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IMP Reference Guide
2.20.1
The Integrative Modeling Platform
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Class for storing model, its restraints, constraints, and particles. More...
#include "IMP/Model.h"
Inheritance diagram for IMP::Model:Class for storing model, its restraints, constraints, and particles.
Proxy of C++ IMP::Model class.
The Model maintains a standard IMP container for each of Particle, ScoreState and Restraint object types.
Each Float attribute has an associated range which reflects the range of values that it is expected to take on during optimization. The optimizer can use these ranges to make the optimization process more efficient. By default, the range estimates are simply the range of values for that attribute in the various particles, but it can be set to another value. For example, an attribute storing an angle could have the range set to (0,PI).
The ranges are not enforced; they are just guidelines. In order to enforce ranges, see, for example, IMP::example::ExampleSingletonModifier.
Public Member Functions | |
| Model (std::string name="Model %1%") | |
| Construct an empty model. More... | |
| ParticleIndex | add_particle (std::string name) |
| Add particle to the model. More... | |
| void | add_undecorator (ParticleIndex pi, Undecorator *d) |
| Add the passed Undecorator to the particle. More... | |
| void | clear_particle_caches (ParticleIndex pi) |
| Clear all the cache attributes of a given particle. More... | |
| unsigned | get_dependencies_updated () |
| Get the model age when ModelObject dependencies were last changed, or 0. More... | |
| def | get_derivatives_numpy |
| Get the model's attribute derivatives array for FloatKey k as a NumPy array. More... | |
| def | get_floats_numpy |
| Get the model's attribute array for FloatKey k as a NumPy array. More... | |
| bool | get_has_particle (ParticleIndex p) const |
| Check whether a given particle index exists. More... | |
| def | get_ints_numpy |
| Get the model's attribute array for IntKey k as a NumPy array. More... | |
| ModelObjectsTemp | get_model_objects () const |
| Get all the ModelObjects associated with this Model. More... | |
| Particle * | get_particle (ParticleIndex p) const |
| Get the particle from an index. More... | |
| ParticleIndexes | get_particle_indexes () |
| Get all particle indexes. More... | |
| std::string | get_particle_name (ParticleIndex pi) |
| Get the name of a particle. More... | |
| unsigned | get_particles_size () const |
| Get an upper bound on the number of particles in the Model. More... | |
| def | get_sphere_derivatives_numpy |
| Get the model's XYZR attribute derivatives arrays as NumPy arrays. More... | |
| def | get_spheres_numpy |
| Get the model's XYZR attribute arrays as NumPy arrays. More... | |
| virtual std::string | get_type_name () const override |
| uint32_t | get_unique_id () const |
| Get the unique ID of this Model. More... | |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| Get information about the module and version of the object. More... | |
| void | remove_particle (ParticleIndex pi) |
| Remove a particle from the Model. More... | |
| void | restore_dependencies () |
| Restore ModelObject dependencies to previous restore point. More... | |
| void | save_dependencies () |
| Mark a 'restore point' for ModelObject dependencies. More... | |
| void | update () |
| Sometimes it is useful to be able to make sure the model is up to date. More... | |
| 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) |
Static Public Member Functions | |
| static Model * | get_by_unique_id (uint32_t id) |
| Return the Model with the given unique ID. More... | |
States | |
ScoreStates maintain invariants in the Model (see ScoreState for more information.) ScoreStates do not need to be explicitly added to the Model, but they can be if desired in order to keep them alive as long as the model is alive.
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| list | score_states |
| A Python list of ScoreStates More... | |
| void | remove_score_state (ScoreState *d) |
| void | remove_score_states (const ScoreStates &d) |
| void | set_score_states (const ScoreStates &ps) |
| void | set_score_states_order (const ScoreStates &objs) |
| unsigned int | add_score_state (ScoreState *obj) |
| void | add_score_states (const ScoreStates &objs) |
| void | clear_score_states () |
| unsigned int | get_number_of_score_states () const |
| bool | get_has_score_states () |
| ScoreState * | get_score_state (unsigned int i) const |
| ScoreStates | get_score_states () const |
| void | erase_score_state (unsigned int i) |
| void | reserve_score_states (unsigned int sz) |
Accessing attributes | |
All the attribute data associated with each Particle are stored in the Model. For each type of attribute, there are the methods detailed below (where, eg, TypeKey is FloatKey or StringKey) | |
| void | add_attribute (TypeKey attribute_key, ParticleIndex particle, Type value) |
| add particle attribute with the specified key and initial value More... | |
| void | remove_attribute (TypeKey attribute_key, ParticleIndex particle) |
| remove particle attribute with the specified key More... | |
| bool | get_has_attribute (TypeKey attribute_key, ParticleIndex particle) const |
| return true if particle has attribute with the specified key More... | |
| void | set_attribute (TypeKey attribute_key, ParticleIndex particle, Type value) |
| set the value of particle attribute with the specified key More... | |
| Type | get_attribute (TypeKey attribute_key, ParticleIndex particle) |
| get the value of the particle attribute with the specified key More... | |
| void | add_cache_attribute (TypeKey attribute_key, ParticleIndex particle, Type value) |
| void | set_is_optimized (TypeKey attribute_key, ParticleIndex particle, bool true_or_false) |
Storing data in the model | |
One can store data associated with the model. This is used, for example, to keep a central ScoreState to normalize rigid body rotational variables. | |
| void | add_data (ModelKey mk, Object *o) |
| Store a piece of data in the model referenced by the key. More... | |
| Object * | get_data (ModelKey mk) const |
| Get back some data stored in the model. More... | |
| void | remove_data (ModelKey mk) |
| Remove data stored in the model. More... | |
| bool | get_has_data (ModelKey mk) const |
| Check if the model has a certain piece of data attached. More... | |
Model triggers | |
Triggers can be used to track when to clear and rebuild caches of derived model properties. For example, a Restraint may restrain two particles as a function of the number of chemical bonds between them. To speed up this restraint, the bond graph can be cached; however, this graph needs to be rebuilt if bonds are created or removed. This can be achieved by checking that the model time (see get_age()) of the cache matches the time when the 'bond added/removed' Trigger was last updated (see get_trigger_last_updated()), either when the Restraint is evaluated or in an associated ScoreState. Triggers are intended for events that are rare during a typical optimization. Triggers can be created by any IMP module in either C++ or Python by creating a new TriggerKey, much as model attributes are handled. To avoid name collisions, it is recommended to prepend the module and/or class name to the trigger, e.g. "atom.Bond.changed". For an example, see IMP::score_functor::OrientedSoap, which uses a cache built from the molecular hierarchy, which is cleared when the IMP::core::Hierarchy::get_changed_key() trigger is updated. | |
| unsigned | get_age () |
| Get the current 'model time'. More... | |
| unsigned | get_trigger_last_updated (TriggerKey tk) |
| Get the time when the given trigger was last updated, or 0. More... | |
| void | set_trigger_updated (TriggerKey tk) |
| Update the given trigger. More... | |
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 () |
| IMP::Model::Model | ( | std::string | name = "Model %1%" | ) |
Construct an empty model.
| void IMP::Model::add_attribute | ( | TypeKey | attribute_key, |
| ParticleIndex | particle, | ||
| Type | value | ||
| ) |
add particle attribute with the specified key and initial value
| void IMP::Model::add_cache_attribute | ( | TypeKey | attribute_key, |
| ParticleIndex | particle, | ||
| Type | value | ||
| ) |
Cache attributes, unlike normal attributes, can be added during evaluation. They are also cleared by the clear_cache_attributes() method. Cache attributes should be used when one is adding data to a particle to aid scoring (eg cache the rigid body collision acceleration structure).
When some pertinent aspect of the particle changes, the clear method should be called (yes, this is a bit vague). Examples where it should be cleared include changing the set of members of a core::RigidBody or their coordinates, changing the members of an atom::Hierarchy.
Store a piece of data in the model referenced by the key.
| ParticleIndex IMP::Model::add_particle | ( | std::string | name | ) |
Add particle to the model.
| void IMP::Model::add_undecorator | ( | ParticleIndex | pi, |
| Undecorator * | d | ||
| ) |
Add the passed Undecorator to the particle.
| void IMP::Model::clear_particle_caches | ( | ParticleIndex | pi | ) |
Clear all the cache attributes of a given particle.
| unsigned IMP::Model::get_age | ( | ) |
| Type IMP::Model::get_attribute | ( | TypeKey | attribute_key, |
| ParticleIndex | particle | ||
| ) |
get the value of the particle attribute with the specified key
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static |
| unsigned IMP::Model::get_dependencies_updated | ( | ) |
Get the model age when ModelObject dependencies were last changed, or 0.
This gives the Model age (see get_age()) when Particles, Restraints, or ScoreStates were last added or removed. It is typically used to help maintain caches that depend on the model's dependency graph.
| def IMP.Model.get_derivatives_numpy | ( | self, | |
| k | |||
| ) |
Get the model's attribute derivatives array for FloatKey k as a NumPy array.
See Model::get_ints_numpy() for more details.
Definition at line 5558 of file __init__.py.
| def IMP.Model.get_floats_numpy | ( | self, | |
| k | |||
| ) |
Get the model's attribute array for FloatKey k as a NumPy array.
See Model::get_ints_numpy() for more details.
Definition at line 5553 of file __init__.py.
| bool IMP::Model::get_has_attribute | ( | TypeKey | attribute_key, |
| ParticleIndex | particle | ||
| ) | const |
return true if particle has attribute with the specified key
| bool IMP::Model::get_has_data | ( | ModelKey | mk | ) | const |
Check if the model has a certain piece of data attached.
| bool IMP::Model::get_has_particle | ( | ParticleIndex | p | ) | const |
| def IMP.Model.get_ints_numpy | ( | self, | |
| k | |||
| ) |
Get the model's attribute array for IntKey k as a NumPy array.
The array is indexed by ParticleIndex; particles that don't have this attribute will either be off the end of the array or will have the value INT_MAX. This is a NumPy view that shares memory with the Model. Thus, any changes to values in this list will be reflected in the Model. Also, if the Model attribute array moves in memory (e.g. if particles or attributes are added) this array will be invalidated, so it is unsafe to keep it around long term.
Definition at line 5540 of file __init__.py.
| ModelObjectsTemp IMP::Model::get_model_objects | ( | ) | const |
Get all the ModelObjects associated with this Model.
| Particle* IMP::Model::get_particle | ( | ParticleIndex | p | ) | const |
| ParticleIndexes IMP::Model::get_particle_indexes | ( | ) |
Get all particle indexes.
| std::string IMP::Model::get_particle_name | ( | ParticleIndex | pi | ) |
Get the name of a particle.
| unsigned IMP::Model::get_particles_size | ( | ) | const |
| def IMP.Model.get_sphere_derivatives_numpy | ( | self | ) |
Get the model's XYZR attribute derivatives arrays as NumPy arrays.
See Model::get_ints_numpy() for more details.
Definition at line 5571 of file __init__.py.
| def IMP.Model.get_spheres_numpy | ( | self | ) |
Get the model's XYZR attribute arrays as NumPy arrays.
The attribute arrays for Cartesian coordinates and radii are stored separately from those for other FloatKeys. This function returns a tuple of two NumPy arrays, the first of coordinates and the second of radii. See Model::get_ints_numpy() for more details.
Definition at line 5565 of file __init__.py.
| unsigned IMP::Model::get_trigger_last_updated | ( | TriggerKey | tk | ) |
| uint32_t IMP::Model::get_unique_id | ( | ) | const |
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
| void IMP::Model::remove_attribute | ( | TypeKey | attribute_key, |
| ParticleIndex | particle | ||
| ) |
remove particle attribute with the specified key
| void IMP::Model::remove_data | ( | ModelKey | mk | ) |
Remove data stored in the model.
| void IMP::Model::remove_particle | ( | ParticleIndex | pi | ) |
Remove a particle from the Model.
The particle will then be inactive and cannot be used for anything and all data stored in the particle is lost.
| void IMP::Model::restore_dependencies | ( | ) |
Restore ModelObject dependencies to previous restore point.
This method, when paired with save_dependencies(), can be used to avoid triggering a model dependency update due to a temporary change in the model dependency graph, for example due to adding a temporary restraint, evaluating it, then removing that same restraint. It should only be called in cases where it is known that the dependency graph is the same as when save_dependencies() was called (this is only checked in debug mode). Save/restore call pairs cannot be nested, although it is OK to skip the call to restore_dependencies(), e.g. if an exception occurs.
| void IMP::Model::save_dependencies | ( | ) |
Mark a 'restore point' for ModelObject dependencies.
| void IMP::Model::set_attribute | ( | TypeKey | attribute_key, |
| ParticleIndex | particle, | ||
| Type | value | ||
| ) |
set the value of particle attribute with the specified key
| void IMP::Model::set_is_optimized | ( | TypeKey | attribute_key, |
| ParticleIndex | particle, | ||
| bool | true_or_false | ||
| ) |
Optimized attributes are the parameters of the model that are allowed to be modified by samplers and optimizers
| void IMP::Model::set_trigger_updated | ( | TriggerKey | tk | ) |
| void IMP::Model::update | ( | ) |
Sometimes it is useful to be able to make sure the model is up to date.
This method updates all the state but does not necessarily compute the score. Use this to make sure that your containers and rigid bodies are up to date.
| list IMP::Model::score_states |