Various classes to hold sets of particles.
Simple conjugate gradients optimizer.
Return all close unordered pairs of particles taken from the SingletonContainer.
Bond create_custom_bond(Bonded a, Bonded b, Float length, Float stiffness=-1)
Connect the two wrapped particles by a custom bond.
static Bonded setup_particle(kernel::Model *m, ParticleIndex pi)
Store a kernel::ParticleIndexes.
XYZRs create_xyzr_particles(kernel::Model *m, unsigned int num, Float radius, Float box_side=10)
Create a set of particles with random coordinates.
Basic functionality that is expected to be used by a wide variety of IMP users.
Functionality for loading, creating, manipulating and scoring atomic structures.
Applies a PairScore to each Pair in a list.
Class for storing model, its restraints, constraints, and particles.