Atom Example files
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python charmm_forcefield.py
python load_protein_restrain_bonds.py
python molecular_hierarchy.py

Core Example files
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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
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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
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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