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protocols::fldsgn::filters::SheetTopologyFilter Class Reference

#include <SheetTopologyFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::SheetTopologyFilter:
Inheritance graph

Public Types

typedef protocols::filters::Filter Super
typedef protocols::filters::Filter Filter
typedef std::string String
typedef core::pose::Pose Pose
typedef utility::tag::TagCOP TagCOP
typedef basic::datacache::DataMap DataMap
typedef std::pair< core::Size,
typedef std::set< ResiduePairingResiduePairingSet
typedef utility::vector1
< ResiduePairingSet

Public Member Functions

 SheetTopologyFilter ()
 SheetTopologyFilter (StrandPairingSetOP const &sps)
 SheetTopologyFilter (String const &sheet_topology)
 SheetTopologyFilter (SheetTopologyFilter const &rval)
 ~SheetTopologyFilter () override
FilterOP clone () const override
FilterOP fresh_instance () const override
void filtered_sheet_topology (StrandPairingSetOP const &sps)
void filtered_sheet_topology (String const &sheet_topology)
void set_secstruct (std::string const &ss)
 set user-specified pose secondary structure More...
void set_use_dssp (bool const use_dssp)
 if true, and secstruct is unset, dssp is used on the input. Otherwise, the pose.secstruct() is used More...
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
 parse xml More...
core::Real compute (Pose const &pose) const
 returns the fraction of pairings that pass the filter More...
core::Real report_sm (Pose const &pose) const override
 returns the fraction of pairings that pass More...
bool apply (Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
std::string name () const override
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 Filter (std::string const &)
 Filter (Filter const &)
 ~Filter () override
virtual void report (std::ostream &, core::pose::Pose const &) const
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)

Private Member Functions

std::string get_filtered_sheet_topology (core::pose::Pose const &pose) const
 Returns the desired strand pairing topology string. More...
std::string get_secstruct (core::pose::Pose const &pose) const
 Returns the pose secondary structure to be used in computation. More...
ResiduePairingSets compute_residue_pairings (topology::StrandPairingSet &spairset, topology::SS_Info2 const &ss_info) const
 Given the filtered strand pairings, compute the number of residue pairings possible. More...
ResiduePairingSet compute_paired_residues (topology::StrandPairing const &pairing, topology::SS_Info2 const &ss_info) const
 Computes number of pairings in the given StrandPairing. More...
core::Size count_residue_pairings (ResiduePairingSets const &pair_sets) const
 Counts total number of residue pairings present in the ResiduePairingSets. More...
core::Size count_good_pairings (ResiduePairingSet const &filtered_pair_set, ResiduePairingSet const &pose_pair_set) const
 Counts number of residue pairs in the filtered_pair_set are present in the pose_pair_set. More...
void replace_register_shifts (topology::StrandPairingSet &spairset, topology::StrandPairingSet &filtered_spairset) const
 Replace register shift of pairings in pose_spairset with 99 if register shift in filtered_spairset is 99. More...

Private Attributes

String filtered_sheet_topology_
String secstruct_input_
bool ignore_register_shift_
bool use_dssp_

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::fldsgn::filters::SheetTopologyFilter::SheetTopologyFilter ( )
protocols::fldsgn::filters::SheetTopologyFilter::SheetTopologyFilter ( StrandPairingSetOP const &  sps)
protocols::fldsgn::filters::SheetTopologyFilter::SheetTopologyFilter ( String const &  sheet_topology)
protocols::fldsgn::filters::SheetTopologyFilter::SheetTopologyFilter ( SheetTopologyFilter const &  rval)
protocols::fldsgn::filters::SheetTopologyFilter::~SheetTopologyFilter ( )

Member Function Documentation

bool protocols::fldsgn::filters::SheetTopologyFilter::apply ( Pose const &  pose) const

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), filtered_sheet_topology_, and tr().

std::string protocols::fldsgn::filters::SheetTopologyFilter::class_name ( )
FilterOP protocols::fldsgn::filters::SheetTopologyFilter::clone ( ) const
core::Real protocols::fldsgn::filters::SheetTopologyFilter::compute ( Pose const &  pose) const

returns the fraction of pairings that pass the filter

[in]posePose to be checked

Pose secondary structure is determined by the user inputs, and must match the pose length.

If the filtered sheet topology doesn't contain and strand pairings, the value returned is 1.0 (i.e. all pairings OK)

If the pose doesn't contain strands, the value returned is 0.0 (i.e. all pairings bad)

If the pose is missing a strand, the value returned is 0.0 (i.e. all pairings bad)

Otherwise, NP_actual/NP_filtered is returned, where NP_actual is the number of good residue pairings in the structure, and NP_filtered is total possible residue pairings in the sheet

References protocols::fldsgn::topology::StrandPairingSet::begin(), protocols::fldsgn::topology::calc_strand_pairing_set(), protocols::fldsgn::filters::compute_max_strand(), compute_residue_pairings(), count_good_pairings(), count_residue_pairings(), protocols::fldsgn::topology::StrandPairingSet::end(), protocols::fldsgn::filters::find_pairing_idx(), core::sequence::get_abego(), get_filtered_sheet_topology(), get_secstruct(), ignore_register_shift_, protocols::fldsgn::topology::StrandPairingSet::name(), protocols::fldsgn::topology::NO_STRANDS, protocols::fldsgn::topology::StrandPairing::orient(), protocols::fldsgn::filters::remove_register_shifts(), replace_register_shifts(), core::pose::Pose::size(), protocols::fldsgn::topology::StrandPairingSet::strand_pairing(), core::pose::Pose::total_residue(), and tr().

Referenced by apply(), and report_sm().

SheetTopologyFilter::ResiduePairingSet protocols::fldsgn::filters::SheetTopologyFilter::compute_paired_residues ( topology::StrandPairing const &  pairing,
topology::SS_Info2 const &  ss_info 
) const
SheetTopologyFilter::ResiduePairingSets protocols::fldsgn::filters::SheetTopologyFilter::compute_residue_pairings ( topology::StrandPairingSet spairset,
topology::SS_Info2 const &  ss_info 
) const

Given the filtered strand pairings, compute the number of residue pairings possible.

[in]spairsetThe strand pairing set to be used to find residue pairings. It is non-const because the pairings are stored as OPs, so begin() and end() are non-const
[in]ss_infoSS_Info2 object describing the secondary structure of the pose
Vector of ResiduePairingSets, one for each strand pairing, in the same order as in spairset

References protocols::fldsgn::topology::StrandPairingSet::begin(), compute_paired_residues(), protocols::fldsgn::topology::StrandPairingSet::end(), core::scoring::pair, and tr().

Referenced by compute().

core::Size protocols::fldsgn::filters::SheetTopologyFilter::count_good_pairings ( ResiduePairingSet const &  filtered_pair_set,
ResiduePairingSet const &  pose_pair_set 
) const

Counts number of residue pairs in the filtered_pair_set are present in the pose_pair_set.

References tr().

Referenced by compute().

core::Size protocols::fldsgn::filters::SheetTopologyFilter::count_residue_pairings ( ResiduePairingSets const &  pair_sets) const

Counts total number of residue pairings present in the ResiduePairingSets.

Referenced by compute().

void protocols::fldsgn::filters::SheetTopologyFilter::filtered_sheet_topology ( StrandPairingSetOP const &  sps)
void protocols::fldsgn::filters::SheetTopologyFilter::filtered_sheet_topology ( String const &  sheet_topology)
FilterOP protocols::fldsgn::filters::SheetTopologyFilter::fresh_instance ( ) const
std::string protocols::fldsgn::filters::SheetTopologyFilter::get_filtered_sheet_topology ( core::pose::Pose const &  pose) const

Returns the desired strand pairing topology string.

Rules for selecting this topology string:

  1. If a user-specified filtered_sheet_topology_ is set, return that
  2. If StructureData is cached in the pose, determine pairings from that
  3. throw error

References filtered_sheet_topology_, protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(), protocols::denovo_design::components::SegmentPairing::get_strand_pairings(), and protocols::denovo_design::components::StructureDataFactory::has_cached_data().

Referenced by compute().

std::string protocols::fldsgn::filters::SheetTopologyFilter::get_secstruct ( core::pose::Pose const &  pose) const

Returns the pose secondary structure to be used in computation.

Rules for selecting the secondary structure:

  1. If a user-specified secstruct_input_ is set, return this
  2. If use_dssp is true, determine secondary structure by DSSP
  3. Return pose secondary stucture otherwise

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::pose::Pose::secstruct(), secstruct_input_, tr(), and use_dssp_.

Referenced by compute().

std::string protocols::fldsgn::filters::SheetTopologyFilter::name ( ) const

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::fldsgn::filters::SheetTopologyFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &   
void protocols::fldsgn::filters::SheetTopologyFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
void protocols::fldsgn::filters::SheetTopologyFilter::replace_register_shifts ( topology::StrandPairingSet spairset,
topology::StrandPairingSet filtered_spairset 
) const

Replace register shift of pairings in pose_spairset with 99 if register shift in filtered_spairset is 99.

References protocols::fldsgn::filters::find_pairing(), core::scoring::pair, and protocols::fldsgn::topology::StrandPairingSet::push_back().

Referenced by compute().

core::Real protocols::fldsgn::filters::SheetTopologyFilter::report_sm ( Pose const &  pose) const

returns the fraction of pairings that pass

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::fldsgn::filters::SheetTopologyFilter::set_secstruct ( std::string const &  ss)

set user-specified pose secondary structure

References secstruct_input_.

Referenced by parse_my_tag().

void protocols::fldsgn::filters::SheetTopologyFilter::set_use_dssp ( bool const  use_dssp)

if true, and secstruct is unset, dssp is used on the input. Otherwise, the pose.secstruct() is used

References use_dssp_.

Referenced by parse_my_tag().

Member Data Documentation

String protocols::fldsgn::filters::SheetTopologyFilter::filtered_sheet_topology_
bool protocols::fldsgn::filters::SheetTopologyFilter::ignore_register_shift_

Referenced by compute(), and parse_my_tag().

String protocols::fldsgn::filters::SheetTopologyFilter::secstruct_input_

Referenced by get_secstruct(), and set_secstruct().

bool protocols::fldsgn::filters::SheetTopologyFilter::use_dssp_

The documentation for this class was generated from the following files: