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IMP Manual  develop.fa29adf,2019/03/22
Glossary

Several of the more common terms used in IMP (often parts of class names) are covered below.

This is not intended to be a complete list of classes in IMP. For that, please see the class list in the Reference Guide.

Model Typically, only a single Model is used in an IMP run. Multiple proteins or conformations can be (and often are) stored in a single model. A single conformation is usually stored in a Hierarchy.

Attributes The Model contains a number of Particles, each of which can have any number of attributes (and different Particles can have different sets of attributes). For example, some Particles can have x, y and z attributes and so act like points, while other Particles can have attributes that point to other Particles and so act like bonds or other connections. Attributes are rarely accessed directly, but instead Decorator objects are used.

ParticleIndex All of the Particles are stored in the Model as a simple one-dimensional array. While they can be accessed as Particle objects, it is more efficient just to use a Model pointer and an index into that array. This index is termed a ParticleIndex. Any function that expects a ParticleIndex can also be passed a Particle in Python, which is automatically converted.

Decorator A Decorator is an object that "wraps" an existing Particle and presents a particular interface to it - it is not a Particle in its own right. These are used rather than accessing Particle attributes directly. For example, the IMP::core::XYZ Decorator is used to access point-like Particles. See also Hierarchy.

Hierarchy While Particles are stored as a simple flat list inside the Model, it is often useful to group them and set up parent-child relationships. This is implemented in IMP with a special "Hierarchy" Decorator. For example, the IMP::atom::Hierarchy Decorator provides for a molecular hierarchy, whereby a single "residue" Particle may contain a number of "atom" Particles as children. See also Leaves.

ScoringFunction This is used to calculate how well a configuration in the Model satisfies the Restraints (i.e. the score or energy of the system). Typically this is just the sum of all Restraints. In most cases, there will only be one ScoringFunction, but it is possible to create multiple such functions (for example to score subsets of the system). Contrast with Score.

Singleton Used to refer to a single Particle, as opposed to a pair, triple or quad of Particles. For example, an IMP::container::ListSingletonContainer contains a list of Particles, while an IMP::container::ListPairContainer contains a list of pairs of Particles.

Container An object that contains a group of related Particles. This allows the same set of Particles to be used in more than one Restraint or Constraint without having to specify them multiple times. Some Containers also can fill themselves automatically, for example with a list of all pairs of Particles that are close in space (see IMP::container::ClosePairContainer).

Modifier A function that changes the attributes of a single Particle or pair, triple or quad (IMP::SingletonModifier, IMP::PairModifier, IMP::TripletModifier, IMP::QuadModifier respectively). For example, IMP::core::TransformationSymmetry is a SingletonModifier that rotates and translates a single Particle. Modifiers are most commonly used by Constraints.

Predicate A function that returns a single integer value, given a single Particle or pair, triple or quad of Particles (IMP::SingletonPredicate, IMP::PairPredicate, IMP::TripletPredicate, IMP::QuadPredicate respectively). Usually this is interpreted as a True/False value (non-zero/zero, respectively). For example, IMP::core::ClosePairsFinder, which returns all pairs of Particles that are nearby in space, can use a PairPredicate to exclude certain pairs from this list. IMP::atom::StereochemistryPairFilter is a PairPredicate that excludes all pairs of atoms that are connected by bonds.

Restraint Every Restraint in IMP is implemented as a function that returns a score for some subset of the Model. Often this delegates to a Score object to make the restraint more flexible. See also ScoringFunction for the total score for the entire Model (which is typically just the sum of all restraints). A Restraint is satisfied by modifying the system to minimize its score.

Constraint Unlike a Restraint, a Constraint defines some invariant of the system that cannot be violated (IMP::core::RigidBody uses a Constraint internally, for example, to keep things rigid). Each Constraint is implemented by changing the Model (using a Modifier) prior to each ScoringFunction evaluation (and in some cases after evaluation too) to ensure that the invariant is not violated. ScoreState is a synonym.

ScoreState This is simply a synonym for Constraint.

Score A Score object calculates a score for a Particle, or pair, triple or quad of Particles. For example, IMP::core::DistancePairScore scores two Particles based on the Cartesian distance between them. Typically these are used internally by Restraints. Do not confuse with Restraint or ScoringFunction.

Mover One of the mechanisms for sampling the ScoringFunction is Monte Carlo (MC) simulation. This relies on a number of Mover objects that perturb the system in some way at each MC step. For example, IMP::core::BallMover is often used with pointlike Particles to move them in Cartesian space.

Leaves The leaves of an IMP Hierarchy are simply the children that don't in turn have their own children. A commonly-used hierarchy is a molecular hierarchy, in which often the atoms are the leaves (although this is not always the case; where atomic information is not available the leaves may be residues, fragments of sequence, or even entire proteins).