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

#include <SheetTopologyFilter.hh>

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

Public Types
typedef protocols::filters::Filter	Super
typedef protocols::filters::Filter	Filter
typedef std::string	String
typedef protocols::filters::FilterOP	FilterOP
typedef core::pose::Pose	Pose
typedef protocols::fldsgn::topology::StrandPairingSet	StrandPairingSet
typedef protocols::fldsgn::topology::StrandPairingSetOP	StrandPairingSetOP
typedef protocols::fldsgn::topology::SS_Info2	SS_Info2
typedef protocols::fldsgn::topology::SS_Info2_OP	SS_Info2_OP
typedef utility::tag::TagCOP	TagCOP
typedef basic::datacache::DataMap	DataMap
typedef std::pair< core::Size, core::Size >	ResiduePairing
typedef std::set< ResiduePairing >	ResiduePairingSet
typedef utility::vector1< ResiduePairingSet >	ResiduePairingSets

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	set_ignore_register_shift (bool const ignore_register_shift)
	Set to true to ignore register shifts. More...
std::string	get_filtered_sheet_topology () const
	get filtered sheet_topology by StrandPairingSetOP More...
std::string	set_secstruct () const
	set user-specified pose secondary structure More...
bool	set_use_dssp () const
	if true, and secstruct is unset, dssp is used on the input. Otherwise, the pose.secstruct() is used More...
bool	set_ignore_register_shift () const
	Set to true to ignore register shifts. 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 () 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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

DataMap

typedef basic::datacache::DataMap protocols::fldsgn::filters::SheetTopologyFilter::DataMap

Filter

typedef protocols::filters::Filter protocols::fldsgn::filters::SheetTopologyFilter::Filter

FilterOP

typedef protocols::filters::FilterOP protocols::fldsgn::filters::SheetTopologyFilter::FilterOP

Pose

typedef core::pose::Pose protocols::fldsgn::filters::SheetTopologyFilter::Pose

ResiduePairing

typedef std::pair< core::Size, core::Size > protocols::fldsgn::filters::SheetTopologyFilter::ResiduePairing

ResiduePairingSet

typedef std::set< ResiduePairing > protocols::fldsgn::filters::SheetTopologyFilter::ResiduePairingSet

ResiduePairingSets

typedef utility::vector1< ResiduePairingSet > protocols::fldsgn::filters::SheetTopologyFilter::ResiduePairingSets

SS_Info2

typedef protocols::fldsgn::topology::SS_Info2 protocols::fldsgn::filters::SheetTopologyFilter::SS_Info2

SS_Info2_OP

typedef protocols::fldsgn::topology::SS_Info2_OP protocols::fldsgn::filters::SheetTopologyFilter::SS_Info2_OP

StrandPairingSet

typedef protocols::fldsgn::topology::StrandPairingSet protocols::fldsgn::filters::SheetTopologyFilter::StrandPairingSet

StrandPairingSetOP

typedef protocols::fldsgn::topology::StrandPairingSetOP protocols::fldsgn::filters::SheetTopologyFilter::StrandPairingSetOP

String

typedef std::string protocols::fldsgn::filters::SheetTopologyFilter::String

Super

typedef protocols::filters::Filter protocols::fldsgn::filters::SheetTopologyFilter::Super

TagCOP

typedef utility::tag::TagCOP protocols::fldsgn::filters::SheetTopologyFilter::TagCOP

Constructor & Destructor Documentation

SheetTopologyFilter() [1/4]

protocols::fldsgn::filters::SheetTopologyFilter::SheetTopologyFilter

(

)

SheetTopologyFilter() [2/4]

protocols::fldsgn::filters::SheetTopologyFilter::SheetTopologyFilter

(

StrandPairingSetOP const &

sps

)

References filtered_sheet_topology_.

SheetTopologyFilter() [3/4]

protocols::fldsgn::filters::SheetTopologyFilter::SheetTopologyFilter

(

String const &

sheet_topology

)

SheetTopologyFilter() [4/4]

protocols::fldsgn::filters::SheetTopologyFilter::SheetTopologyFilter ( SheetTopologyFilter const &  rval )

default

~SheetTopologyFilter()

protocols::fldsgn::filters::SheetTopologyFilter::~SheetTopologyFilter ( )

inlineoverride

Member Function Documentation

apply()

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

overridevirtual

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

Implements protocols::filters::Filter.

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

class_name()

std::string protocols::fldsgn::filters::SheetTopologyFilter::class_name ( )

static

Referenced by protocols::fldsgn::filters::SheetTopologyFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

FilterOP protocols::fldsgn::filters::SheetTopologyFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::fldsgn::filters::SheetTopologyFilter::compute

(

Pose const &

pose

)

const

returns the fraction of pairings that pass the filter

Parameters

[in]

pose

Pose 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().

compute_paired_residues()

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

private

Computes number of pairings in the given StrandPairing.

Parameters

[in]	pairing	StrandPairing which contains residue pairing information
[in]	ss_info	SS_Info2 object describing the secondary structure of the pose

Returns

ResiduePairingSet containing pairs of residues

References protocols::fldsgn::topology::StrandPairing::begin1(), protocols::fldsgn::topology::StrandPairing::end1(), protocols::fldsgn::topology::StrandPairing::has_paired_residue(), protocols::fldsgn::topology::StrandPairing::residue_pair(), protocols::fldsgn::topology::StrandPairing::rgstr_shift(), protocols::fldsgn::topology::StrandPairing::s1(), protocols::fldsgn::topology::StrandPairing::s2(), protocols::fldsgn::topology::SS_Info2::strand(), and tr().

Referenced by compute_residue_pairings().

compute_residue_pairings()

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

private

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

Parameters

[in]	spairset	The 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_info	SS_Info2 object describing the secondary structure of the pose

Returns

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().

count_good_pairings()

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

private

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

References tr().

Referenced by compute().

count_residue_pairings()

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

private

Counts total number of residue pairings present in the ResiduePairingSets.

Referenced by compute().

filtered_sheet_topology() [1/2]

void protocols::fldsgn::filters::SheetTopologyFilter::filtered_sheet_topology

(

StrandPairingSetOP const &

sps

)

References filtered_sheet_topology_.

filtered_sheet_topology() [2/2]

void protocols::fldsgn::filters::SheetTopologyFilter::filtered_sheet_topology

(

String const &

sheet_topology

)

References filtered_sheet_topology_.

fresh_instance()

FilterOP protocols::fldsgn::filters::SheetTopologyFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

get_filtered_sheet_topology() [1/2]

std::string protocols::fldsgn::filters::SheetTopologyFilter::get_filtered_sheet_topology

(

)

const

get filtered sheet_topology by StrandPairingSetOP

References filtered_sheet_topology_.

Referenced by compute().

get_filtered_sheet_topology() [2/2]

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

private

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().

get_secstruct()

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

private

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::pose::Pose::secstruct(), secstruct_input_, tr(), and use_dssp_.

Referenced by compute().

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

void protocols::fldsgn::filters::SheetTopologyFilter::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &    )

overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References filtered_sheet_topology_, ignore_register_shift_, protocols::fldsgn::topology::StrandPairingSet::name(), protocols::parser::BluePrint::secstruct(), set_secstruct(), set_use_dssp(), protocols::parser::BluePrint::strand_pairings(), tr(), and use_dssp_.

provide_xml_schema()

void protocols::fldsgn::filters::SheetTopologyFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::fldsgn::filters::SheetTopologyFilterCreator::provide_xml_schema().

replace_register_shifts()

void protocols::fldsgn::filters::SheetTopologyFilter::replace_register_shifts ( topology::StrandPairingSet &  spairset, topology::StrandPairingSet &  filtered_spairset  ) const

private

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().

report_sm()

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

overridevirtual

returns the fraction of pairings that pass

Reimplemented from protocols::filters::Filter.

References compute().

set_ignore_register_shift() [1/2]

bool protocols::fldsgn::filters::SheetTopologyFilter::set_ignore_register_shift

(

)

const

Set to true to ignore register shifts.

References ignore_register_shift_.

set_ignore_register_shift() [2/2]

void protocols::fldsgn::filters::SheetTopologyFilter::set_ignore_register_shift

(

bool const

ignore_register_shift

)

Set to true to ignore register shifts.

References ignore_register_shift_.

set_secstruct() [1/2]

std::string protocols::fldsgn::filters::SheetTopologyFilter::set_secstruct

(

)

const

set user-specified pose secondary structure

References secstruct_input_.

Referenced by parse_my_tag().

set_secstruct() [2/2]

void protocols::fldsgn::filters::SheetTopologyFilter::set_secstruct

(

std::string const &

ss

)

set user-specified pose secondary structure

References secstruct_input_.

set_use_dssp() [1/2]

bool protocols::fldsgn::filters::SheetTopologyFilter::set_use_dssp

(

)

const

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().

set_use_dssp() [2/2]

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_.

Member Data Documentation

filtered_sheet_topology_

String protocols::fldsgn::filters::SheetTopologyFilter::filtered_sheet_topology_

private

Referenced by apply(), filtered_sheet_topology(), get_filtered_sheet_topology(), parse_my_tag(), and SheetTopologyFilter().

ignore_register_shift_

bool protocols::fldsgn::filters::SheetTopologyFilter::ignore_register_shift_

private

Referenced by compute(), parse_my_tag(), and set_ignore_register_shift().

secstruct_input_

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

private

Referenced by get_secstruct(), and set_secstruct().

use_dssp_

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

private

Referenced by get_secstruct(), parse_my_tag(), and set_use_dssp().

---

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

• src/protocols/fldsgn/filters/SheetTopologyFilter.hh
• src/protocols/fldsgn/filters/SheetTopologyFilter.cc