seamm_ff_util

• seamm_ff_util package
  • Submodules
  • seamm_ff_util.dreiding module
    • DreidingMixin
      • DreidingMixin.dreiding_angles()
      • DreidingMixin.dreiding_bonds()
      • DreidingMixin.dreiding_dihedrals()
      • DreidingMixin.dreiding_hydrogen_bonds()
      • DreidingMixin.eex_dreiding_atomic_parameters()
  • seamm_ff_util.eex module
    • EEX_Mixin
      • EEX_Mixin.eex_1_3_bond_bond()
      • EEX_Mixin.eex_angle()
      • EEX_Mixin.eex_angle_angle()
      • EEX_Mixin.eex_angle_torsion_angle()
      • EEX_Mixin.eex_atomic_charge()
      • EEX_Mixin.eex_atoms()
      • EEX_Mixin.eex_bond()
      • EEX_Mixin.eex_bond_angle()
      • EEX_Mixin.eex_bond_bond()
      • EEX_Mixin.eex_bond_charge_increment()
      • EEX_Mixin.eex_charge()
      • EEX_Mixin.eex_compare_values()
      • EEX_Mixin.eex_out_of_plane()
      • EEX_Mixin.eex_pair()
      • EEX_Mixin.eex_shell_model()
      • EEX_Mixin.eex_torsion()
      • EEX_Mixin.eex_torsion_angle()
      • EEX_Mixin.eex_torsion_end_bond()
      • EEX_Mixin.eex_torsion_middle_bond()
  • seamm_ff_util.ff_assigner module
    • FFAssigner
      • FFAssigner.assign()
      • FFAssigner.draw_atom_types()
    • ForcefieldAssignmentError
  • seamm_ff_util.forcefield module
    • Forcefield
      • Forcefield.a_b_to_sigma_eps()
      • Forcefield.angle_angle_parameters()
      • Forcefield.angle_angle_torsion_1_parameters()
      • Forcefield.angle_parameters()
      • Forcefield.angle_torsion_3_parameters()
      • Forcefield.ar_br_to_sigma_eps()
      • Forcefield.assign_forcefield()
      • Forcefield.bond_angle_parameters()
      • Forcefield.bond_bond_1_3_parameters()
      • Forcefield.bond_bond_parameters()
      • Forcefield.bond_increments()
      • Forcefield.bond_parameters()
      • Forcefield.charge_method
      • Forcefield.charges()
      • Forcefield.cite_parameter()
      • Forcefield.clear()
      • Forcefield.current_forcefield
      • Forcefield.element()
      • Forcefield.end_bond_torsion_3_parameters()
      • Forcefield.energy_expression()
      • Forcefield.ff_form
      • Forcefield.fftype
      • Forcefield.filename
      • Forcefield.files_visited
      • Forcefield.forcefields
      • Forcefield.get_fragments()
      • Forcefield.get_templates()
      • Forcefield.initialize_biosym_forcefield()
      • Forcefield.make_canonical()
      • Forcefield.mass()
      • Forcefield.middle_bond_torsion_3_parameters()
      • Forcefield.no_transform()
      • Forcefield.nonbond_parameters()
      • Forcefield.nonbond_transformation()
      • Forcefield.oop_parameters()
      • Forcefield.references
      • Forcefield.rmin_eps_to_sigma_eps()
      • Forcefield.rmin_to_sigma()
      • Forcefield.setup_topology()
      • Forcefield.shell_model()
      • Forcefield.sigma_to_rmin()
      • Forcefield.terms
      • Forcefield.torsion_parameters()
    • ForcefieldChargeError
    • NonbondForms
      • NonbondForms.AR_BR
      • NonbondForms.A_B
      • NonbondForms.RMIN_EPS
      • NonbondForms.SIGMA_EPS
  • seamm_ff_util.metadata module
  • seamm_ff_util.reaxff module
    • ReaxFFMixin
      • ReaxFFMixin.eex_reaxff_angle_parameters()
      • ReaxFFMixin.eex_reaxff_atomic_parameters()
      • ReaxFFMixin.eex_reaxff_bond_parameters()
      • ReaxFFMixin.eex_reaxff_general_parameters()
      • ReaxFFMixin.eex_reaxff_hydrogen_bond_parameters()
      • ReaxFFMixin.eex_reaxff_off_diagonal_parameters()
      • ReaxFFMixin.eex_reaxff_torsion_parameters()
    • import_reaxff()
    • parse_reax_data()
    • read_reaxff_parameters()
    • reaxff_to_molssi_format()
    • run()
    • write_ff_file()
  • seamm_ff_util.tabulate_function module
    • tabulate_angle()
  • Module contents