Decorator for helping deal with a hierarchy.
Various important functionality for implementing decorators.
Simple conjugate gradients optimizer.
Simple Monte Carlo optimizer.
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 kernel::ParticlePairsTemp to maintain an invariant.
A 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.
Angle restraint between three particles.
Use a SingletonModifier applied to a kernel::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.
Angle restraint between three particles.
Use a hierarchy of grids to find close pairs.
Return the hierarchy children of 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 paricles.
A mover that apply other movers one at a time.
Apply a PairScore to close pairs.
A particle with a user-defined type.
Closed cubic spline function.
A particle refiner which returns a fixed set of particles.
A prevent spheres from inter-penetrating.
Accumulate the derivatives of the refined particles.
Log the restraint scores and things.
A mover that transform a rigid body.
Various important functionality for implementing decorators.
functionality only availble in python.
functionality for defining rigid bodies
The base class for movers for MC optimization.
Various important functionality for implementing decorators.
A mover that transform a rigid body.
Decorator to hold Gaussian3D.
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 based on the unmodified value of an attribute.
A score on the distance between the surfaces of two spheres.
Cover a bond with a sphere.
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.
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 kernel::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 kernel::ParticleQuadsTemp to maintain an invariant.
Apply a PairScore to a Pair.
Dihedral restraint between four particles.
Harmonic upper bound function.
Set the coordinates of the particle to be the centoid of the refined particles.
A modifier which perturbs a point with a normal distribution.
A Score on the angle between three particles.
