parmed.structure.Structure
==========================

.. currentmodule:: parmed.structure

.. autoclass:: Structure

   
   .. automethod:: __init__

   
   .. rubric:: Methods

   .. autosummary::
   
      ~Structure.__init__
      ~Structure.add_atom
      ~Structure.add_atom_to_residue
      ~Structure.assign_bonds
      ~Structure.copy
      ~Structure.createSystem
      ~Structure.get_box
      ~Structure.get_coordinates
      ~Structure.has_NBFIX
      ~Structure.is_changed
      ~Structure.join_dihedrals
      ~Structure.load_dataframe
      ~Structure.omm_add_constraints
      ~Structure.omm_angle_force
      ~Structure.omm_bond_force
      ~Structure.omm_cmap_force
      ~Structure.omm_dihedral_force
      ~Structure.omm_gbsa_force
      ~Structure.omm_improper_force
      ~Structure.omm_nonbonded_force
      ~Structure.omm_out_of_plane_bend_force
      ~Structure.omm_pi_torsion_force
      ~Structure.omm_rb_torsion_force
      ~Structure.omm_set_virtual_sites
      ~Structure.omm_stretch_bend_force
      ~Structure.omm_torsion_torsion_force
      ~Structure.omm_trigonal_angle_force
      ~Structure.omm_urey_bradley_force
      ~Structure.prune_empty_terms
      ~Structure.save
      ~Structure.split
      ~Structure.strip
      ~Structure.to_dataframe
      ~Structure.unchange
      ~Structure.update_dihedral_exclusions
      ~Structure.visualize
      ~Structure.write_cif
      ~Structure.write_pdb
      ~Structure.write_psf
   
   

   
   
   .. rubric:: Attributes

   .. autosummary::
   
      ~Structure.ANGLE_FORCE_GROUP
      ~Structure.BOND_FORCE_GROUP
      ~Structure.CMAP_FORCE_GROUP
      ~Structure.DIHEDRAL_FORCE_GROUP
      ~Structure.IMPROPER_FORCE_GROUP
      ~Structure.NONBONDED_FORCE_GROUP
      ~Structure.OUT_OF_PLANE_BEND_FORCE_GROUP
      ~Structure.PI_TORSION_FORCE_GROUP
      ~Structure.RB_TORSION_FORCE_GROUP
      ~Structure.STRETCH_BEND_FORCE_GROUP
      ~Structure.TORSION_TORSION_FORCE_GROUP
      ~Structure.TRIGONAL_ANGLE_FORCE_GROUP
      ~Structure.UREY_BRADLEY_FORCE_GROUP
      ~Structure.box
      ~Structure.box_vectors
      ~Structure.combining_rule
      ~Structure.coordinates
      ~Structure.positions
      ~Structure.topology
      ~Structure.velocities
      ~Structure.view