| apply(core::pose::Pose const &pose) const override | protocols::peptide_deriver::PeptideDeriverFilter | virtual |
| assign(PeptideDeriverFilter &, PeptideDeriverFilter const &) | protocols::peptide_deriver::PeptideDeriverFilter | privatestatic |
| build_receptor_peptide_pose(core::pose::Pose const &receptor_pose, core::pose::Pose const &partner_pose, core::Size peptide_start, core::Size peptide_end, core::Size &jump_id) const | protocols::peptide_deriver::PeptideDeriverFilter | |
| calculate_interface_score(core::pose::Pose const &pose, core::Size const jump_id) const | protocols::peptide_deriver::PeptideDeriverFilter | |
| calculate_per_residue_interface_score(core::pose::Pose &chain_pair_pose, std::set< core::Size > interface_residues, std::ostream &report_out, core::Size const jump_id) const | protocols::peptide_deriver::PeptideDeriverFilter | |
| class_name() | protocols::peptide_deriver::PeptideDeriverFilter | static |
| clear() | protocols::filters::Filter | inlinevirtual |
| clone() const override | protocols::peptide_deriver::PeptideDeriverFilter | inlinevirtual |
| derive_peptide(PeptideDeriverOutputter &output, core::pose::Pose const &pose, core::Size const first_chain_index, core::Size const second_chain_index, bool const both_ways) const | protocols::peptide_deriver::PeptideDeriverFilter | |
| derive_peptide(PeptideDeriverOutputter &output, core::pose::Pose const &receptor_pose, core::pose::Pose const &partner_pose, core::Real const total_isc) const | protocols::peptide_deriver::PeptideDeriverFilter | |
| Filter() | protocols::filters::Filter | |
| Filter(std::string const &) | protocols::filters::Filter | |
| Filter(Filter const &) | protocols::filters::Filter | |
| find_interface_residues(core::pose::Pose const &chain_pair_pose) | protocols::peptide_deriver::PeptideDeriverFilter | privatestatic |
| fresh_instance() const override | protocols::peptide_deriver::PeptideDeriverFilter | inlinevirtual |
| generate_N2C_cyclic_peptide_protein_complex(core::pose::PoseOP const receptor_peptide_pose, core::Size const pep_nter_idx, core::Size const pep_cter_idx, core::scoring::ScoreFunctionOP const scorefxn_N2C_minimize) const | protocols::peptide_deriver::PeptideDeriverFilter | |
| get_chain_indices(core::pose::Pose const &pose, utility::vector1< char > const &restrict_to_chains) | protocols::peptide_deriver::PeptideDeriverFilter | privatestatic |
| get_is_do_minimize() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_is_dump_cyclic_poses() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_is_dump_peptide_pose() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_is_dump_prepared_pose() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_is_dump_report_file() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_is_report_gzip() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_is_skip_zero_isc() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_optimize_cyclic_threshold() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_pep_lengths() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_report_format() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_restrict_partners_to_chains() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_restrict_receptors_to_chains() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_scorefxn_deriver() const | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| get_type() const | protocols::filters::Filter | inlinevirtual |
| get_user_defined_name() const | protocols::filters::Filter | inline |
| is_do_minimize_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| is_dump_cyclic_poses_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| is_dump_peptide_pose_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| is_dump_prepared_pose_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| is_dump_report_file_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| is_report_gzip_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| is_skip_zero_isc_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| minimize(core::pose::Pose &) const | protocols::peptide_deriver::PeptideDeriverFilter | private |
| name() const override | protocols::peptide_deriver::PeptideDeriverFilter | virtual |
| normalize_isc(core::Real const isc) | protocols::peptide_deriver::PeptideDeriverFilter | privatestatic |
| operator=(PeptideDeriverFilter const &rhs) | protocols::peptide_deriver::PeptideDeriverFilter | |
| optimize_cyclic_threshold_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data) override | protocols::peptide_deriver::PeptideDeriverFilter | virtual |
| parse_options() | protocols::peptide_deriver::PeptideDeriverFilter | private |
| parse_report_format_string(std::string const &value) | protocols::peptide_deriver::PeptideDeriverFilter | static |
| pep_lengths_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| PeptideDeriverFilter() | protocols::peptide_deriver::PeptideDeriverFilter | |
| PeptideDeriverFilter(PeptideDeriverFilter const &) | protocols::peptide_deriver::PeptideDeriverFilter | |
| prepare_pose(PeptideDeriverOutputter &output, core::pose::Pose &pose) const | protocols::peptide_deriver::PeptideDeriverFilter | |
| provide_citation_info(basic::citation_manager::CitationCollectionList &) const | protocols::filters::Filter | virtual |
| provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd) | protocols::peptide_deriver::PeptideDeriverFilter | static |
| push_chain_residue_indices(core::pose::Pose const &many_chain_pose, core::Size const chain_index, utility::vector1< core::Size > &residue_indices) | protocols::peptide_deriver::PeptideDeriverFilter | privatestatic |
| report(std::ostream &out, core::pose::Pose const &pose) const override | protocols::peptide_deriver::PeptideDeriverFilter | virtual |
| report_format_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| report_sm(core::pose::Pose const &) const | protocols::filters::Filter | inlinevirtual |
| restrict_partners_to_chains_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| restrict_receptors_to_chains_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| score(core::pose::Pose &pose) | protocols::filters::Filter | virtual |
| scorefxn_deriver_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| scorefxn_minimizer_ | protocols::peptide_deriver::PeptideDeriverFilter | private |
| scorename_ | protocols::filters::Filter | protected |
| set_is_do_minimize(bool const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_is_dump_cyclic_poses(bool const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_is_dump_peptide_pose(bool const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_is_dump_prepared_pose(bool const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_is_dump_report_file(bool const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_is_report_gzip(bool const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_is_skip_zero_isc(bool const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_optimize_cyclic_threshold(core::Real const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_pep_lengths(utility::vector1< core::Size > const &values) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_report_format(PeptideDeriverReportFormat const value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_restrict_partners_to_chains(utility::vector1< char > const &values) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_restrict_receptors_to_chains(utility::vector1< char > const &values) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_scorefxn_deriver(core::scoring::ScoreFunctionOP value) | protocols::peptide_deriver::PeptideDeriverFilter | inline |
| set_user_defined_name(std::string const &name) | protocols::filters::Filter | inline |
| ~Filter() override | protocols::filters::Filter | |
1.8.7