| aa_matrices() const | protocols::mean_field::FlexBBDesignMeanField | inline |
| aa_matrices_ | protocols::mean_field::FlexBBDesignMeanField | private |
| aa_matrix() const | protocols::mean_field::FlexBBDesignMeanField | |
| alt_rot_matrix() const | protocols::mean_field::MeanField | inline |
| alt_rot_matrix_ | protocols::mean_field::MeanField | private |
| bb_boltz_probs() | protocols::mean_field::FlexBBMeanField | inline |
| bb_boltz_probs_ | protocols::mean_field::FlexBBMeanField | protected |
| bb_boltz_probs_per_aa() | protocols::mean_field::FlexBBMeanField | inline |
| bb_boltz_probs_per_aa_ | protocols::mean_field::FlexBBMeanField | protected |
| bb_boltz_weights_ | protocols::mean_field::FlexBBMeanField | private |
| build_rot_matrix_for_pose(core::Size pose_ind) | protocols::mean_field::MeanField | |
| calc_alt_rot_matrix() | protocols::mean_field::MeanField | private |
| calc_bb_boltz_probs() override | protocols::mean_field::FlexBBDesignMeanField | virtual |
| calc_energies_matrix() | protocols::mean_field::MeanField | private |
| calc_exp_value_aa_matrix() | protocols::mean_field::FlexBBDesignMeanField | |
| calc_exp_value_rot_matrix() | protocols::mean_field::FlexBBMeanField | |
| converge() | protocols::mean_field::MeanField | |
| convert_energies_to_alt_rm() | protocols::mean_field::MeanField | private |
| delete_pose(core::Size pose_ind) override | protocols::mean_field::FlexBBDesignMeanField | virtual |
| energies_matrix() const | protocols::mean_field::MeanField | inline |
| energies_matrix_ | protocols::mean_field::MeanField | private |
| energy_matrices() const | protocols::mean_field::FlexBBMeanField | inline |
| energy_matrices_ | protocols::mean_field::FlexBBMeanField | private |
| energy_matrix() const | protocols::mean_field::FlexBBMeanField | inline |
| exp_aa_matrix_ | protocols::mean_field::FlexBBDesignMeanField | private |
| exp_energy_matrix_ | protocols::mean_field::FlexBBMeanField | private |
| exp_rot_matrix_ | protocols::mean_field::FlexBBMeanField | private |
| FlexBBDesignMeanField(core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > tasks, core::scoring::ScoreFunctionOP scfxn) | protocols::mean_field::FlexBBDesignMeanField | |
| FlexBBDesignMeanField(core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > tasks, core::scoring::ScoreFunctionOP scfxn, core::Real lambda_mem, core::Real tolerance, core::Real temp, core::Real threshold) | protocols::mean_field::FlexBBDesignMeanField | |
| FlexBBDesignMeanField() | protocols::mean_field::FlexBBDesignMeanField | private |
| FlexBBDesignMeanField(FlexBBDesignMeanField const &object_to_copy) | protocols::mean_field::FlexBBDesignMeanField | private |
| FlexBBMeanField(core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > tasks, core::scoring::ScoreFunctionOP scfxn) | protocols::mean_field::FlexBBMeanField | |
| FlexBBMeanField(core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > tasks, core::scoring::ScoreFunctionOP scfxn, core::Real lambda_mem, core::Real tolerance, core::Real temp, core::Real threshold) | protocols::mean_field::FlexBBMeanField | |
| FlexBBMeanField() | protocols::mean_field::FlexBBMeanField | private |
| FlexBBMeanField(FlexBBMeanField const &object_to_copy) | protocols::mean_field::FlexBBMeanField | private |
| has_converged() const | protocols::mean_field::MeanField | private |
| init_option() const | protocols::mean_field::MeanField | inline |
| init_option_ | protocols::mean_field::MeanField | private |
| lambda_memory() const | protocols::mean_field::MeanField | inline |
| lambda_memory_ | protocols::mean_field::MeanField | private |
| MeanField(core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > const &tasks, core::scoring::ScoreFunctionOP scfxn) | protocols::mean_field::MeanField | |
| MeanField(core::Size const option, core::pose::PoseOPs &poses, utility::vector1< core::pack::task::PackerTaskOP > const &tasks, core::scoring::ScoreFunctionOP scfxn, core::Real lambda_mem, core::Real tolerance, core::Real temp, core::Real threshold) | protocols::mean_field::MeanField | |
| MeanField() | protocols::mean_field::MeanField | private |
| MeanField(MeanField const &object_to_copy) | protocols::mean_field::MeanField | private |
| nrot_per_pos_ | protocols::mean_field::FlexBBMeanField | private |
| num_packed() const | protocols::mean_field::MeanField | |
| num_poses() const | protocols::mean_field::MeanField | inline |
| operator<<(std::ostream &output, FlexBBDesignMeanField const &object_to_output) | protocols::mean_field::FlexBBDesignMeanField | friend |
| operator=(FlexBBDesignMeanField const &object_to_copy) | protocols::mean_field::FlexBBDesignMeanField | private |
| pig_ | protocols::mean_field::MeanField | private |
| poses_ | protocols::mean_field::MeanField | private |
| process() override | protocols::mean_field::FlexBBDesignMeanField | virtual |
| renumber_rotamers() | protocols::mean_field::FlexBBMeanField | |
| rot_matrices() const | protocols::mean_field::FlexBBMeanField | inline |
| rot_matrices_ | protocols::mean_field::FlexBBMeanField | private |
| rot_matrix() const override | protocols::mean_field::FlexBBMeanField | virtual |
| rot_matrix_ | protocols::mean_field::MeanField | private |
| scfxn_ | protocols::mean_field::MeanField | private |
| show(std::ostream &output=std::cout) const | protocols::mean_field::FlexBBDesignMeanField | |
| tasks_ | protocols::mean_field::MeanField | private |
| temperature() const | protocols::mean_field::MeanField | inline |
| temperature_ | protocols::mean_field::MeanField | private |
| threshold() const | protocols::mean_field::MeanField | inline |
| threshold_ | protocols::mean_field::MeanField | private |
| tolerance() const | protocols::mean_field::MeanField | inline |
| tolerance_ | protocols::mean_field::MeanField | private |
| ~FlexBBDesignMeanField() override | protocols::mean_field::FlexBBDesignMeanField | |
| ~FlexBBMeanField() override | protocols::mean_field::FlexBBMeanField | |
| ~MeanField() override | protocols::mean_field::MeanField | |
