| acc() const | protocols::md::MDBase | inline |
| acc(core::Size idof) | protocols::md::MDBase | inline |
| acc_ | protocols::md::MDBase | private |
| add_trj(core::optimization::Multivec xyz) | protocols::md::MDBase | inline |
| add_trj_scratch(core::optimization::Multivec xyz) | protocols::md::MDBase | inline |
| apply(core::pose::Pose &pose) override | protocols::md::CartesianMD | virtual |
| Berendsen_Integrator(core::pose::Pose &pose, core::optimization::CartesianMinimizerMap &min_map) | protocols::md::CartesianMD | private |
| CartesianMD() | protocols::md::CartesianMD | |
| CartesianMD(core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP sfxn, core::kinematics::MoveMapCOP movemap=nullptr) | protocols::md::CartesianMD | |
| CartesianMD(core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn) | protocols::md::CartesianMD | |
| CartesianMD(core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MoveMap const &movemap) | protocols::md::CartesianMD | |
| clear_info() | protocols::moves::Mover | inlinevirtual |
| clone() const override | protocols::md::CartesianMD | virtual |
| context_update_step() const | protocols::md::MDBase | inline |
| context_update_step_ | protocols::md::MDBase | private |
| create() | protocols::moves::Mover | virtual |
| cst_on_pose_dynamic(core::pose::Pose &pose, core::optimization::Multivec const &ref_xyz, core::optimization::Multivec const &curr_eqxyz, core::optimization::Multivec &prv_eqxyz, core::optimization::CartesianMinimizerMap const &min_map) const | protocols::md::CartesianMD | |
| cst_on_pose_simple(core::pose::Pose &pose) const | protocols::md::CartesianMD | |
| cst_sdev() const | protocols::md::MDBase | inline |
| cst_sdev_ | protocols::md::MDBase | private |
| cummulative_time() const | protocols::md::MDBase | inline |
| cummulative_time_ | protocols::md::MDBase | private |
| current_job_ | protocols::moves::Mover | private |
| current_tag_ | protocols::moves::Mover | private |
| do_initialize(core::pose::Pose &pose) | protocols::md::CartesianMD | private |
| do_MD(core::pose::Pose &pose, core::Size const &nstep, core::Real const &temp0=300, bool const &initialize=false) | protocols::md::CartesianMD | private |
| do_minimize(core::pose::Pose &pose, core::optimization::MinimizerOptions const &options, bool const &show_energy) | protocols::md::CartesianMD | private |
| dt() const | protocols::md::MDBase | inline |
| dt_ | protocols::md::MDBase | private |
| dump_poses(core::pose::Pose const &pose_ref) const | protocols::md::CartesianMD | |
| Emin_obj() const | protocols::md::MDBase | inline |
| Emin_obj_ | protocols::md::MDBase | private |
| fresh_instance() const override | protocols::md::CartesianMD | inlinevirtual |
| Gamma() const | protocols::md::MDBase | inline |
| Gamma_ | protocols::md::MDBase | private |
| get_additional_output() | protocols::moves::Mover | virtual |
| get_current_eqxyz() const | protocols::md::CartesianMD | |
| get_current_job() const | protocols::moves::Mover | |
| get_current_tag() const | protocols::moves::Mover | inline |
| get_input_pose() const | protocols::moves::Mover | |
| get_last_move_status() const | protocols::moves::Mover | |
| get_name() const override | protocols::md::CartesianMD | virtual |
| get_native_info(core::pose::Pose const &pose) | protocols::md::CartesianMD | private |
| get_native_pose() const | protocols::moves::Mover | |
| get_self_ptr() const | protocols::moves::Mover | inline |
| get_self_ptr() | protocols::moves::Mover | inline |
| get_self_weak_ptr() const | protocols::moves::Mover | inline |
| get_self_weak_ptr() | protocols::moves::Mover | inline |
| get_type() const | protocols::moves::Mover | inline |
| info() | protocols::moves::Mover | inlinevirtual |
| info() const | protocols::moves::Mover | inlinevirtual |
| info_ | protocols::moves::Mover | private |
| init() | protocols::md::MDBase | |
| initialize_velocity(core::Real const &temperature) | protocols::md::CartesianMD | private |
| inittime_ | protocols::md::CartesianMD | private |
| input_pose_ | protocols::moves::Mover | private |
| Kappa() const | protocols::md::MDBase | inline |
| Kappa_ | protocols::md::MDBase | private |
| kinetic_energy() const | protocols::md::MDBase | inline |
| kinetic_energy_ | protocols::md::MDBase | private |
| last_proposal_density_ratio() | protocols::moves::Mover | inlinevirtual |
| last_status_ | protocols::moves::Mover | private |
| mass() const | protocols::md::MDBase | inline |
| mass(core::Size iatm) const | protocols::md::MDBase | inline |
| mass_ | protocols::md::MDBase | private |
| md_energy_report_stepsize() const | protocols::md::MDBase | inline |
| md_energy_report_stepsize_ | protocols::md::MDBase | private |
| md_report_stepsize() const | protocols::md::MDBase | inline |
| md_report_stepsize_ | protocols::md::MDBase | private |
| md_rsr_update_stepsize() const | protocols::md::MDBase | inline |
| md_rsr_update_stepsize_ | protocols::md::MDBase | private |
| MDBase() | protocols::md::MDBase | |
| mdsch() const | protocols::md::MDBase | inline |
| mdsch(core::Size istep) const | protocols::md::MDBase | inline |
| mdsch_ | protocols::md::MDBase | private |
| min_map_ | protocols::md::CartesianMD | private |
| movemap() const | protocols::md::MDBase | inline |
| movemap_ | protocols::md::MDBase | private |
| movemap_factory_ | protocols::md::CartesianMD | private |
| Mover() | protocols::moves::Mover | |
| Mover(std::string const &type_name) | protocols::moves::Mover | |
| mover_name() | protocols::md::CartesianMD | static |
| n_dof() const | protocols::md::MDBase | inline |
| n_dof_ | protocols::md::MDBase | private |
| n_dof_temp() const | protocols::md::MDBase | inline |
| n_dof_temp_ | protocols::md::MDBase | private |
| name() | protocols::moves::Mover | inlinestatic |
| native_ | protocols::md::CartesianMD | private |
| native_given_ | protocols::md::CartesianMD | private |
| native_pose_ | protocols::moves::Mover | private |
| native_resmap_ | protocols::md::CartesianMD | private |
| ncyc_postmin() const | protocols::md::MDBase | inline |
| ncyc_postmin_ | protocols::md::MDBase | private |
| ncyc_premin() const | protocols::md::MDBase | inline |
| ncyc_premin_ | protocols::md::MDBase | private |
| nstep() const | protocols::md::MDBase | inline |
| nstep_ | protocols::md::MDBase | private |
| parent typedef | protocols::md::MDBase | |
| parse_movemap(TagCOP tag, basic::datacache::DataMap &data) | protocols::md::CartesianMD | |
| parse_my_tag(TagCOP, basic::datacache::DataMap &) override | protocols::md::CartesianMD | virtual |
| parse_opts(TagCOP tag, basic::datacache::DataMap &data) | protocols::md::CartesianMD | |
| parse_schfile(std::string const schfile) | protocols::md::MDBase | |
| Pose typedef | protocols::moves::Mover | |
| pose0() const | protocols::md::MDBase | inline |
| pose0_ | protocols::md::MDBase | private |
| pose_minobj() const | protocols::md::MDBase | inline |
| pose_minobj_ | protocols::md::MDBase | private |
| PoseCOP typedef | protocols::moves::Mover | |
| potential_energy() const | protocols::md::MDBase | inline |
| potential_energy_ | protocols::md::MDBase | private |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::moves::Mover | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::md::CartesianMD | static |
| prv_eqxyz() const | protocols::md::MDBase | inline |
| prv_eqxyz_ | protocols::md::MDBase | private |
| ref_xyz() const | protocols::md::MDBase | inline |
| ref_xyz_ | protocols::md::MDBase | private |
| register_options() | protocols::moves::Mover | inlinestatic |
| reinitialize_for_each_job() const | protocols::moves::Mover | virtual |
| reinitialize_for_new_input() const | protocols::moves::Mover | virtual |
| renew_trj_scratch() | protocols::md::MDBase | inline |
| report_as_silent() const | protocols::md::MDBase | inline |
| report_as_silent_ | protocols::md::MDBase | private |
| report_MD(core::pose::Pose &pose, core::optimization::CartesianMinimizerMap const &min_map, bool const report_trj) | protocols::md::CartesianMD | private |
| report_scorecomp() const | protocols::md::MDBase | inline |
| report_scorecomp_ | protocols::md::MDBase | private |
| report_silent(core::pose::Pose &pose, core::Real rmsd=-1.0, core::Real gdttm=-1.0, core::Real gdtha=-1.0) | protocols::md::MDBase | |
| reset_status() | protocols::moves::Mover | |
| resize_natm_variables() | protocols::md::MDBase | |
| rsrfilename() const | protocols::md::MDBase | inline |
| rsrfilename_ | protocols::md::MDBase | private |
| scheduled() const | protocols::md::MDBase | inline |
| scheduled_ | protocols::md::MDBase | private |
| scorefxn() const | protocols::md::MDBase | inline |
| scorefxn_ | protocols::md::MDBase | private |
| scorefxn_obj() const | protocols::md::MDBase | inline |
| scorefxn_obj_ | protocols::md::MDBase | private |
| selectmode() const | protocols::md::MDBase | inline |
| selectmode_ | protocols::md::MDBase | private |
| set_acc(core::optimization::Multivec setting) | protocols::md::MDBase | inline |
| set_constraint(core::Real const sdev) | protocols::md::MDBase | |
| set_context_update_step(core::Size setting) | protocols::md::MDBase | inline |
| set_cst_sdev(core::Real setting) | protocols::md::MDBase | inline |
| set_cummulative_time(core::Real setting) | protocols::md::MDBase | inline |
| set_current_job(protocols::jobdist::BasicJobCOP job) | protocols::moves::Mover | |
| set_current_tag(std::string const &new_tag) | protocols::moves::Mover | inlinevirtual |
| set_defaults() | protocols::md::MDBase | inline |
| set_dt(core::Real setting) | protocols::md::MDBase | inline |
| set_Emin_obj(core::Real setting) | protocols::md::MDBase | inline |
| set_Gamma(core::Real setting) | protocols::md::MDBase | inline |
| set_input_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_Kappa(core::Real setting) | protocols::md::MDBase | inline |
| set_kinetic_energy(core::Real setting) | protocols::md::MDBase | inline |
| set_last_move_status(MoverStatus status) | protocols::moves::Mover | protected |
| set_mass(core::Size iatm, core::Real setting) | protocols::md::MDBase | inline |
| set_md_energy_report_stepsize(core::Size setting) | protocols::md::MDBase | inline |
| set_md_report_stepsize(core::Size setting) | protocols::md::MDBase | inline |
| set_md_rsr_update_stepsize(core::Size setting) | protocols::md::MDBase | inline |
| set_mdsch(utility::vector1< MDscheduleData > setting) | protocols::md::MDBase | inline |
| set_movemap(core::pose::Pose const &pose, core::kinematics::MoveMapCOP movemap) | protocols::md::MDBase | virtual |
| set_n_dof(core::Size setting) | protocols::md::MDBase | inline |
| set_n_dof_temp(core::Size setting) | protocols::md::MDBase | inline |
| set_native_pose(PoseCOP pose) | protocols::moves::Mover | virtual |
| set_ncyc_postmin(core::Size setting) | protocols::md::MDBase | inline |
| set_ncyc_premin(core::Size setting) | protocols::md::MDBase | inline |
| set_nstep(core::Size setting) | protocols::md::MDBase | inline |
| set_pose0(core::pose::Pose setting) | protocols::md::MDBase | inline |
| set_pose_minobj(core::pose::Pose setting) | protocols::md::MDBase | inline |
| set_potential_energy(core::Real setting) | protocols::md::MDBase | inline |
| set_prv_eqxyz(core::optimization::Multivec setting) | protocols::md::MDBase | inline |
| set_ref_xyz(core::optimization::Multivec setting) | protocols::md::MDBase | inline |
| set_report_as_silent(bool setting) | protocols::md::MDBase | inline |
| set_report_scorecomp(bool setting) | protocols::md::MDBase | inline |
| set_rsrfilename(std::string setting) | protocols::md::MDBase | inline |
| set_scheduled(bool setting) | protocols::md::MDBase | inline |
| set_scorefxn(core::scoring::ScoreFunctionCOP setting) | protocols::md::MDBase | inline |
| set_scorefxn(core::scoring::ScoreFunction const &setting) | protocols::md::MDBase | inline |
| set_scorefxn_obj(core::scoring::ScoreFunctionCOP setting) | protocols::md::MDBase | inline |
| set_scorefxn_obj(core::scoring::ScoreFunction const &setting) | protocols::md::MDBase | inline |
| set_selectmode(std::string setting) | protocols::md::MDBase | inline |
| set_silentname(std::string setting) | protocols::md::MDBase | inline |
| set_store_trj(bool setting) | protocols::md::MDBase | inline |
| set_temp0(core::Real setting) | protocols::md::MDBase | inline |
| set_temperature(core::Real setting) | protocols::md::MDBase | inline |
| set_time_minobj(core::Real setting) | protocols::md::MDBase | inline |
| set_trj(utility::vector1< core::optimization::Multivec > setting) | protocols::md::MDBase | inline |
| set_trj_score_only(bool setting) | protocols::md::MDBase | inline |
| set_trj_scratch(utility::vector1< core::optimization::Multivec > setting) | protocols::md::MDBase | inline |
| set_type(std::string const &setting) | protocols::moves::Mover | inline |
| set_uniform_coord_constrained(bool setting) | protocols::md::MDBase | inline |
| set_vel(core::optimization::Multivec setting) | protocols::md::MDBase | inline |
| set_write_dynamic_rsr(bool setting) | protocols::md::MDBase | inline |
| set_write_dynamic_rsr(std::string const filename) | protocols::md::MDBase | inline |
| set_xyz(core::optimization::Multivec setting) | protocols::md::MDBase | inline |
| show(std::ostream &output=std::cout) const | protocols::moves::Mover | virtual |
| silentname() const | protocols::md::MDBase | inline |
| silentname_ | protocols::md::MDBase | private |
| store_trj() const | protocols::md::MDBase | inline |
| store_trj_ | protocols::md::MDBase | private |
| Strings typedef | protocols::moves::Mover | |
| TagCOP typedef | protocols::moves::Mover | |
| temp0() const | protocols::md::MDBase | inline |
| temp0_ | protocols::md::MDBase | private |
| temperature() const | protocols::md::MDBase | inline |
| temperature_ | protocols::md::MDBase | private |
| test_move(Pose &pose) | protocols::moves::Mover | inlinevirtual |
| time_minobj() const | protocols::md::MDBase | inline |
| time_minobj_ | protocols::md::MDBase | private |
| trj() const | protocols::md::MDBase | inline |
| trj(core::Size itrj) const | protocols::md::MDBase | inline |
| trj_ | protocols::md::MDBase | private |
| trj_score_only() const | protocols::md::MDBase | inline |
| trj_score_only_ | protocols::md::MDBase | private |
| trj_scratch() const | protocols::md::MDBase | inline |
| trj_scratch_ | protocols::md::MDBase | private |
| type(const std::string &type_in) | protocols::moves::Mover | inline |
| type() const | protocols::moves::Mover | inline |
| type_ | protocols::moves::Mover | private |
| uniform_coord_constrained() const | protocols::md::MDBase | inline |
| uniform_coord_constrained_ | protocols::md::MDBase | private |
| update_restraint(core::pose::Pose &pose, core::optimization::CartesianMinimizerMap const &min_map) | protocols::md::CartesianMD | |
| use_rattle(bool const value) | protocols::md::CartesianMD | |
| use_rattle_ | protocols::md::CartesianMD | private |
| vel() const | protocols::md::MDBase | inline |
| vel(core::Size idof) | protocols::md::MDBase | inline |
| vel_ | protocols::md::MDBase | private |
| VelocityVerlet_Integrator(core::pose::Pose &pose, core::optimization::CartesianMinimizerMap &min_map, md::Rattle &rattle, bool const update_score=false) | protocols::md::CartesianMD | private |
| write_dynamic_rsr() const | protocols::md::MDBase | inline |
| write_dynamic_rsr_ | protocols::md::MDBase | private |
| xyz() const | protocols::md::MDBase | inline |
| xyz(core::Size idof) | protocols::md::MDBase | inline |
| xyz_ | protocols::md::MDBase | private |
| ~CartesianMD() override | protocols::md::CartesianMD | |
| ~MDBase() override | protocols::md::MDBase | |
