Decorator for helping deal with a hierarchy.
Various important functionality for implementing decorators.
Simple conjugate gradients optimizer.
Decorator to hold Gaussian3D.
Score model efficiently when a small number of particles are changed.
Classes to track how the model was created.
Accumulate the derivatives of the refined particles.
Act on the distance between two rigid bodies.
Distance restraint between two particles.
Test all pairs of particles to find close pairs.
Use a PairModifier applied to a ParticlePairsTemp to maintain an invariant.
Constrain orientation of surfaces with respect to rigid bodies.
Prevent spheres from inter-penetrating.
Mass Spec Connectivity restraint.
Test all pairs of particles to find close pairs.
functionality for defining rigid bodies
Simple Monte Carlo optimizer.
Open cubic spline function.
A restraint to maintain the diameter of a set of points.
A Score on the distance to a fixed point.
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Use a SingletonModifier applied to a ParticlesTemp to maintain an invariant.
A modifier which variables within a ball.
Apply a QuadScore to a Quad.
Write geometry to a file during optimization.
A mover that applies a random subset of movers.
Angle restraint between three particles.
Use a hierarchy of grids to find close pairs.
Copies derivatives from coarse grained particle to its refined set of particles using weights indicat...
A score on the distance between a surface and a sphere.
Score on surface-to-end distance of chain tethered to impenetrable surface.
Return the hierarchy leaves under a particle.
Delegate to another PairScore depending on particle types.
Score particles based on a bounding box.
Angle restraint between three particles.
Generate pairs by applying a Refiner to the particles.
Weighted sum of unary functions.
A mover that applies other movers one at a time.
Apply a PairScore to close pairs.
A mover that transforms a Surface.
A particle with a user-defined type.
Closed cubic spline function.
A modifier that perturbs a point with a log-normal distribution.
A particle refiner which returns a fixed set of particles.
A restraint that prevents spheres from inter-penetrating.
Accumulate the derivatives of the refined particles.
A Score on the crossing angle between two rigid bodies.
Write the scores of the passed restraints to a file.
A mover that transforms a rigid body.
Various important functionality for implementing decorators.
Simple surface decorator.
Functionality only available in Python.
A score based on the unmodified value of an attribute.
Score particles based on a bounding sphere - score would typically increase as particles are exiting ...
functionality for defining rigid bodies
The base class for movers for Monte Carlo optimization.
Various important functionality for implementing decorators.
Distance restraint between two particles.
A mover that transform a rigid body.
Decorators for directions and the angle between them.
Apply a TripletScore to a Triplet.
Harmonic lower bound function.
A modifier which variables within a ball.
A Score on the distance between a pair of particles.
A score on the distance between the surfaces of two spheres.
Set the position and radius of a particle to enclose the refined.
Score particles based on a bounding box.
A lookup based particle refiner.
Handle rigid bodies by looking at their members.
Test all pairs of particles to find close pairs.
A base class for algorithms to detect proximities.
Negative logarithm of weighted sum of negative exponential of unary functions.
Simple steepest descent optimizer.
Implement various types of symmetry.
A Monte Carlo/Conjugate Gradients based sampler.
Storage of a model, its restraints, constraints and particles.
Use a TripletModifier applied to a ParticleTripletsTemp to maintain an invariant. ...
Return the hierarchy children of a particle.
Score based on the k minimum restraints.
Apply a SingletonScore to a Singleton.
Decorator for a sphere-like particle.
Use a QuadModifier applied to a ParticleQuadsTemp to maintain an invariant.
Modeller-style multiple binormal (phi/psi) restraint.
A mover that transforms a Direction.
Apply a PairScore to a Pair.
Dihedral restraint between four particles.
Harmonic upper bound function.
Set the coordinates of the particle to be the centroid of the refined particles.
A modifier which perturbs a point with a normal distribution.
A Score on the angle between three particles.
