parmed.amber.AmoebaParm
=======================

.. currentmodule:: parmed.amber

.. autoclass:: AmoebaParm

   
   .. automethod:: __init__

   
   .. rubric:: Methods

   .. autosummary::
   
      ~AmoebaParm.__init__
      ~AmoebaParm.add_atom
      ~AmoebaParm.add_atom_to_residue
      ~AmoebaParm.add_flag
      ~AmoebaParm.assign_bonds
      ~AmoebaParm.copy
      ~AmoebaParm.createSystem
      ~AmoebaParm.delete_flag
      ~AmoebaParm.fill_LJ
      ~AmoebaParm.from_rawdata
      ~AmoebaParm.from_structure
      ~AmoebaParm.get_box
      ~AmoebaParm.get_coordinates
      ~AmoebaParm.has_1012
      ~AmoebaParm.has_NBFIX
      ~AmoebaParm.id_format
      ~AmoebaParm.initialize_topology
      ~AmoebaParm.is_changed
      ~AmoebaParm.join_dihedrals
      ~AmoebaParm.load_atom_info
      ~AmoebaParm.load_dataframe
      ~AmoebaParm.load_pointers
      ~AmoebaParm.load_rst7
      ~AmoebaParm.load_structure
      ~AmoebaParm.mdin_skeleton
      ~AmoebaParm.omm_add_constraints
      ~AmoebaParm.omm_angle_force
      ~AmoebaParm.omm_bond_force
      ~AmoebaParm.omm_cmap_force
      ~AmoebaParm.omm_dihedral_force
      ~AmoebaParm.omm_gbsa_force
      ~AmoebaParm.omm_improper_force
      ~AmoebaParm.omm_nonbonded_force
      ~AmoebaParm.omm_out_of_plane_bend_force
      ~AmoebaParm.omm_pi_torsion_force
      ~AmoebaParm.omm_rb_torsion_force
      ~AmoebaParm.omm_set_virtual_sites
      ~AmoebaParm.omm_stretch_bend_force
      ~AmoebaParm.omm_torsion_torsion_force
      ~AmoebaParm.omm_trigonal_angle_force
      ~AmoebaParm.omm_urey_bradley_force
      ~AmoebaParm.parse
      ~AmoebaParm.prune_empty_terms
      ~AmoebaParm.ptr
      ~AmoebaParm.rdparm
      ~AmoebaParm.rdparm_old
      ~AmoebaParm.rdparm_slow
      ~AmoebaParm.recalculate_LJ
      ~AmoebaParm.rediscover_molecules
      ~AmoebaParm.remake_parm
      ~AmoebaParm.save
      ~AmoebaParm.set_version
      ~AmoebaParm.split
      ~AmoebaParm.strip
      ~AmoebaParm.to_dataframe
      ~AmoebaParm.unchange
      ~AmoebaParm.update_dihedral_exclusions
      ~AmoebaParm.view_as
      ~AmoebaParm.visualize
      ~AmoebaParm.write_cif
      ~AmoebaParm.write_parm
      ~AmoebaParm.write_pdb
      ~AmoebaParm.write_psf
      ~AmoebaParm.write_rst7
   
   

   
   
   .. rubric:: Attributes

   .. autosummary::
   
      ~AmoebaParm.ANGLE_FORCE_GROUP
      ~AmoebaParm.BOND_FORCE_GROUP
      ~AmoebaParm.CMAP_FORCE_GROUP
      ~AmoebaParm.DIHEDRAL_FORCE_GROUP
      ~AmoebaParm.IMPROPER_FORCE_GROUP
      ~AmoebaParm.NONBONDED_FORCE_GROUP
      ~AmoebaParm.OUT_OF_PLANE_BEND_FORCE_GROUP
      ~AmoebaParm.PI_TORSION_FORCE_GROUP
      ~AmoebaParm.RB_TORSION_FORCE_GROUP
      ~AmoebaParm.STRETCH_BEND_FORCE_GROUP
      ~AmoebaParm.TORSION_TORSION_FORCE_GROUP
      ~AmoebaParm.TRIGONAL_ANGLE_FORCE_GROUP
      ~AmoebaParm.UREY_BRADLEY_FORCE_GROUP
      ~AmoebaParm.amoeba
      ~AmoebaParm.angles_inc_h
      ~AmoebaParm.angles_without_h
      ~AmoebaParm.bonds_inc_h
      ~AmoebaParm.bonds_without_h
      ~AmoebaParm.box
      ~AmoebaParm.box_vectors
      ~AmoebaParm.chamber
      ~AmoebaParm.combining_rule
      ~AmoebaParm.coordinates
      ~AmoebaParm.dihedrals_inc_h
      ~AmoebaParm.dihedrals_without_h
      ~AmoebaParm.has_cmap
      ~AmoebaParm.positions
      ~AmoebaParm.topology
      ~AmoebaParm.velocities
      ~AmoebaParm.view