IMP::Particle Class Reference

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Detailed Description

Class to handle individual model particles.

Note:

Direct manipuation of particles is considered advanced and Particles should only be manipulated through IMP::Decorator derived classes.

A IMP::Particle is a mapping between keys and values.

Four possible types of values:

• Float (float)
• String (std::string or Python string)
• Int (int)
• Particle (A pointer to another IMP::Particle)

To use an attribute you first create a key

   f= IMP.FloatKey("MyAttribute")
   

Creating a key is expensive and should not be done often.

Then use it to manipulate the attribute.

   p.add_attribute(f, initial_value, whether_attribute_is_optimized)
   p.set_attribute(f, new_value)
   p.remove_attribute(f)
   

This class contains particle methods and indexes to particle attributes. To prevent a particle from being moved by the optimizer during optimization, mark all of its attributes as being non-optimizable (set_is_optimized method). Note that this only affects the optimizer, ScoreStates may still change the particle attributes.

A particle may only belong to one model.

Any attempt to access or change an attribute which the particle does not have results is undefined. It will throw an exception if checks are on or possibly just crash if they are not. Likewise an attempt to touch an inactive particle is also undefined (and will throw an exception if checks are enabled).

Inheritance diagram for IMP::Particle:

List of all members.

Public Member Functions
	Particle (Model *m, std::string name)
	Construct a particle and add it to the Model.
	Particle (Model *m)
	Construct a particle and add it to the Model.
ParticleIndex	get_index () const
bool	get_is_active () const
	Get whether the particle is active.
Static Public Member Functions
static Particle *	get_from (IMP::base::Object *o)
Attribute manipulation
For each type of attribute and their corresponding key type, the Particle provides the following methods. The Type is the type of the attribute (Float, Int, Particle * etc.) and KeyType is the type of the key (FloatKey, IntKey, ParticleKey etc.).
void	add_attribute (KeyType name, Type initial_value)
void	remove_attribute (KeyType name)
bool	has_attribute (KeyType name) const
Type	get_value (KeyType name) const
Float Attributes
Float attributes can be optimized, meaning the optimizer is allowed to change their value in order to improve the score. As a result, there are a number of extra methods to manipulate them. All distances are assumed to be in angstroms and derivatives in kcal/mol angstrom. This is not enforced.
void	add_attribute (FloatKey name, const Float initial_value, bool optimized)
void	add_to_derivative (FloatKey key, Float value, const DerivativeAccumulator &da)
void	set_is_optimized (FloatKey k, bool tf)
bool	get_is_optimized (FloatKey k) const
Float	get_derivative (FloatKey name) const
Particle attributes
void	add_attribute (ParticleKey k, Particle *v)
bool	has_attribute (ParticleKey k)
void	set_value (ParticleKey k, Particle *v)
Particle *	get_value (ParticleKey k) const
void	remove_attribute (ParticleKey k)
ParticleKeys	get_particle_keys () const

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Constructor & Destructor Documentation

IMP::Particle::Particle	(	Model *	m,
		std::string	name
	)

Construct a particle and add it to the Model.

IMP::Particle::Particle

(

Model *

m

)

Construct a particle and add it to the Model.

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Member Function Documentation

bool IMP::Particle::get_is_active

(

)

const

Get whether the particle is active.

Restraints referencing the particle are only evaluated for 'active' particles.

Returns:

true it the particle is active.

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

• Particle.h