Atom Example files ------------------------------------------------------------------ python charmm_forcefield.py python load_protein_restrain_bonds.py python molecular_hierarchy.py Core Example files ------------------------------------------------------------------ python connectivity_restraint.py python cover_particles.py python excluded_volume.py python pair_restraint.py python restrain_diameter.py python rigid_bodies.py python rigid_collisions.py python XYZ_Decorator.py python XYZR_Decorator.py Atom Test files ------------------------------------------------------------------ python test_bd.py python test_bd_singleton_score.py python test_bond_decorator_particle_pair_container.py python test_bond_refiner.py python test_bonds.py python test_charged_decorator.py python test_charmm_atom.py python test_charmm_parameters.py python test_charmm_topology.py python test_clone.py python test_coulomb.py python test_cover_bond.py python test_create_protein.py python test_distance.py python test_element.py python test_estimates.py python test_force_switch.py python test_fragment.py python test_get_residue.py python test_hierarchy.py python test_lennard_jones_decorator.py python test_lennard_jones_pair_score.py python test_md_optimizer.py python test_mol2.py python test_pdb.py python test_pdb_string.py python test_protein_ligand_score.py python test_ref_optimizer_states.py python test_rmsd_and_no.py python test_simplify.py python test_stereo_pair_filter.py Core Test files ------------------------------------------------------------------ python test_angle.py python test_box.py python test_centroid.py python test_cg_optimizer.py python test_children.py python test_close_pair_finders.py python test_close_pairs_ps.py python test_connectivity.py python test_cosine.py python test_cover.py python test_cover_refiner.py python test_diameter.py python test_dihedral.py python test_distance.py python test_ev_restraint.py python test_harmonic.py python test_hierarchy.py python test_linear.py python test_mccg.py python test_mc_rigid_bodies.py python test_particles.py python test_refcount.py python test_refined_pairs_ps.py python test_ref_states.py python test_rigid_bodies.py python test_rigid_distance.py python test_sd_optimizer.py python test_splines.py python test_table.py python test_to_from_refined.py python test_transform_particles.py python test_transform.py python test_truncated_harmonic.py python test_typed_pair_score.py python test_volume.py python test_xyzr.py