apply(core::pose::Pose const &pose) const | protocols::analysis::PeptideDeriverFilter | virtual |
assign(PeptideDeriverFilter &, PeptideDeriverFilter const &) | protocols::analysis::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::analysis::PeptideDeriverFilter | |
calculate_interface_score(core::pose::Pose const &pose, core::Size const jump_id) const | protocols::analysis::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::analysis::PeptideDeriverFilter | |
clear() | protocols::filters::Filter | inlinevirtual |
clone() const | protocols::analysis::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::analysis::PeptideDeriverFilter | |
derive_peptide(PeptideDeriverOutputter &output, core::pose::Pose const &receptor_pose, core::pose::Pose const &partner_pose, core::Real const total_isc) const | protocols::analysis::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::analysis::PeptideDeriverFilter | privatestatic |
fresh_instance() const | protocols::analysis::PeptideDeriverFilter | inlinevirtual |
get_chain_indices(core::pose::Pose const &pose, utility::vector1< char > const &restrict_to_chains) | protocols::analysis::PeptideDeriverFilter | privatestatic |
get_is_do_minimize() const | protocols::analysis::PeptideDeriverFilter | inline |
get_is_dump_cyclic_poses() const | protocols::analysis::PeptideDeriverFilter | inline |
get_is_dump_peptide_pose() const | protocols::analysis::PeptideDeriverFilter | inline |
get_is_dump_prepared_pose() const | protocols::analysis::PeptideDeriverFilter | inline |
get_is_dump_report_file() const | protocols::analysis::PeptideDeriverFilter | inline |
get_is_report_gzip() const | protocols::analysis::PeptideDeriverFilter | inline |
get_is_skip_zero_isc() const | protocols::analysis::PeptideDeriverFilter | inline |
get_optimize_cyclic_threshold() const | protocols::analysis::PeptideDeriverFilter | inline |
get_pep_lengths() const | protocols::analysis::PeptideDeriverFilter | inline |
get_report_format() const | protocols::analysis::PeptideDeriverFilter | inline |
get_restrict_partners_to_chains() const | protocols::analysis::PeptideDeriverFilter | inline |
get_restrict_receptors_to_chains() const | protocols::analysis::PeptideDeriverFilter | inline |
get_scorefxn_deriver() const | protocols::analysis::PeptideDeriverFilter | inline |
get_type() const | protocols::filters::Filter | inlinevirtual |
get_user_defined_name() const | protocols::filters::Filter | inline |
is_do_minimize_ | protocols::analysis::PeptideDeriverFilter | private |
is_dump_cyclic_poses_ | protocols::analysis::PeptideDeriverFilter | private |
is_dump_peptide_pose_ | protocols::analysis::PeptideDeriverFilter | private |
is_dump_prepared_pose_ | protocols::analysis::PeptideDeriverFilter | private |
is_dump_report_file_ | protocols::analysis::PeptideDeriverFilter | private |
is_report_gzip_ | protocols::analysis::PeptideDeriverFilter | private |
is_skip_zero_isc_ | protocols::analysis::PeptideDeriverFilter | private |
minimize(core::pose::Pose &) const | protocols::analysis::PeptideDeriverFilter | private |
name() const | protocols::analysis::PeptideDeriverFilter | inlinevirtual |
normalize_isc(core::Real const isc) | protocols::analysis::PeptideDeriverFilter | privatestatic |
operator=(PeptideDeriverFilter const &rhs) | protocols::analysis::PeptideDeriverFilter | |
optimize_cyclic_threshold_ | protocols::analysis::PeptideDeriverFilter | private |
parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose) | protocols::analysis::PeptideDeriverFilter | virtual |
parse_options() | protocols::analysis::PeptideDeriverFilter | private |
parse_report_format_string(std::string const value) | protocols::analysis::PeptideDeriverFilter | static |
pep_lengths_ | protocols::analysis::PeptideDeriverFilter | private |
PeptideDeriverFilter() | protocols::analysis::PeptideDeriverFilter | |
PeptideDeriverFilter(PeptideDeriverFilter const &) | protocols::analysis::PeptideDeriverFilter | |
prepare_pose(PeptideDeriverOutputter &output, core::pose::Pose &pose) const | protocols::analysis::PeptideDeriverFilter | |
push_chain_residue_indices(core::pose::Pose const &many_chain_pose, core::Size const chain_index, utility::vector1< core::Size > &residue_indices) | protocols::analysis::PeptideDeriverFilter | privatestatic |
report(std::ostream &out, core::pose::Pose const &pose) const | protocols::analysis::PeptideDeriverFilter | virtual |
report_format_ | protocols::analysis::PeptideDeriverFilter | private |
report_sm(core::pose::Pose const &) const | protocols::filters::Filter | inlinevirtual |
restrict_partners_to_chains_ | protocols::analysis::PeptideDeriverFilter | private |
restrict_receptors_to_chains_ | protocols::analysis::PeptideDeriverFilter | private |
score(core::pose::Pose &pose) | protocols::filters::Filter | virtual |
scorefxn_deriver_ | protocols::analysis::PeptideDeriverFilter | private |
scorefxn_minimizer_ | protocols::analysis::PeptideDeriverFilter | private |
scorename_ | protocols::filters::Filter | protected |
set_is_do_minimize(bool const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_is_dump_cyclic_poses(bool const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_is_dump_peptide_pose(bool const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_is_dump_prepared_pose(bool const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_is_dump_report_file(bool const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_is_report_gzip(bool const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_is_skip_zero_isc(bool const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_optimize_cyclic_threshold(core::Real const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_pep_lengths(utility::vector1< core::Size > const &values) | protocols::analysis::PeptideDeriverFilter | inline |
set_report_format(PeptideDeriverReportFormat const value) | protocols::analysis::PeptideDeriverFilter | inline |
set_restrict_partners_to_chains(utility::vector1< char > const &values) | protocols::analysis::PeptideDeriverFilter | inline |
set_restrict_receptors_to_chains(utility::vector1< char > const &values) | protocols::analysis::PeptideDeriverFilter | inline |
set_scorefxn_deriver(core::scoring::ScoreFunctionOP value) | protocols::analysis::PeptideDeriverFilter | inline |
set_user_defined_name(std::string const &name) | protocols::filters::Filter | inline |
~Filter() | protocols::filters::Filter | virtual |