Index A | B | C | D | E | F | G | H | K | M | N | O | P | R | S | U A add_all_default_ener_function() (openmicron.forcefield.aicgmodel.AICG2Model method) add_debye_huckel() (openmicron.forcefield.aicgmodel.AICG2Model method) add_excluded() (openmicron.forcefield.aicgmodel.AICG2Model method) add_flexible_loc_angle() (openmicron.forcefield.aicgmodel.AICG2Model method) add_flexible_loc_dihedral() (openmicron.forcefield.aicgmodel.AICG2Model method) add_kim_hummer() (openmicron.forcefield.aicgmodel.AICG2Model method) add_protein_aicg13_angle() (openmicron.forcefield.aicgmodel.AICG2Model method) add_protein_aicg_dihedral() (openmicron.forcefield.aicgmodel.AICG2Model method) add_protein_bond() (openmicron.forcefield.aicgmodel.AICG2Model method) add_protein_harmonic_angle() (openmicron.forcefield.aicgmodel.AICG2Model method) add_protein_native_dihedral() (openmicron.forcefield.aicgmodel.AICG2Model method) add_protein_native_pair() (openmicron.forcefield.aicgmodel.AICG2Model method) add_reporters() (openmicron.forcefield.simulationsystem.SimulationSystem method) aicg13_ang_array_to_pd() (openmicron.utils.parser_ninfo.ParserNinfo method) aicg13_angle_term() (in module openmicron.forcefield.functionterms) AICG2Model (class in openmicron.forcefield.aicgmodel) aicg_dihd_array_to_pd() (openmicron.utils.parser_ninfo.ParserNinfo method) aicg_dihd_term() (in module openmicron.forcefield.functionterms) append_ff_params() (openmicron.forcefield.simulationsystem.SimulationSystem method) ashbaugh_hatch() (in module openmicron.forcefield.functionterms) auto_get_charged_atom() (openmicron.forcefield.simulationsystem.SimulationSystem method) B bonds_array_to_pd() (openmicron.utils.parser_ninfo.ParserNinfo method) C convert_str_to_number_array() (openmicron.utils.parser_ninfo.ParserNinfo method) correct_flex_ang_force_para() (openmicron.utils.parser_flp_para.parser_flp_para method) create_system() (openmicron.forcefield.simulationsystem.SimulationSystem method) cubic_spline() (openmicron.utils.parser_flp_para.parser_flp_para method) D debye_Huckel_bond_form() (in module openmicron.forcefield.functionterms) debye_Huckel_nonbonded_form() (in module openmicron.forcefield.functionterms) diff_cubic_spline() (openmicron.utils.parser_flp_para.parser_flp_para method) E excluded_term() (in module openmicron.forcefield.functionterms) F flex_angle_term() (in module openmicron.forcefield.functionterms) flex_dihd_term() (in module openmicron.forcefield.functionterms) flexi_dihd_energy() (openmicron.utils.parser_flp_para.parser_flp_para method) G gene_psf() (in module openmicron.utils) get_corr_flex_ang_para() (openmicron.utils.parser_flp_para.parser_flp_para method) get_exclusion() (openmicron.forcefield.simulationsystem.SimulationSystem method) get_mini_component_set() (openmicron.utils.redefinetop.RedefineTopology method) get_ninfo() (openmicron.utils.parser_ninfo.ParserNinfo method) go_contact_term() (in module openmicron.forcefield.functionterms) H harm_ang_array_to_pd() (openmicron.utils.parser_ninfo.ParserNinfo method) harmonic_angle_term() (in module openmicron.forcefield.functionterms) harmonic_bond_term() (in module openmicron.forcefield.functionterms) K kh_and_ex_term() (in module openmicron.forcefield.functionterms) kim_hummer_term() (in module openmicron.forcefield.functionterms) M module openmicron.forcefield.aicgmodel openmicron.forcefield.simulationsystem openmicron.utils.parser_flp_para openmicron.utils.parser_ninfo openmicron.utils.redefinetop move_COM_to_box_center() (openmicron.forcefield.simulationsystem.SimulationSystem method) N native_dihd_array_to_pd() (openmicron.utils.parser_ninfo.ParserNinfo method) native_dihd_term() (in module openmicron.forcefield.functionterms) native_pair_array_to_pd() (openmicron.utils.parser_ninfo.ParserNinfo method) O openmicron.forcefield.aicgmodel module openmicron.forcefield.simulationsystem module openmicron.utils.parser_flp_para module openmicron.utils.parser_ninfo module openmicron.utils.redefinetop module P parser_exv_params() (in module openmicron.utils) parser_flp_para (class in openmicron.utils.parser_flp_para) parser_kh_params() (in module openmicron.utils) parser_ninfo() (openmicron.utils.parser_ninfo.ParserNinfo method) ParserNinfo (class in openmicron.utils.parser_ninfo) R read_flexible_local_para() (openmicron.utils.parser_flp_para.parser_flp_para method) redefine_bond() (openmicron.utils.redefinetop.RedefineTopology method) RedefineTopology (class in openmicron.utils.redefinetop) S save_state() (openmicron.forcefield.simulationsystem.SimulationSystem method) save_system() (openmicron.forcefield.simulationsystem.SimulationSystem method) set_flex_dihd_corr() (openmicron.utils.parser_flp_para.parser_flp_para method) set_simulation() (openmicron.forcefield.simulationsystem.SimulationSystem method) SimulationSystem (class in openmicron.forcefield.simulationsystem) U umbrella_sampling_contact() (in module openmicron.forcefield.functionterms)
