Store all parameters for a simulation. More...

#include <IMP/npctransport/SimulationData.h>

Inheritance diagram for IMP::npctransport::SimulationData:

Detailed Description

Store all parameters for a simulation.

Definition at line 47 of file SimulationData.h.

Public Member Functions
	SimulationData (std::string prev_output_file, bool quick, std::string rmf_file_name=std::string(), std::string new_output_file="")

void	activate_statistics ()
	by adding all appropriate optimizer states, if they weren't already More...

void	add_interaction (const ::npctransport_proto::Assignment_InteractionAssignment &idata)

void	dump_geometry ()

double	get_angular_d_factor () const

bool	get_are_floaters_on_one_slab_side ()

double	get_backbone_tau_ns () const

atom::BrownianDynamics *	get_bd (bool recreate=false)

ParticlesTemp	get_beads ()

Particles &	get_beads_byref ()

algebra::BoundingBox3D	get_box () const

double	get_box_size () const

algebra::Cylinder3D	get_cylinder () const

ParticleTypeSet const &	get_fg_bead_types () const

atom::Hierarchies	get_fg_chain_roots () const

ParticleTypeSet const &	get_fg_chain_types () const

atom::Hierarchies	get_fg_chains () const

ParticleTypeSet const &	get_floater_types () const

bool	get_has_bounding_box () const

bool	get_has_slab () const

double	get_initial_simulation_time_ns () const

bool	get_is_backbone_harmonic () const

bool	get_is_exclude_floaters_from_slab_initially ()

bool	get_is_fg_bead (ParticleIndex pi) const

bool	get_is_fg_bead (core::ParticleType pt) const

bool	get_is_fg_chain (ParticleIndex pi) const

bool	get_is_fg_chain (core::ParticleType pt) const

bool	get_is_pore_radius_dynamic () const
	returns true if pore radius can change dynamically More...

bool	get_is_slab_with_cylindrical_pore () const

bool	get_is_slab_with_toroidal_pore () const

bool	get_is_xyz_hist_stats ()

double	get_maximum_number_of_minutes () const
	Return the maximum number of minutes the simulation can run. More...

Model *	get_model ()

Model *	get_model () const

ParticlesTemp	get_non_optimizable_beads ()

unsigned int	get_number_of_frames () const

unsigned int	get_number_of_trials () const

ParticlesTemp	get_obstacle_particles () const

ParticleTypeSet const &	get_obstacle_types () const

ParticlesTemp	get_optimizable_beads ()

double	get_output_npctransport_version () const

int	get_output_statistics_interval_frames ()

double	get_pore_anchored_beads_k () const

double	get_pore_radius () const
	alias to get_tunnel_radius More...

double	get_pore_radius_k () const
	alias to get_tunnel_radius_k More...

double	get_range () const

int	get_rmf_dump_interval_frames () const

std::string	get_rmf_file_name () const

rmf::SaveOptimizerState *	get_rmf_sos_writer ()

atom::Hierarchy	get_root () const

atom::Hierarchy	get_root_of_type (core::ParticleType type) const

Scoring *	get_scoring ()

Scoring const *	get_scoring () const

algebra::Vector3Ds	get_site_centers (core::ParticleType t0) const

double	get_site_display_radius (core::ParticleType) const

algebra::Sphere3Ds	get_sites (core::ParticleType t0) const

Particle *	get_slab_particle () const

double	get_slab_thickness () const

display::Geometry *	get_static_geometry ()

Statistics *	get_statistics ()

Statistics const *	get_statistics () const

double	get_statistics_fraction () const

double	get_temperature_k () const

double	get_tunnel_radius () const
	returns te current tunnel radius More...

double	get_tunnel_radius_k () const

virtual std::string	get_type_name () const

virtual ::IMP::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

void	initialize_positions_from_rmf (RMF::FileConstHandle fh, int frame_number=-1)

void	link_rmf_file_handle (RMF::FileHandle fh, bool is_restraints=true)

void	remove_fgs_with_prefix (std::string s_fg_type)
	remove all FGs of specified type. More...

void	remove_particle_type (core::ParticleType pt)

void	reset_rmf ()

void	set_box_size (double box_size)

void	set_rmf_file (const std::string &new_name, bool is_save_restraints_to_rmf=true, bool is_force_restart=false)

void	set_sites (core::ParticleType t0, int n, double r, double sr)

void	set_sites (core::ParticleType t0, const algebra::Sphere3Ds &sites)

void	switch_suspend_rmf (bool suspend)

void	write_geometry (std::string out)

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)

Additional Inherited Members
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::SimulationData::SimulationData	(	std::string	prev_output_file,
		bool	quick,
		std::string	rmf_file_name = `std::string()`,
		std::string	new_output_file = `""`
	)

Parameters

[in]	prev_output_file	name of protobuf file that encapsulates the assignment data for initializing the simulation params and the output statistics file. The output file is assumed to already exist at this point and contain the assignment. If it contains an rmf_conformation or conformation field, it will be used to initialize particle positions, in that priority.
[in]	quick	if true, perform a very short simulation, typically for calibration or for initial testing
[out]	rmf_file_name	RMF file to which simulation trajectory is recorded (if empty, no RMF file is created upon construction)

See Also: set_rmf_file()

Parameters

[in] new_output_file new protobuf file for subsequent output and statistics If it is "", then prev_output_file is being rewritten (= default).

Member Function Documentation

void IMP::npctransport::SimulationData::activate_statistics ( )

by adding all appropriate optimizer states, if they weren't already

activates Brownian Dynamics statistics tracking

void IMP::npctransport::SimulationData::add_interaction ( const ::npctransport_proto::Assignment_InteractionAssignment & idata )

add the specified interaction to the scoring. In additions, adds statistics optimizer state about pairs of this type.

Parameters

idata the protobuf data about the interaction (particle types, interaction coefficients, etc.)

double IMP::npctransport::SimulationData::get_angular_d_factor ( ) const

returns the simulation angular d factor

Definition at line 104 of file SimulationData.h.

bool IMP::npctransport::SimulationData::get_are_floaters_on_one_slab_side ( )

returns whether should exclude floaters from one slab side, if excluded at all

Definition at line 97 of file SimulationData.h.

atom::BrownianDynamics* IMP::npctransport::SimulationData::get_bd ( bool recreate = false )

gets the Brownian Dynamics object that is capable of simulating this data. Statistics are not yet active for the simulation.

Parameters

recreate if true, forces recreation of the bd object

ParticlesTemp IMP::npctransport::SimulationData::get_beads ( )

returns all diffusing fine-level beads in this simulation data object (or an empty list if none exists)

Definition at line 366 of file SimulationData.h.

Particles& IMP::npctransport::SimulationData::get_beads_byref ( )

returns all diffusing fine-level beads in this simulation data object (or an empty list if none exists)

Note: efficient - returns an existing container by ref

Definition at line 359 of file SimulationData.h.

ParticleTypeSet const& IMP::npctransport::SimulationData::get_fg_bead_types ( ) const

return all the types of fg beads that were added via create_fgs() including the suffix appended to their chain type name

Definition at line 311 of file SimulationData.h.

atom::Hierarchies IMP::npctransport::SimulationData::get_fg_chain_roots ( ) const

retrieve fg chain hierarchies

Returns: all the fg hierarchies in the simulation data object that stand for individual FG chains

ParticleTypeSet const& IMP::npctransport::SimulationData::get_fg_chain_types ( ) const

return all the types of fg chains that were added via create_fgs(), i.e. the types of chain roots

Definition at line 317 of file SimulationData.h.

atom::Hierarchies IMP::npctransport::SimulationData::get_fg_chains ( ) const

Deprecated:: As of IMP release 2.2. See the IMP Deprecation Policy for more information about deprecation in IMP., use get_fg_chain_roots() instead

Definition at line 344 of file SimulationData.h.

ParticleTypeSet const& IMP::npctransport::SimulationData::get_floater_types ( ) const

return all the types of floaters that were added via create_floaters()

Definition at line 324 of file SimulationData.h.

double IMP::npctransport::SimulationData::get_initial_simulation_time_ns ( ) const

get time from which simulation begins

Definition at line 394 of file SimulationData.h.

bool IMP::npctransport::SimulationData::get_is_exclude_floaters_from_slab_initially ( )

returns whether should exclude floaters from slab during initialization

Definition at line 91 of file SimulationData.h.

bool IMP::npctransport::SimulationData::get_is_fg_bead ( ParticleIndex pi ) const

returns true if bead has an fg type that is, particle was added within create_fgs()

bool IMP::npctransport::SimulationData::get_is_fg_bead ( core::ParticleType pt ) const

returns true if particle type is of fg type (that is, it is one of the types added via create_fgs())

Definition at line 288 of file SimulationData.h.

bool IMP::npctransport::SimulationData::get_is_fg_chain ( ParticleIndex pi ) const

returns true if particle has an fg chain type that is, particle has the same type as the root of an fg chain that was added via create_fgs()

bool IMP::npctransport::SimulationData::get_is_fg_chain ( core::ParticleType pt ) const

returns true if particle type is an fg chain type (that is, it is one of the types of a chain added via create_fgs())

Definition at line 303 of file SimulationData.h.

bool IMP::npctransport::SimulationData::get_is_pore_radius_dynamic ( ) const

returns true if pore radius can change dynamically

Definition at line 640 of file SimulationData.h.

bool IMP::npctransport::SimulationData::get_is_slab_with_cylindrical_pore ( ) const

returns true if a slab is defined and has a cylindrical pore

Definition at line 508 of file SimulationData.h.

bool IMP::npctransport::SimulationData::get_is_slab_with_toroidal_pore ( ) const

returns true if a slab is defined and has a toroidal pore

Definition at line 512 of file SimulationData.h.

double IMP::npctransport::SimulationData::get_maximum_number_of_minutes ( ) const

Return the maximum number of minutes the simulation can run.

Or 0 for no limit.

Definition at line 459 of file SimulationData.h.

ParticlesTemp IMP::npctransport::SimulationData::get_non_optimizable_beads ( )

returns all fine-level beads that currently exist in this simulation data object get_sd(), which are also non-optimizable (or an empty list if no such bead exists)

ParticlesTemp IMP::npctransport::SimulationData::get_obstacle_particles ( ) const

return all the obstacle particles

ParticleTypeSet const& IMP::npctransport::SimulationData::get_obstacle_types ( ) const

return all the types of obstacles that were added via create_obstacles()

Definition at line 330 of file SimulationData.h.

ParticlesTemp IMP::npctransport::SimulationData::get_optimizable_beads ( )

returns all fine-level beads that currently exist in this simulation data object get_sd(), which are also optimizable (or an empty list if no such bead exists)

double IMP::npctransport::SimulationData::get_pore_radius ( ) const

alias to get_tunnel_radius

Definition at line 624 of file SimulationData.h.

double IMP::npctransport::SimulationData::get_pore_radius_k ( ) const

alias to get_tunnel_radius_k

Definition at line 635 of file SimulationData.h.

double IMP::npctransport::SimulationData::get_range ( ) const

returns the maximal interaction range between particles

Definition at line 85 of file SimulationData.h.

rmf::SaveOptimizerState* IMP::npctransport::SimulationData::get_rmf_sos_writer ( )

Returns the internal periodic SaveOptimizerState writer that periodically outputs the particles hierarchy and restraints, using the file name returned by SimulationData::get_rmf_file_name(), which is assumed to be non empty. If the writer does not exist, then it is constructed first.

Exceptions

RMF::IOException couldn't create RMF file

atom::Hierarchy IMP::npctransport::SimulationData::get_root_of_type ( core::ParticleType type ) const

Returns the root of all chains of type 'type'

Scoring* IMP::npctransport::SimulationData::get_scoring ( )

returns a scoring object that is updated with the current particles hierarch and associated with this sd

Scoring const* IMP::npctransport::SimulationData::get_scoring ( ) const

returns a scoring object that is updated with the current particles hierarchy and associated with this sd

algebra::Vector3Ds IMP::npctransport::SimulationData::get_site_centers ( core::ParticleType t0 ) const

returns a list of 3D coordinates for the interaction sites associated with particles of type t0. The site coordinates are in the particles local reference frame

Definition at line 416 of file SimulationData.h.

double IMP::npctransport::SimulationData::get_site_display_radius ( core::ParticleType ) const

Returns the effective interaction range radius of a site on a floater

Definition at line 455 of file SimulationData.h.

algebra::Sphere3Ds IMP::npctransport::SimulationData::get_sites ( core::ParticleType t0 ) const

returns a list of Spheres3D for the interaction sites associated with particles of type t0. The site coordinates are in the particles local reference frame.

Definition at line 434 of file SimulationData.h.

Particle* IMP::npctransport::SimulationData::get_slab_particle ( ) const

returns the slab particle, initializing it based on current parameters if needed

Definition at line 518 of file SimulationData.h.

Statistics* IMP::npctransport::SimulationData::get_statistics ( )

returns a Statistics object that is updated by this simulation data

Statistics const* IMP::npctransport::SimulationData::get_statistics ( ) const

returns a Statistics object that is updated by this simulation data

double IMP::npctransport::SimulationData::get_statistics_fraction ( ) const

returns the requested fraction of time for taking statistics

Definition at line 277 of file SimulationData.h.

double IMP::npctransport::SimulationData::get_tunnel_radius ( ) const

returns te current tunnel radius

double IMP::npctransport::SimulationData::get_tunnel_radius_k ( ) const

returns the force coefficient for keeping the tunnel radius in equilibrium (radius is dynamic only if this coefficient is positive)

Definition at line 630 of file SimulationData.h.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 675 of file SimulationData.h.

void IMP::npctransport::SimulationData::initialize_positions_from_rmf	(	RMF::FileConstHandle	fh,
		int	frame_number = `-1`
	)

Open the specified RMF file, links it to the hierarchies of this object, and copy the XYZ coordinates from its last frame into the particles of this object.

Note: this method assumes that the hierarchies that are stored in the RMF file was constructed in the same way as the hierarchies within this SimulationData object. The only major difference between the two is assumed to be the coordinates of the various particles. Otherwise, results might be unexpected, and it is not guaranteed that a mismatch would be detected at runtime.

See Also: IMP::rmf::link_hierarchies(); IMP::rmf::load_frame()

The frame number is the frame in the file to use, if, eg, there are several initial frames to use. If it is -1, the last frame is used.

Exceptions

RMF::IOException if couldn't open RMF file, or unsupported file format

void IMP::npctransport::SimulationData::link_rmf_file_handle	(	RMF::FileHandle	fh,
		bool	is_restraints = `true`
	)

Links a handle to an open rmf file with the hierarchy and constraints of this simulation data, so that writing frames into this handle will write the updated state of the simulation

Parameters

fh	the handle to be linked
is_restraints	if true, save restraints to RMF

Exceptions

RMF::IOException IO error with RMF file handle

void IMP::npctransport::SimulationData::remove_fgs_with_prefix ( std::string s_fg_type )

remove all FGs of specified type.

Remove any FG chain if the prefix of its string representation matches s_fg_type (= begins with s_fg_type, followed by an empty string or a non-digit character) from the simulation, including model particles, statistics and associated interaction, as well as related assignemnt and statistics data from the output protobuf file

Parameters

s_fg_type The FG type prefix (chain name, to which a suffix could be added for children beads)

See Also: remove_particle_type

void IMP::npctransport::SimulationData::remove_particle_type ( core::ParticleType pt )

remove particle of type pt from simulation, including all model particles, statistics and interactions associated with it

Note: this does not update the protobuf assignment or protobuf statistics

See Also: remove_fgs_with_prefix

void IMP::npctransport::SimulationData::reset_rmf ( )

Resets the RMF file to which the internal periodic SaveOptimizerState writer dumps the output. If it does not exist, create it.

Exceptions

RMF::IOException couldn't create RMF file or other IO related problems with RMF

void IMP::npctransport::SimulationData::set_rmf_file	(	const std::string &	new_name,
		bool	is_save_restraints_to_rmf = `true`,
		bool	is_force_restart = `false`
	)

resets the name of the RMF file that records the simulation. If an old one exists from a previous call with a different name and different restraints settings, then the previous RMF writer is invalidated by this action (closed and flushed). If the Brownian Dynamics object has already been initialized, a new writer with the new name is added as an optimizer state to it instead of the existing one. TODO: make sure the old writer is indeed closed and flushed

Parameters

new_name	the new name of the rmf file
is_save_restraints_to_rmf	whether to save restraints to this rmf file
is_force_reset	if true, force reset even if new_name and is_save_restraints_to_rmf are equal to their old values.

void IMP::npctransport::SimulationData::set_sites	(	core::ParticleType	t0,
		int	n,
		double	r,
		double	sr
	)

Create n interaction sites spread around the surface of a ball of radius r, and associate these sites with all particles of type t0

If n==-1, creates a single site, centered at the bead, and r is ignored

Parameters

t0	type of particle to associate with sites
n	number of sites
r	radius at which to position sites relative to t0 origin
sr	radius from site center within which site has maximal interaction energy

void IMP::npctransport::SimulationData::set_sites	(	core::ParticleType	t0,
		const algebra::Sphere3Ds &	sites
	)

Set the sites explicitly.

Definition at line 443 of file SimulationData.h.

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void IMP::npctransport::SimulationData::write_geometry ( std::string out )

Write the geometry to the file path 'out'

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

SimulationData.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation