Examples

Here is a list of all examples:

• algebra/geometry.py
• algebra/grid_space.py
• atom/assess_dope.py
• atom/brownian_statistics.py
• atom/cg_pdb.py
• atom/charmm_forcefield.py
• atom/charmm_forcefield_verbose.py
• atom/charmm_topology.py
• atom/Diffusion_decorator.py
• atom/dope_and_excluded_volume.cpp
• atom/edit_molecular_hierarchy.py
• atom/load_protein_restrain_bonds.py
• atom/markers.py
• atom/molecular_hierarchy.py
• atom/multiresolution.py
• atom/rigid_brownian_dynamics.py
• atom/score_protein_with_ligand.py
• atom/structure_from_sequence.py
• BallMover.py
• container/bipartite_nonbonded_interactions.py
• container/connectivity.py
• container/filter_close_pairs.py
• container/nonbonded_interactions.py
• container/restrain_in_sphere.py
• container/statistical.py
• core/connectivity_restraint.py
• core/cover_particles.py
• core/custom_hierarchy.py
• core/excluded_volume.py
• core/linear_and_harmonic_scores.py
• core/model_numpy.py
• core/move_aware_mc.py
• core/ms_connectivity_restraint.py
• core/optimize_balls.py
• core/pair_restraint.py
• core/randomize_rigid_body.py
• core/restrain_diameter.py
• core/restrain_in_sphere.py
• core/restrain_minimum_distance.py
• core/rigid_bodies.py
• core/rigid_collisions.py
• core/simple.cpp
• core/simple.py
• core/symmetry.py
• core/XYZ_Decorator.py
• core/XYZR_Decorator.py
• display/basic_geometry.py
• display/display_log.py
• display/displaying_ensembles.py
• display/show_particles_as_spheres.py
• domino/custom_filter.py
• domino/domino_approach.py
• domino/interactive.py
• domino/interactive_with_containers.py
• domino/marina_party.py
• domino/merge_tree.py
• domino/multiscale.py
• domino/restraint_cache.py
• domino/rigid_body_excluded_volume.py
• domino/save_assignments.py
• domino/six_particles_optimization.py
• em/analyze_convergence.py
• em/cube.py
• em/fit_restraint.py
• em/generate_density_map_of_fixed_dimension.py
• em/local_fitting.py
• em/numpy_data.py
• em/pdb2density.py
• em2d/clustering_of_pdb_models.py
• em2d/collision_cross_section.py
• em2d/em_images_conversion.py
• em2d/optimize_em2d_with_montecarlo.py
• example/range_restriction.py
• flags.cpp
• grid.cpp
• gsl/simplex.py
• kernel/basic_optimization.py
• kernel/chain.py
• kernel/dependency_graph.py
• kernel/flags.py
• kernel/graph.py
• kernel/setup.py
• kernel/write_a_restraint.py
• kernel/write_an_optimizer_state.py
• kmeans/kmeans_example.py
• log.py
• misc/decay.py
• modeller/imp_restraints_in_modeller.py
• modeller/load_modeller_model.py
• modeller/modeller_restraints_in_imp.py
• multistate.py
• parallel/local_distance.py
• parallel/tasks.py
• pmi/ambiguity.py
• pmi/atomistic.py
• pmi/automatic.py
• pmi/em.py
• pmi/ideal_helix.py
• pmi/membrane.py
• pmi/multiscale.py
• pmi/protein_residue_binding.py
• pmi/selection.py
• pmi/symmetry.py
• rmf/geometry.py
• rmf/link.py
• rmf/multiresolution.py
• rmf/pdb.py
• rmf/simulation.py
• rotamer/rotamer_pdb.py
• rotamer/rotamer_pdb2.py
• saxs/profile.py
• saxs/profile_fit.py
• statistics/kmeans.py
• statistics/write_a_metric.py
• temperature_rem.py