Topology Status

[CalCraven]

A summary of the question or discussion topic.
Topology is a pretty bulky object with lots of methods. This is a mix of forward facing methods, deprecated methods, and just can be difficult to parse through. This list of Topology attributes provides a place for some discussion of ways to trim this down and only present information that would be useful. Also, parsing a topology would be much easier if we included a default bond_graph with the topology, which will enable fast searching of attributes by bond neighbors and would perhaps simplify some of the many parsing methods in Topology.

Keep

1. '_name'
2. 'name'
3. 'angle_types'
4. 'atom_types'
5. 'bond_types'
6. 'dihedral_types'
7. 'improper_types'
8. '_pairpotential_types'
9. 'pairpotential_types'
10. '_sites'
11. 'sites'
12. '_virtual_sites'
13. 'virtual_sites'
14. '_bonds'
15. 'bonds'
16. '_box'
17. 'box'
18. '_scaling_factors'
19. 'scaling_factors'
20. '_combining_rule'
21. 'combining_rule'
22. 'connection_types'
23. 'connections'
24. 'identify_connections'
25. 'positions'
26. 'unique_site_labels'
27. '_unit_system'
28. 'unit_system'

Conversions

1. 'to_dataframe'
2. 'load'
3. 'save'
4. 'write_forcefield'

Garbage Handlers

1. 'remove_connection'
2. 'remove_pairpotentialtype'
3. 'remove_site'

Adders

1. 'add_connection'
2. 'add_pairpotentialtype'
3. 'add_site'
4. '_add_virtual_site'

Getters

1. 'get_lj_scale'
2. 'get_scaling_factors'
3. 'get_electrostatics_scale'
4. 'get_forcefield'
5. 'get_index`
6. '_get_untyped_sites'
7. '_get_scaling_factor'

Setters

1. 'set_electrostatics_scale'
2. 'set_lj_scale'
3. 'set_rigid'
4. 'set_scaling_factors'
5. '_set_scaling_factor'

iter methods

1. 'iter_connections_by_site'
2. 'iter_sites'
3. 'iter_sites_by_molecule'
4. 'iter_sites_by_residue'

Methods we can remove

1. '_bookkeep_potentials'
2. '_potentials_count'
3. 'is_updated'
4. 'update_angle_types'
5. 'update_atom_types'
6. 'update_bond_types'
7. 'update_connection_types'
8. 'update_dihedral_types'
9. 'update_improper_types'
10. 'update_topology'
11. 'n_angles'
12. 'n_bonds'
13. 'n_connections'
14. 'n_dihedrals'
15. 'n_impropers'
16. 'n_sites'
17. 'n_virtual_sites'

Discuss

1. '_angles'
2. 'angles'
3. '_dihedrals'
4. 'dihedrals'
5. '_impropers'
6. 'impropers'
7. '_unique_connections' # uncertain if this is used enough
8. 'create_subtop' # not sure this is useful for anything

Condense

1. '_get_angles_for' # replace if we have implement bond_graph
2. '_get_bonds_for' # replace if we have implement bond_graph
3. '_get_dihedrals_for' # replace if we have implement bond_graph
4. '_get_untyped_angles' # condense into get_untyped_connections
5. '_get_untyped_bonds' # condense into get_untyped_connections
6. '_get_untyped_dihedrals' # condense into get_untyped_connections
7. '_get_untyped_impropers' # condense into get_untyped_connections
8. 'angle_type_expressions' # topology expressions
9. 'atom_type_expressions'
10. 'bond_type_expressions'
11. 'connection_type_expressions'
12. 'dihedral_type_expressions'
13. 'improper_type_expressions'
14. 'pairpotential_type_expressions'
15. 'is_fully_typed' # some get_istyped method
16. 'is_typed' # some get_istyped method
17. 'get_untyped' # some get_istyped method
18. '_typed' # some get_istyped method
19. 'typed' # some get_istyped method

Extract into other modules

1. '_molecule_scaling_factors' # can we condense molecule information into a single class that has this information
2. 'molecule_scaling_factors'
3. '_pandas_from_parameters' # This should just be a function that takes a topology
4. '_parse_dataframe_attrs' # This should just be a function that takes a topology
5. '_parse_parameter_expression' # move to some sort of topology parser utils or the units module
6. 'convert_potential_styles' # move to conversions.py
7. 'convert_unit_styles' # move to conversions.py