mstk.topology.Topology
======================

.. currentmodule:: mstk.topology

.. autoclass:: Topology

   
   
   .. rubric:: Methods

   .. autosummary::
   
      ~Topology.__init__
      ~Topology.generate_angle_dihedral_improper
      ~Topology.generate_drude_particles
      ~Topology.generate_virtual_sites
      ~Topology.get_12_13_14_pairs
      ~Topology.get_drude_pairs
      ~Topology.get_unique_molecules
      ~Topology.get_virtual_site_pairs
      ~Topology.guess_bonds_from_ff
      ~Topology.init_from_omm_topology
      ~Topology.open
      ~Topology.register_format
      ~Topology.remove_drude_particles
      ~Topology.remove_virtual_sites
      ~Topology.save_to
      ~Topology.scale_box
      ~Topology.scale_with_packmol
      ~Topology.set_positions
      ~Topology.to_omm_topology
      ~Topology.update_molecules
      ~Topology.write
   
   

   
   
   .. rubric:: Attributes

   .. autosummary::
   
      ~Topology.angles
      ~Topology.atoms
      ~Topology.bonds
      ~Topology.dihedrals
      ~Topology.has_position
      ~Topology.has_virtual_site
      ~Topology.impropers
      ~Topology.is_drude
      ~Topology.molecules
      ~Topology.n_angle
      ~Topology.n_atom
      ~Topology.n_bond
      ~Topology.n_dihedral
      ~Topology.n_improper
      ~Topology.n_molecule
      ~Topology.n_residue
      ~Topology.positions
      ~Topology.residues
      ~Topology.virtual_site_classes