

Definition at line 70 of file BodyStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::WeakPointer< BodyStatisticsOptimizerState > > IMP::npctransport::BodyStatisticsOptimizerStatesTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: BodyStatisticsOptimizerState

Definition at line 70 of file BodyStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::Pointer< ChainStatisticsOptimizerState > > IMP::npctransport::ChainStatisticsOptimizerStates

A vector of reference-counting object pointers.

Definition at line 115 of file ChainStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::WeakPointer< ChainStatisticsOptimizerState > > IMP::npctransport::ChainStatisticsOptimizerStatesTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: ChainStatisticsOptimizerState

Definition at line 115 of file ChainStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::Pointer< FGChain > > IMP::npctransport::FGChains

A vector of reference-counting object pointers.

Definition at line 190 of file FGChain.h.

typedef IMP::Vector<IMP::WeakPointer< FGChain > > IMP::npctransport::FGChainsTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: FGChain

Definition at line 190 of file FGChain.h.

typedef IMP::Vector<IMP::Pointer< GlobalStatisticsOptimizerState > > IMP::npctransport::GlobalStatisticsOptimizerStates

A vector of reference-counting object pointers.

Definition at line 52 of file GlobalStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::WeakPointer< GlobalStatisticsOptimizerState > > IMP::npctransport::GlobalStatisticsOptimizerStatesTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: GlobalStatisticsOptimizerState

Definition at line 52 of file GlobalStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::Pointer< HarmonicSpringSingletonScore > > IMP::npctransport::HarmonicSpringSingletonScores

A vector of reference-counting object pointers.

Definition at line 152 of file HarmonicSpringSingletonScore.h.

typedef IMP::Vector<IMP::WeakPointer< HarmonicSpringSingletonScore > > IMP::npctransport::HarmonicSpringSingletonScoresTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: HarmonicSpringSingletonScore

Definition at line 152 of file HarmonicSpringSingletonScore.h.

typedef IMP::Vector<IMP::Pointer< HarmonicWellPairScore > > IMP::npctransport::HarmonicWellPairScores

A vector of reference-counting object pointers.

Definition at line 114 of file harmonic_distance_pair_scores.h.

typedef IMP::Vector<IMP::WeakPointer< HarmonicWellPairScore > > IMP::npctransport::HarmonicWellPairScoresTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: HarmonicWellPairScore

Definition at line 114 of file harmonic_distance_pair_scores.h.

typedef std::pair<IMP::core::ParticleType, IMP::core::ParticleType> IMP::npctransport::InteractionType

an interaction that involves particles of two types

Definition at line 21 of file typedefs.h.

typedef IMP::Vector< InteractionType > IMP::npctransport::InteractionTypes

Pass or store a set of InteractionType .

Definition at line 22 of file typedefs.h.

typedef IMP::Vector<IMP::Pointer< LinearInteraction > > IMP::npctransport::LinearInteractions

A vector of reference-counting object pointers.

Definition at line 85 of file functor_linear_distance_pair_scores_typedefs.h.

typedef IMP::Vector<IMP::WeakPointer< LinearInteraction > > IMP::npctransport::LinearInteractionsTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: LinearInteraction

Definition at line 85 of file functor_linear_distance_pair_scores_typedefs.h.

typedef IMP::Vector<IMP::Pointer< LinearWellPairScore > > IMP::npctransport::LinearWellPairScores

A vector of reference-counting object pointers.

Definition at line 468 of file linear_distance_pair_scores.h.

typedef IMP::Vector<IMP::WeakPointer< LinearWellPairScore > > IMP::npctransport::LinearWellPairScoresTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: LinearWellPairScore

Definition at line 468 of file linear_distance_pair_scores.h.

typedef IMP::Vector<IMP::Pointer< ParticleTransportStatisticsOptimizerState > > IMP::npctransport::ParticleTransportStatisticsOptimizerStates

A vector of reference-counting object pointers.

Definition at line 113 of file ParticleTransportStatisticsOptimizerState.h.

typedef IMP::Vector<IMP::WeakPointer< ParticleTransportStatisticsOptimizerState > > IMP::npctransport::ParticleTransportStatisticsOptimizerStatesTemp

A vector of weak (non reference-counting) pointers to specified objects.

See Also: ParticleTransportStatisticsOptimizerState

Definition at line 113 of file ParticleTransportStatisticsOptimizerState.h.

typedef IMP::Vector< SitesPairScoreParameters > IMP::npctransport::SitesPairScoreParametersList

Pass or store a set of SitesPairScoreParameters .

Definition at line 97 of file SitesPairScoreParameters.h.

Function Documentation

void IMP::npctransport::add_hierarchies_with_sites	(	RMF::FileHandle	fh,
		const atom::Hierarchies &	hs
	)

Functions for adding a hierarchy to an RMF file or linking an RMF file to an existing hierarchy, including support for particles with sites.

These functions are practically identical to the add / link methods in modules/rmf/include/hierarchy_io.h, such as IMP::rmf::link_hierarchies(), except here NPC particle sites support is included.Add objects to the file.

Note: This does not save a configuration; make sure you use save_frame() to do that.

void IMP::npctransport::add_hierarchies_with_sites	(	RMF::NodeHandle	fh,
		const atom::Hierarchies &	hs
	)

Add objects to the file under the specified node.

Note: This does not save a configuration; make sure you use save_frame() to do that.

void IMP::npctransport::add_hierarchy_with_sites	(	RMF::FileHandle	fh,
		atom::Hierarchy	hs
	)

Add a single HierarchyWithSites object to the RMF file.

Note: This does not save a configuration; make sure you use save_frame() to do that.

void IMP::npctransport::add_test_sites	(	RMF::FileHandle	fh,
		core::ParticleType	t,
		double	display_radius,
		algebra::Vector3Ds	sites
	)

for testing - adds the list of sites with specified radius, to be associated with particle type t. The file handle fh relies on this list only if it doesn't have particles with simulation data keys

void IMP::npctransport::add_test_sites	(	RMF::FileHandle	fh,
		core::ParticleType	t,
		algebra::Sphere3Ds	sites
	)

for testing - adds the list of sites with specified display radius, to be associated with particle type t. The file handle fh relies on this list only if it doesn't have particles with simulation data keys

int IMP::npctransport::assign_ranges	(	std::string	input_config_fname,
		std::string	output_assignment_fname,
		unsigned int	work_unit,
		bool	show_steps,
		boost::uint64_t	random_seed
	)

reads the protobuf message in [input_config_fname], which may contain submessages with ranges of values (indicated by presence of .upper and .lower fields, with .steps possible steps for each such field). The output is a message with the [work_unit]'th possible combination of these ranges, to the file [output_assignment_fname].

Note: the range values are enumerated as if they lie on a grid with log-evenly distributed axis-aligned grid points, using the .base field as the log base for each ranged field, such that e.g. iterating over the range [1..8] with 3 steps and base 2 will be enumerated as (1,4,8)

Parameters

fname	input_config_fname configuration file name
output	output_assignment_fname assignment file name
work_unit	the index of combination of range values to be used. If the total of possible combinations of all fields with ranges is k, it is guaranteed that iterating over work_unit between 0..k-1 will enumerate over all possible combinations, and that work_unit and (work_unit % k) will return the same output for the same input.
show_steps	show the steps that occur
random_seed	the random seed used to initialize the IMP random number generator for this simulation

Exceptions

IMP::ValueException if any of the values in the configuration file are in conflict (e.g., simulation time and maximal number of frames)

void IMP::npctransport::copy_FGs_coordinates	(	SimulationData const *	src_sd,
		SimulationData *	trg_sd
	)

copy coordinates of src_sd to trg_sd for FG repeats only

void IMP::npctransport::copy_hierarchy_reference_frame_recursive	(	Particle *	src_p,
		Particle *	trg_p
	)

Copy XYZ coordinates or RigidBody reference frame from src_pi to trg_pi if applicable, and if src_pi and trg_pi are an atom hierarchy, proceed recursively to their children. If so, assumes identical topology of hierarchies for src_pi and trg_pi

void IMP::npctransport::copy_particle_reference_frame_if_applicable	(	Particle *	src_p,
		Particle *	trg_p
	)

Copy XYZ coordinates or RigidBody reference frame from src_p to trg_p, if it is decorated with XYZ or RigidBody. Do nothing otherwise.

FGChain* IMP::npctransport::create_fg_chain	(	IMP::npctransport::SimulationData *	sd,
		atom::Hierarchy	parent,
		const ::npctransport_proto::Assignment_FGAssignment &	fg_data,
		display::Color	c
	)

Create a chain particle hierarchy, to be owned by the model of sd, with restraint bonding consecutive particles added to sd, according to the parameters specified in fg_data.

Notes:

The type of the chain root is specified in fg_data.type(). Individual particles may have different types if fg_data.type_suffix_list is non-empty. In this case, the type of particle i is suffixed with fg_data.type_suffix_list[i], or remains fg_data.type() if the suffix is "".

The rest length between two consecutive chain beads is fg_data.radius() * 2.0 * fg_data.rest_length_factor() and the spring constant is the simulation backbone_k parameter.

If fg_data.is_tamd() is true, created a TAMD hierarchy, otherwise a simple parent + beads structure. In the TAMD case, the custom restraint are added to sd->get_scoring() and the tamd images are added to sd->root()

Parameters

[in,out]	sd	the simulation data whose model is associated with the new chain. The chain is also added to the simulation data scoring object.
	parent	parent hierarchy to which chain is added
[in]	fg_data	data about the FG chain
[in]	c	color of chain particles

Returns: chain structure (with root and chain beads)

atom::Hierarchies IMP::npctransport::create_hierarchies_with_sites	(	RMF::FileConstHandle	fh,
		Model *	m
	)

Create HierarchyWithSites objects from the RMF file.

Note: This does not load a frame. Make sure you call IMP::rmf::load_frame() before using.

double IMP::npctransport::do_evaluate_index	(	algebra::Sphere3D &	d_xyzr0,
		algebra::Sphere3D &	d_xyzr1,
		DerivativeAccumulator *	da,
		const algebra::Vector3D &	delta,
		double	delta_length,
		double	x0,
		double	k
	)

Evaluates a linear pair potential, such that score = k * (delta_length - x0) is returned. Also, updates the derivative vectors of the particles if da is not null.

Parameters

[out]	d_xyzr0	pointer to derivative of particle 0
[out]	d_xyzr1	pointer to derivative of particle 1
[in,out]	da	accumulator for score derivatives to be updated
[in]	delta	a vector that represents the displacement between the two particles
	delta_length	the cached length of delta, assumed correct, and required for faster calculation
	x0	resting distance (where score = 0)
	k	score linear coefficient. Note that the score is attractive for a positive k, and repulsive for a negative k (assuming the lower the score the better).

Returns: the score

Definition at line 41 of file linear_distance_pair_scores.h.

double IMP::npctransport::do_evaluate_index_harmonic	(	Model *	m,
		const ParticleIndexPair &	pp,
		DerivativeAccumulator *	da,
		const algebra::Vector3D &	delta,
		double	delta_length,
		double	x0,
		double	k
	)

Evaluates a linear pair potential, such that force = k * (delta_length - x0) is returned. Also, updates the derivative vectors of the particles in the model m.

Parameters

[out]	m	a model for the particles, in which particle derivatives are updated
[in]	pp	a pair of particle indices for fast access through internal model methods
[in,out]	da	accumulator for score derivatives to be updated
[in]	delta	a vector from pp[1] to pp[0]
	delta_length	the cached length of delta, assumed correct, and required for faster calculation
	x0	resting distance (where score = 0)
	k	score linear coefficient. Note that the score is attractive for a positive k, and repulsive for a negative k (assuming the lower the score the better).

Returns: the score

Definition at line 41 of file harmonic_distance_pair_scores.h.

void IMP::npctransport::do_main_loop	(	SimulationData *	sd,
		const RestraintsTemp &	init_restraints
	)

Run simulation using preconstructed SimulationData object sd.

Parameters

sd	SimulationData object to optimize
init_restraints	ad-hoc restraints during initialization only

unsigned int IMP::npctransport::find_or_add_fg_bead_of_type	(	::npctransport_proto::Statistics *	s,
		IMP::core::ParticleType	pt
	)

finds the index of s.fg_beads() whose type equals pt.get_string() if it does not exist, add it to s

Parameters

s	the statistics message for searching the fg
pt	the type of fg to look for

unsigned int IMP::npctransport::find_or_add_fg_chain_of_type	(	::npctransport_proto::Statistics *	s,
		IMP::core::ParticleType	pt
	)

finds the index of s.fgs() whose type equals pt.get_string() if it does not exist, add it to s

Parameters

s	the statistics message for searching the fg
pt	the type of fg to look for

unsigned int IMP::npctransport::find_or_add_floater_of_type	(	::npctransport_proto::Statistics *	s,
		IMP::core::ParticleType	pt
	)

finds the index of s->floaters() whose type equals pt.get_string() if it does not exist, add it to s

Parameters

s	the statistics message for searching t
pt	the type to look for

unsigned int IMP::npctransport::find_or_add_interaction_of_type	(	::npctransport_proto::Statistics *	s,
		IMP::npctransport::InteractionType	it
	)

finds the index of s.interactions() whose type0 and type1 particle type equivalents are equale to it. If it does not exist, add it to s

Parameters

s	the statistics message for searching t
it	the type to look for

Returns: the index of the interaction type in s.interaction()

double IMP::npctransport::get_close_pairs_range ( const ::npctransport_proto::Assignment & config )

returns an upper bound on the contact range (maximal sphere-sphere distance that enables a contact) between any two particles in the system

std::string IMP::npctransport::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

std::ifstream in(IMP::npctransport::get_data_path("data_library"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note: Each module has its own data directory, so be sure to use this function from the correct module.

int IMP::npctransport::get_dump_interval_in_frames	(	const ::npctransport_proto::Assignment &	config,
		double	time_step
	)

computes the number of frames for the specified dump_interval, which is normalized by the time step if the interval is specified in ns

Parameters

config	the simulation parameters
time_step	the time step in femtoseconds

std::string IMP::npctransport::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

std::ifstream in(IMP::npctransport::get_example_path("example_protein.pdb"));

This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.

Note: Each module has its own example directory, so be sure to use this function from the correct module.

FGChain* IMP::npctransport::get_fg_chain ( atom::Hierarchy root )

gets a newly allocated chain structure from a root of an FG nup (by adding its ordered leaves)

FGChain* IMP::npctransport::get_fg_chain ( Particle * p_root )

gets a newly allocated chain structure from a root of an FG nup (by adding its ordered leaves)

Parameters

p_root a particle that is assumed to be Hierarchy decorated

int IMP::npctransport::get_frames_from_ns	(	double	ns,
		double	time_step
	)

computes the number of frames that approximate a certain number of nanoseconds using the specified time_step per step in fs

Parameters

ns	time in ns
time_step	step in fs per frame

algebra::Vector3D IMP::npctransport::get_global_from_local_v3	(	Particle *	p,
		const algebra::Vector3D &	local
	)

Parameters

p	a rigid body particle
local	the vector in local coordinates

Returns: the global coordinates of local based on the reference frame of the rigid body p

Definition at line 111 of file util.h.

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template<class t_ordered_set >

boost::tuple<unsigned int, unsigned int> IMP::npctransport::get_n_lost_and_gained	(	t_ordered_set	old,
		t_ordered_set	cur
	)

returns |old/core| and |cur/old|, i.e., the number of items lost from old, and the ones gained in cur.

Note: it is assumed that old and cur are ordered iteratable objects (e.g. std::set) whose begin() and end() methods qualify as valid inputs for std::set_difference

Definition at line 138 of file util.h.

ParticlesTemp IMP::npctransport::get_non_optimizable_particles ( ParticlesTemp const & particles )

returns particles with non-optimizable coordinates from particles

int IMP::npctransport::get_number_of_frames	(	const ::npctransport_proto::Assignment &	config,
		double	time_step
	)

computes the number of frames needed to achieve simulation time required in the configuration time, with time step computed from config.

Parameters

config	the simulation parameters
time_step	the time step in femtoseconds

Exceptions

ValueException if maximum number of frames specified in config is exceeded

ParticlesTemp IMP::npctransport::get_optimizable_particles ( ParticlesTemp const & particles )

returns particles with optimizable coordinates from particles

int IMP::npctransport::get_output_statistics_interval_in_frames	(	const ::npctransport_proto::Assignment &	assign,
		double	time_step,
		double	default_value_ns = `1.0`
	)

computes the maximal interval for outputting statistics to output file (and to dump order params) in frames, for the output_statistics_interval_ns param in assignment, based on specified time_step

Parameters

assign	the simulation assignment parameters
time_step	the time step in femtoseconds
default_value_ns	interval in ns to use if none specified in assignment parameters

ParticleIndexes IMP::npctransport::get_particle_indexes ( ParticlesTemp const & particles )

returns particle indexes from a list of particles

void IMP::npctransport::get_protobuf_configuration_from_text	(	std::string	config_txt,
		std::string	config_pb
	)

Converts protobuf configuration file config_txt (which is in pretty protobuf textual output format) to binary protobuf format (in file config_pb)

Parameters

config_txt	the input textual protobuf config file
config_pb	the output binary protobuf file

template<typename V3iter >

algebra::Sphere3Ds IMP::npctransport::get_spheres_from_vectors	(	V3iter	first,
		V3iter	last,
		double	radius
	)

convert vectors to spheres of passed radius

Definition at line 169 of file util.h.

algebra::Sphere3Ds IMP::npctransport::get_spheres_from_vectors	(	algebra::Vector3Ds const &	vs,
		double	radius
	)

convert vectors to spheres of passed radius

int IMP::npctransport::get_statistics_interval_in_frames	(	const ::npctransport_proto::Assignment &	assign,
		double	time_step,
		double	default_value_ns = `0.1`
	)

computes the number of frames for the specified statistics_interval, normalized by the time step if the interval is specified in ns

Parameters

assign	the simulation assignment parameters
time_step	the time step in femtoseconds
default_value_ns	interval in ns to use if none specified in assignment parameters

double IMP::npctransport::get_time_step	(	double	max_d_factor,
		double	max_k,
		double	min_radius,
		double	min_range,
		double	max_trans_relative_to_radius = `0.1`,
		double	time_step_factor = `1.0`
	)

Computes the time step size that is required for a stable simulation. Formally, first computes the time step size that restricts the estimated translation size of any particle, at any given simulation step to [max_trans_relative_to_radius * min_radius], given the simulation parameters max_d_factor and max_k. This base time step is then multiplied by time_step_factor.

Parameters

max_d_factor	the maximal diffusion factor of any particle in the system, which factors the Einstein diffusion coefficient)
max_k	the maximal force applied on any particle in the simulation
min_radius	the minimal radius of any interaction in the system
min_range	the minimal range of any interaction
max_trans_relative_to_radius	the maximal estimated translation allowed for any particle as fraction of min_radius (before factoring by time_step_factor)
time_step_factor	multiply final time step in this factor

Returns: time step size in femtoseconds required for stable simulation

double IMP::npctransport::get_time_step	(	const ::npctransport_proto::Assignment &	config,
		double	max_trans_relative_to_radius = `0.1`
	)

computes the time step size that is required for a stable simulation, where the translation of any particle at any simulation time step is restricted, based on the simulation parameters in config.

Parameters

config	the simulation parameters used to compute the time step size
max_trans_relative_to_radius	the maximal estimated translation allowed for any particle as fraction of its radius (before factoring by time step factor, specified in config)

Returns: time step size in femtoseconds required for stable simulation

void IMP::npctransport::inflate_floater	(	SimulationData *	sd,
		const std::string	floater_name,
		const float	new_radius
	)

inflate floater of specified type to new_radius

void IMP::npctransport::initialize_positions	(	SimulationData *	sd,
		const RestraintsTemp &	extra_restraints = `RestraintsTemp()`,
		bool	debug = `false`,
		double	short_init_factor = `1.0`,
		bool	is_disable_randomize = `false`,
		bool	are_fgs_pre_initialized = `false`
	)

pre-optimize the positions of all diffusing particles in 'sd' whose coordinates are optimizable, using only chain restraints, excluded volumes and bounding box restraints (but not interaction restraints).

The initialization data is dumped to the RMF file sd->get_rmf_file_name() using dump interval sd->get_rmf_dump_interval_frames() * 100, or every frame in case that debug is true.

Parameters

sd	the SimulationData object containing diffusing particles
extra_restraints	a list of additional ad-hoc restraints that will be used only throughout initialization
debug	if true, the initialization will dump much more output (e.g. every frame to RMF file)
short_init_factor	a factor between >0 and 1 for decreasing the number of optimization cycles at each round
is_disable_randomize	if true, do not initially randomize particle positions, essentially performing an extended relaxation from the starting coordinates
are_fgs_pre_initialized	if true, do not try to pre-optimize FGs before adding diffusers

void IMP::npctransport::link_hierarchies_with_sites	(	RMF::FileConstHandle	fh,
		const atom::Hierarchies &	hs
	)

Link HierarchyWithSites objects with the RMF file, possibly overwriting an existing link for loading from the file. This does not alter the object, but will affect the behavior of functions like load_frame() and save_frame(). See IMP::rmf::link_hierarchies() for more details. The only difference is the addition of particle sites support.

bool IMP::npctransport::load_output_protobuf	(	std::string	output_fname,
		::npctransport_proto::Output &	output
	)

load file output_fname into protobuf output object output return true if succesful

void IMP::npctransport::load_pb_conformation	(	const ::npctransport_proto::Conformation &	conformation,
		IMP::SingletonContainerAdaptor	beads,
		boost::unordered_map< core::ParticleType, algebra::Sphere3Ds > &	sites
	)

Loads a protobuf conformation into the diffusers and sites

Parameters

conformation	the saved conformation protobuf message
beads	corresponding diffusers to be updated
sites	a map of sites for each diffuser particle type to be updated

Note: the beads and sites must have the same structure as the ones used when saving (e.g. their non-changing variables are expected to be identical, and they differ only in the dynamic ones)

See Also: save_pb_conformation

InteractionType IMP::npctransport::make_ordered_interaction_type	(	IMP::core::ParticleType	t0,
		IMP::core::ParticleType	t1
	)

convenience method for creating and interaction type in swig

Definition at line 26 of file typedefs.h.

InteractionType IMP::npctransport::make_unordered_interaction_type	(	IMP::core::ParticleType	t0,
		IMP::core::ParticleType	t1
	)

an interaction type canonized to (t0,t1) s.t. t0 >= t1, so order doesn't matter

Definition at line 35 of file typedefs.h.

template<class t_value >

std::pair<t_value, t_value> IMP::npctransport::make_unordered_pair	(	t_value	v0,
		t_value	v1
	)

Canonize such that v0>=v1 so order doesn't matter.

Definition at line 160 of file util.h.

IMP::ParticleIndexPair IMP::npctransport::make_unordered_particle_index_pair	(	IMP::ParticleIndex	pi0,
		IMP::ParticleIndex	pi1
	)

ParticleIndexPair canonized to (pi0',pi1') s.t. pi0' >= pi1' so order doesn't matter

Definition at line 45 of file typedefs.h.

ParticleIndexPair IMP::npctransport::make_unordered_particle_index_pair ( ParticleIndexPair pip )

ParticleIndexPair canonized to (pi0',pi1') s.t. pi0' >= pi1' so order doesn't matter

Definition at line 55 of file typedefs.h.

template<class ParticlesList , class BoundingVolume >

void IMP::npctransport::randomize_particles	(	const ParticlesList &	ps,
		const BoundingVolume &	bv
	)

Randomize the positions of a set of particles within a bounding volume. Rigid bodies have their orientation randomized too.

Note: Particles are randomized only if their coordinates are optimizable, that is, get_coordinates_are_optimized() == true)

Definition at line 35 of file randomize_particles.h.

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void IMP::npctransport::remove_Nup42 ( SimulationData * sd )

remove nup42 and its anchors (also from obstacles)

void IMP::npctransport::reset_box_size	(	SimulationData *	sd,
		double	box_size
	)

change box size sd to specified box size and update output file

void IMP::npctransport::save_pb_conformation	(	IMP::SingletonContainerAdaptor	beads,
		const boost::unordered_map< core::ParticleType, algebra::Sphere3Ds > &	sites,
		::npctransport_proto::Conformation *	conformation
	)

Saves a protobuf conformation from the diffusers and sites

Parameters

beads	beads to save
sites	a map of sites for each diffuser particle type to be saved
conformation	the conformation protobuf message to be save

See Also: load_pb_conformation

IMP::npctransport::SimulationData* IMP::npctransport::startup	(	int	argc,
		char *	argv[]
	)

initialize and return a simulation data object based on program command line parameters

Exceptions

IMP::IOException if there was any IO problem

Detailed Description

fg_simulation: run NPC transport simulations

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Typedefs

Functions

Variables

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