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protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter Class Reference

This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds. More...

#include <OversaturatedHbondAcceptorFilter.hh>

Inheritance diagram for protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter:
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Public Member Functions

 OversaturatedHbondAcceptorFilter ()
 Default constructor. More...
 
 OversaturatedHbondAcceptorFilter (OversaturatedHbondAcceptorFilter const &src)
 Copy constructor. More...
 
 ~OversaturatedHbondAcceptorFilter () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
 
protocols::filters::FilterOP clone () const override
 Required in the context of the parser/scripting scheme. More...
 
protocols::filters::FilterOP fresh_instance () const override
 Required in the context of the parser/scripting scheme. More...
 
virtual std::string get_name () const
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the structure passes the filter, false otherwise. More...
 
core::Real report_sm (core::pose::Pose const &pose) const override
 Required for reporting score values. More...
 
void report (std::ostream &os, core::pose::Pose const &pose) const override
 Allows printing a summary of this filter to a stream. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Parse XML tag (to use this Mover in RosettaScripts). More...
 
void set_max_allowed_oversaturated (core::Size const max_allowed)
 Set the maximum allowed number of instances of an oversaturated hydrogen bond acceptor. More...
 
core::Size max_allowed_oversaturated () const
 Get the maximum allowed number of instances of an oversaturated hydrogen bond acceptor. More...
 
void set_hbond_energy_cutoff (core::Real const &input_value)
 Set the threshold for considering something to be a hydrogen bond. More...
 
core::Real const & hbond_energy_cutoff () const
 Get the threshold for considering something to be a hydrogen bond. More...
 
void set_consider_mainchain_only (bool const input_setting)
 Set whether we only consider mainchain hydrogen bond donors and acceptors. More...
 
bool consider_mainchain_only () const
 Get whether we only consider mainchain hydrogen bond donors and acceptors. More...
 
void set_donor_selector (core::select::residue_selector::ResidueSelectorCOP donor_selector_in)
 Set the residue selector for donor residues. More...
 
core::select::residue_selector::ResidueSelectorCOP donor_selector () const
 Get the residue selector for donor residues. More...
 
void set_acceptor_selector (core::select::residue_selector::ResidueSelectorCOP acceptor_selector_in)
 Set the residue selector for acceptor residues. More...
 
core::select::residue_selector::ResidueSelectorCOP acceptor_selector () const
 Get the residue selector for acceptor residues. More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
 Set the scorefunction. More...
 
core::scoring::ScoreFunctionCOP scorefxn () const
 Get the scorefunction. 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 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

core::Size max_allowed_hbonds (core::pose::Pose const &pose, core::Size const res_index, core::Size const atom_index) const
 Given an atom, return the maximum number of hydrogen bonds that an atom of this type is allowed to receive. More...
 
core::Size compute (core::pose::Pose const &pose) const
 The function that actually calculates the value that this filter returns, called by the apply(), report(), and report_sm() functions. More...
 

Private Attributes

core::Size max_allowed_oversaturated_
 What is the maximum allowed number of instances of an oversaturated hydrogen bond acceptor? More...
 
core::Real hbond_energy_cutoff_
 The energy cutoff for considering something to be a hydrogen bond. More...
 
bool consider_mainchain_only_
 Should we only consider mainchain hydrogen bond donors and acceptors? More...
 
core::select::residue_selector::ResidueSelectorCOP donor_selector_
 Optional residue selector for the residues that could possibly be donating hydrogen bonds. More...
 
core::select::residue_selector::ResidueSelectorCOP acceptor_selector_
 Optional residue selector for the residues that could possibly be accepting hydrogen bonds. More...
 
core::scoring::ScoreFunctionOP scorefxn_
 The scorefunction to use for hydrogen bond scoring. More...
 

Additional Inherited Members

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

Detailed Description

This filter flags poses containing more than two hydrogen bonds to an oxygen atom, a common pathology that results from Rosetta's pairwise-decomposible scorefunction, which can't penalize excessive hydrogen bonds.

Constructor & Destructor Documentation

protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::OversaturatedHbondAcceptorFilter ( )

Default constructor.

protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::OversaturatedHbondAcceptorFilter ( OversaturatedHbondAcceptorFilter const &  src)

Copy constructor.

References acceptor_selector_, donor_selector_, and scorefxn_.

protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::~OversaturatedHbondAcceptorFilter ( )
overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::acceptor_selector ( ) const

Get the residue selector for acceptor residues.

References acceptor_selector_.

bool protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

Returns true if the structure passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), and max_allowed_oversaturated().

std::string protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::class_name ( )
static
protocols::filters::FilterOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::clone ( ) const
overridevirtual

Required in the context of the parser/scripting scheme.

Make a copy of this object and return an owning pointer to the copy.

Implements protocols::filters::Filter.

Referenced by compute().

core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::compute ( core::pose::Pose const &  pose) const
private
bool protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::consider_mainchain_only ( ) const

Get whether we only consider mainchain hydrogen bond donors and acceptors.

References consider_mainchain_only_.

Referenced by compute(), and parse_my_tag().

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::donor_selector ( ) const

Get the residue selector for donor residues.

References donor_selector_.

protocols::filters::FilterOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::fresh_instance ( ) const
overridevirtual

Required in the context of the parser/scripting scheme.

Implements protocols::filters::Filter.

std::string protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::get_name ( ) const
virtual

References class_name().

core::Real const & protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::hbond_energy_cutoff ( ) const

Get the threshold for considering something to be a hydrogen bond.

References hbond_energy_cutoff_.

Referenced by compute(), and parse_my_tag().

core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_hbonds ( core::pose::Pose const &  pose,
core::Size const  res_index,
core::Size const  atom_index 
) const
private

Given an atom, return the maximum number of hydrogen bonds that an atom of this type is allowed to receive.

For now, this function returns 0 if this is not an acceptor, 2 if it is. This is crude, of course. Ultimately, it should figure out how many hbonds an atom can actually receive.

References core::chemical::ResidueType::heavyatom_is_an_acceptor(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by compute().

core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_oversaturated ( ) const

Get the maximum allowed number of instances of an oversaturated hydrogen bond acceptor.

References max_allowed_oversaturated_.

Referenced by apply(), parse_my_tag(), and report().

std::string protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::report ( std::ostream &  os,
core::pose::Pose const &  pose 
) const
overridevirtual

Allows printing a summary of this filter to a stream.

Reimplemented from protocols::filters::Filter.

References compute(), and max_allowed_oversaturated().

core::Real protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::report_sm ( core::pose::Pose const &  pose) const
overridevirtual

Required for reporting score values.

Reimplemented from protocols::filters::Filter.

References compute().

core::scoring::ScoreFunctionCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::scorefxn ( ) const

Get the scorefunction.

References scorefxn_.

Referenced by compute().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_acceptor_selector ( core::select::residue_selector::ResidueSelectorCOP  acceptor_selector_in)

Set the residue selector for acceptor residues.

Clones the input.

References acceptor_selector_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_consider_mainchain_only ( bool const  input_setting)

Set whether we only consider mainchain hydrogen bond donors and acceptors.

References consider_mainchain_only_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_donor_selector ( core::select::residue_selector::ResidueSelectorCOP  donor_selector_in)

Set the residue selector for donor residues.

Clones the input.

References donor_selector_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_hbond_energy_cutoff ( core::Real const &  input_value)

Set the threshold for considering something to be a hydrogen bond.

References hbond_energy_cutoff_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_max_allowed_oversaturated ( core::Size const  max_allowed)

Set the maximum allowed number of instances of an oversaturated hydrogen bond acceptor.

References max_allowed_oversaturated_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::set_scorefxn ( core::scoring::ScoreFunctionCOP  sfxn_in)

Set the scorefunction.

Clones the input.

References scorefxn_.

Referenced by parse_my_tag().

Member Data Documentation

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::acceptor_selector_
private

Optional residue selector for the residues that could possibly be accepting hydrogen bonds.

Referenced by acceptor_selector(), compute(), OversaturatedHbondAcceptorFilter(), and set_acceptor_selector().

bool protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::consider_mainchain_only_
private

Should we only consider mainchain hydrogen bond donors and acceptors?

Defaults to true.

Referenced by compute(), consider_mainchain_only(), and set_consider_mainchain_only().

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::donor_selector_
private

Optional residue selector for the residues that could possibly be donating hydrogen bonds.

Referenced by compute(), donor_selector(), OversaturatedHbondAcceptorFilter(), and set_donor_selector().

core::Real protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::hbond_energy_cutoff_
private

The energy cutoff for considering something to be a hydrogen bond.

Defaults to -0.1.

Referenced by hbond_energy_cutoff(), and set_hbond_energy_cutoff().

core::Size protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::max_allowed_oversaturated_
private

What is the maximum allowed number of instances of an oversaturated hydrogen bond acceptor?

Defaults to 0.

Referenced by max_allowed_oversaturated(), and set_max_allowed_oversaturated().

core::scoring::ScoreFunctionOP protocols::cyclic_peptide::OversaturatedHbondAcceptorFilter::scorefxn_
private

The scorefunction to use for hydrogen bond scoring.

If no scorefunction is provided, then the default scorefunction is used.

Referenced by compute(), OversaturatedHbondAcceptorFilter(), scorefxn(), and set_scorefxn().


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