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IMP Reference Guide  develop.d3e3923077,2019/12/11
The Integrative Modeling Platform
IMP::npctransport Namespace Reference

Detailed Description

Build Status codecov

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< SlabWithPoreSlabsWithPores
 
typedef IMP::Vector
< SlabWithToroidalPore
SlabsWithToroidalPores
 
typedef IMP::Vector< TransportingTransportings
 

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 ()
 
FGChaincreate_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)
 
FGChainget_fg_chain (atom::Hierarchy root)
 
FGChainget_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::SimulationDatastartup (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

Pass or store a set of Avro2PBReader .

Definition at line 90 of file Avro2PBReader.h.

A vector of reference-counting object pointers.

Definition at line 70 of file BodyStatisticsOptimizerState.h.

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

See Also
BodyStatisticsOptimizerState

Definition at line 70 of file BodyStatisticsOptimizerState.h.

A vector of reference-counting object pointers.

Definition at line 115 of file ChainStatisticsOptimizerState.h.

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

See Also
ChainStatisticsOptimizerState

Definition at line 115 of file ChainStatisticsOptimizerState.h.

A vector of reference-counting object pointers.

Definition at line 190 of file FGChain.h.

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

See Also
FGChain

Definition at line 190 of file FGChain.h.

A vector of reference-counting object pointers.

Definition at line 52 of file GlobalStatisticsOptimizerState.h.

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

See Also
GlobalStatisticsOptimizerState

Definition at line 52 of file GlobalStatisticsOptimizerState.h.

A vector of reference-counting object pointers.

Definition at line 152 of file HarmonicSpringSingletonScore.h.

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

See Also
HarmonicSpringSingletonScore

Definition at line 152 of file HarmonicSpringSingletonScore.h.

A vector of reference-counting object pointers.

Definition at line 114 of file harmonic_distance_pair_scores.h.

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.

an interaction that involves particles of two types

Definition at line 21 of file typedefs.h.

Pass or store a set of InteractionType .

Definition at line 22 of file typedefs.h.

A vector of reference-counting object pointers.

Definition at line 85 of file functor_linear_distance_pair_scores_typedefs.h.

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.

A vector of reference-counting object pointers.

Definition at line 468 of file linear_distance_pair_scores.h.

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.

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
fnameinput_config_fname configuration file name
outputoutput_assignment_fname assignment file name
work_unitthe 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_stepsshow the steps that occur
random_seedthe random seed used to initialize the IMP random number generator for this simulation
Exceptions
IMP::ValueExceptionif 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]sdthe simulation data whose model is associated with the new chain. The chain is also added to the simulation data scoring object.
parentparent hierarchy to which chain is added
[in]fg_datadata about the FG chain
[in]ccolor 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_xyzr0pointer to derivative of particle 0
[out]d_xyzr1pointer to derivative of particle 1
[in,out]daaccumulator for score derivatives to be updated
[in]deltaa vector that represents the displacement between the two particles
delta_lengththe cached length of delta, assumed correct, and required for faster calculation
x0resting distance (where score = 0)
kscore 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]ma model for the particles, in which particle derivatives are updated
[in]ppa pair of particle indices for fast access through internal model methods
[in,out]daaccumulator for score derivatives to be updated
[in]deltaa vector from pp[1] to pp[0]
delta_lengththe cached length of delta, assumed correct, and required for faster calculation
x0resting distance (where score = 0)
kscore 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
sdSimulationData object to optimize
init_restraintsad-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
sthe statistics message for searching the fg
ptthe 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
sthe statistics message for searching the fg
ptthe 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
sthe statistics message for searching t
ptthe 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
sthe statistics message for searching t
itthe 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
configthe simulation parameters
time_stepthe 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_roota 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
nstime in ns
time_stepstep in fs per frame
algebra::Vector3D IMP::npctransport::get_global_from_local_v3 ( Particle *  p,
const algebra::Vector3D &  local 
)
Parameters
pa rigid body particle
localthe 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
configthe simulation parameters
time_stepthe time step in femtoseconds
Exceptions
ValueExceptionif 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
assignthe simulation assignment parameters
time_stepthe time step in femtoseconds
default_value_nsinterval 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_txtthe input textual protobuf config file
config_pbthe 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
assignthe simulation assignment parameters
time_stepthe time step in femtoseconds
default_value_nsinterval 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_factorthe maximal diffusion factor of any particle in the system, which factors the Einstein diffusion coefficient)
max_kthe maximal force applied on any particle in the simulation
min_radiusthe minimal radius of any interaction in the system
min_rangethe minimal range of any interaction
max_trans_relative_to_radiusthe maximal estimated translation allowed for any particle as fraction of min_radius (before factoring by time_step_factor)
time_step_factormultiply 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
configthe simulation parameters used to compute the time step size
max_trans_relative_to_radiusthe 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
sdthe SimulationData object containing diffusing particles
extra_restraintsa list of additional ad-hoc restraints that will be used only throughout initialization
debugif true, the initialization will dump much more output (e.g. every frame to RMF file)
short_init_factora factor between >0 and 1 for decreasing the number of optimization cycles at each round
is_disable_randomizeif true, do not initially randomize particle positions, essentially performing an extended relaxation from the starting coordinates
are_fgs_pre_initializedif 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
conformationthe saved conformation protobuf message
beadscorresponding diffusers to be updated
sitesa 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
beadsbeads to save
sitesa map of sites for each diffuser particle type to be saved
conformationthe 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::IOExceptionif there was any IO problem