parmed.amber.AmberParm
======================

.. currentmodule:: parmed.amber

.. autoclass:: AmberParm

   
   .. automethod:: __init__

   
   .. rubric:: Methods

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

   
   
   .. rubric:: Attributes

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