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Rosetta
2020.11
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#include <NMerSVMEnergyFilter.hh>
Public Member Functions | |
NMerSVMEnergyFilter () | |
NMerSVMEnergyFilter (core::Real const score_type_threshold, std::string string_resnums) | |
bool | apply (core::pose::Pose const &pose) const override |
Returns true if the given pose passes the filter, false otherwise. More... | |
filters::FilterOP | clone () const override |
filters::FilterOP | fresh_instance () const override |
void | report (std::ostream &out, core::pose::Pose const &pose) const override |
core::Real | report_sm (core::pose::Pose const &pose) const override |
used to report filter internals through a score or silent file More... | |
core::Real | compute (core::pose::Pose const &pose) const |
~NMerSVMEnergyFilter () override | |
void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override |
std::string | name () const override |
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Filter () | |
Filter (std::string const &) | |
Filter (Filter const &) | |
~Filter () override | |
virtual std::string | get_type () const |
std::string | get_user_defined_name () const |
void | set_user_defined_name (std::string const &name) |
virtual void | clear () |
used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More... | |
virtual core::Real | score (core::pose::Pose &pose) |
virtual bool | filter_provides_citation_info () const |
Does this filter provide information about how to cite it? More... | |
virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP > | provide_citation_info () const |
Provide the citation. More... | |
virtual bool | filter_is_unpublished () const |
Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More... | |
virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP > | provide_authorship_info_for_unpublished () const |
Provide a list of authors and their e-mail addresses, as strings. More... | |
Static Public Member Functions | |
static std::string | class_name () |
static void | provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd) |
Additional Inherited Members | |
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std::string | scorename_ |
protocols::simple_filters::NMerSVMEnergyFilter::NMerSVMEnergyFilter | ( | ) |
protocols::simple_filters::NMerSVMEnergyFilter::NMerSVMEnergyFilter | ( | core::Real const | score_type_threshold, |
std::string | string_resnums | ||
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References score_type_threshold_, and string_resnums_.
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overridedefault |
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overridevirtual |
Returns true if the given pose passes the filter, false otherwise.
Implements protocols::filters::Filter.
References compute(), protocols::filters::Filter::score(), score_type_threshold_, and protocols::simple_filters::TR().
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static |
Referenced by protocols::simple_filters::NMerSVMEnergyFilterCreator::keyname(), name(), and provide_xml_schema().
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inlineoverridevirtual |
Implements protocols::filters::Filter.
core::Real protocols::simple_filters::NMerSVMEnergyFilter::compute | ( | core::pose::Pose const & | pose | ) | const |
References count_eps_, dump_table_, protocols::simple_filters::nmer_svm_res_data::energy, energy_method_, ep_cutoff_, core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), core::pose::get_resnum_list_ordered(), core::scoring::methods::NMerSVMEnergy::n_svms(), core::scoring::methods::NMerSVMEnergy::nmer_length(), protocols::simple_filters::nmer_svm_res_data::nmer_seq, core::pose::Pose::pdb_info(), protocols::simple_filters::nmer_svm_res_data::pdb_seqpos, protocols::simple_filters::print_nmer_svm_energy_data(), rank_as_score_, protocols::filters::Filter::score(), protocols::simple_filters::nmer_svm_res_data::seqpos, core::pose::Pose::sequence(), core::pose::Pose::size(), string_resnums_, protocols::simple_filters::nmer_svm_res_data::svm_energies, protocols::simple_filters::nmer_svm_res_data::svm_rank_avg, protocols::simple_filters::nmer_svm_res_data::svm_ranks, and core::id::to_string().
Referenced by apply(), report(), and report_sm().
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inlineoverridevirtual |
Implements protocols::filters::Filter.
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References class_name().
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References count_eps_, dump_table_, energy_method_, ep_cutoff_, core::scoring::methods::NMerSVMEnergy::gate_svm_scores(), core::scoring::methods::NMerSVMEnergy::nmer_length(), core::scoring::methods::NMerSVMEnergy::nmer_svm_scorecut(), rank_as_score_, core::scoring::methods::NMerSVMEnergy::read_nmer_svm(), core::scoring::methods::NMerSVMEnergy::read_nmer_svm_list(), score_type_threshold_, and string_resnums_.
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static |
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overridevirtual |
Reimplemented from protocols::filters::Filter.
References compute().
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overridevirtual |
used to report filter internals through a score or silent file
Reimplemented from protocols::filters::Filter.
References compute().
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private |
Referenced by compute(), and parse_my_tag().
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private |
Referenced by compute(), and parse_my_tag().
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private |
Referenced by compute(), and parse_my_tag().
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private |
Referenced by compute(), and parse_my_tag().
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private |
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private |
Referenced by compute(), and parse_my_tag().
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private |
Referenced by apply(), NMerSVMEnergyFilter(), and parse_my_tag().
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private |
Referenced by compute(), NMerSVMEnergyFilter(), and parse_my_tag().