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protocols::protein_interface_design::filters::HbondsToResidueFilter Class Reference

returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class More...

#include <HbondsToResidueFilter.hh>

Inheritance diagram for protocols::protein_interface_design::filters::HbondsToResidueFilter:
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Public Types

typedef core::Real Real
 
typedef core::Size Size
 

Public Member Functions

 HbondsToResidueFilter ()
 Default constructor. More...
 
 HbondsToResidueFilter (core::Size const resnum, core::Size const partners, Real const &energy_cutoff=-0.5, bool const backbone=false, bool const sidechain=true, bool const bb_bb=true, bool const from_other_chains=true, bool const from_same_chain=true)
 Constructor. More...
 
 HbondsToResidueFilter (HbondsToResidueFilter const &src)
 Copy constructor. More...
 
bool apply (core::pose::Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
protocols::filters::FilterOP clone () const override
 
protocols::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::Size compute (core::pose::Pose const &pose, core::Size const resnum_rosetta) const
 Actually compute the number of hydrogen bonds to the target residue. More...
 
 ~HbondsToResidueFilter () override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
void set_partners (core::Size const val)
 Set the minimum number of H-bond partners that this residue must have for the filter to pass. More...
 
core::Size partners () const
 Get the minimum number of H-bond partners that this residue must have for the filter to pass. More...
 
void set_energy_cutoff (core::Real const val)
 Set the threshold for the hbond score term at which two residues are counted as being hydrogen bonded. More...
 
core::Real energy_cutoff () const
 Get the threshold for the hbond score term at which two residues are counted as being hydrogen bonded. More...
 
void set_backbone (bool const val)
 Set whether to include backbone hydrogen bonds. More...
 
void set_sidechain (bool const val)
 Set whether to include backbone hydrogen bonds. More...
 
void set_bb_bb (bool const val)
 Set whether to include backbone-backbone hydrogen bonds. More...
 
bool backbone () const
 Get whether to include backbone hydrogen bonds. More...
 
bool sidechain () const
 Get whether to include backbone hydrogen bonds. More...
 
bool bb_bb () const
 Get whether to include backbone-backbone hydrogen bonds. More...
 
void set_resnum (std::string const &input)
 Set the residue number (as a string to be parsed at apply time). More...
 
void set_resnum (core::Size const val)
 Set the residue number (as an integer – Rosetta numbering). More...
 
std::string resnum () const
 Get the residue number (a string to be parsed at apply time). More...
 
void set_from_other_chains (bool const val)
 Set whether hydrogen bonds from other chains should be counted. More...
 
bool from_other_chains () const
 Get whether hydrogen bonds from other chains should be counted. More...
 
void set_from_same_chain (bool const val)
 Set whether hydrogen bonds from the same chain should be counted. More...
 
bool from_same_chain () const
 Get whether hydrogen bonds from the same chain should be counted. More...
 
void set_scorefxn (core::scoring::ScoreFunctionCOP sfxn_in)
 Set the scorefunction to use for hbond calculation. More...
 
void set_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
 Set the ResidueSelector to use. 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 Attributes

std::string resnum_
 The current residue, stored as a string to be parsed at apply time. More...
 
core::Size partners_
 The minimum number of H-bond partners that this residue must have for the filter to pass. More...
 
Real energy_cutoff_
 The threshold for the hbond score term at which two residues are counted as being hydrogen bonded. More...
 
bool backbone_
 Include backbone hydrogen bonds? More...
 
bool sidechain_
 Include sidechain hydrogen bonds? More...
 
bool bb_bb_
 Include backbone-backbone hydrogen bonds? More...
 
bool from_other_chains_
 If true, hydrogen bonds from other chains will be counted. True by default. More...
 
bool from_same_chain_
 If true, hydrogen bonds from the same chain will be counted. True by default. More...
 
core::scoring::ScoreFunctionOP sfxn_
 Owning pointer to the scorefunction to use. More...
 
core::select::residue_selector::ResidueSelectorCOP selector_
 Owning pointer to a ResidueSelector, optionally used to select the residues to count. More...
 

Additional Inherited Members

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

Detailed Description

returns true if the number of hbonding partners to a particular residue exceeds a certain value This filter is useful in conjunction with DesignMinimizeHbonds class

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::protein_interface_design::filters::HbondsToResidueFilter::HbondsToResidueFilter ( )

Default constructor.

protocols::protein_interface_design::filters::HbondsToResidueFilter::HbondsToResidueFilter ( core::Size const  resnum,
core::Size const  partners,
Real const &  energy_cutoff = -0.5,
bool const  backbone = false,
bool const  sidechain = true,
bool const  bb_bb = true,
bool const  from_other_chains = true,
bool const  from_same_chain = true 
)

Constructor.

References energy_cutoff_, resnum(), and resnum_.

protocols::protein_interface_design::filters::HbondsToResidueFilter::HbondsToResidueFilter ( HbondsToResidueFilter const &  src)

Copy constructor.

References sfxn_.

protocols::protein_interface_design::filters::HbondsToResidueFilter::~HbondsToResidueFilter ( )
overridedefault

Member Function Documentation

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual

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

Implements protocols::filters::Filter.

References compute(), core::pose::parse_resnum(), partners_, resnum_, and protocols::protein_interface_design::filters::TR().

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::backbone ( ) const
inline

Get whether to include backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References backbone_.

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::bb_bb ( ) const
inline

Get whether to include backbone-backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References bb_bb_.

std::string protocols::protein_interface_design::filters::HbondsToResidueFilter::class_name ( )
static
protocols::filters::FilterOP protocols::protein_interface_design::filters::HbondsToResidueFilter::clone ( ) const
inlineoverridevirtual
core::Size protocols::protein_interface_design::filters::HbondsToResidueFilter::compute ( core::pose::Pose const &  pose,
core::Size const  resnum_rosetta 
) const
core::Real protocols::protein_interface_design::filters::HbondsToResidueFilter::energy_cutoff ( ) const
inline

Get the threshold for the hbond score term at which two residues are counted as being hydrogen bonded.

References energy_cutoff_.

protocols::filters::FilterOP protocols::protein_interface_design::filters::HbondsToResidueFilter::fresh_instance ( ) const
inlineoverridevirtual
bool protocols::protein_interface_design::filters::HbondsToResidueFilter::from_other_chains ( ) const
inline

Get whether hydrogen bonds from other chains should be counted.

References from_other_chains_.

Referenced by compute(), and parse_my_tag().

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::from_same_chain ( ) const
inline

Get whether hydrogen bonds from the same chain should be counted.

References from_same_chain_.

Referenced by compute(), and parse_my_tag().

std::string protocols::protein_interface_design::filters::HbondsToResidueFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
core::Size protocols::protein_interface_design::filters::HbondsToResidueFilter::partners ( ) const
inline

Get the minimum number of H-bond partners that this residue must have for the filter to pass.

References partners_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::protein_interface_design::filters::HbondsToResidueFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual
core::Real protocols::protein_interface_design::filters::HbondsToResidueFilter::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), core::pose::parse_resnum(), and resnum().

std::string protocols::protein_interface_design::filters::HbondsToResidueFilter::resnum ( ) const
inline

Get the residue number (a string to be parsed at apply time).

References resnum_.

Referenced by HbondsToResidueFilter(), parse_my_tag(), report(), and report_sm().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_backbone ( bool const  val)
inline

Set whether to include backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References backbone_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_bb_bb ( bool const  val)
inline

Set whether to include backbone-backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References bb_bb_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_energy_cutoff ( core::Real const  val)
inline

Set the threshold for the hbond score term at which two residues are counted as being hydrogen bonded.

References energy_cutoff_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_from_other_chains ( bool const  val)
inline

Set whether hydrogen bonds from other chains should be counted.

References from_other_chains_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_from_same_chain ( bool const  val)
inline

Set whether hydrogen bonds from the same chain should be counted.

References from_same_chain_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_partners ( core::Size const  val)
inline

Set the minimum number of H-bond partners that this residue must have for the filter to pass.

References partners_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_resnum ( std::string const &  input)
inline

Set the residue number (as a string to be parsed at apply time).

References resnum_.

Referenced by parse_my_tag(), and set_resnum().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_resnum ( core::Size const  val)

Set the residue number (as an integer – Rosetta numbering).

References set_resnum(), and protocols::hybridization::val.

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_scorefxn ( core::scoring::ScoreFunctionCOP  sfxn_in)

Set the scorefunction to use for hbond calculation.

References sfxn_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_selector ( core::select::residue_selector::ResidueSelectorCOP  selector_in)

Set the ResidueSelector to use.

Only hydrogen bonds between this residue and the residues selected by the ResidueSelector will be counted, if a ResidueSelector is provided.

References selector_.

Referenced by parse_my_tag().

void protocols::protein_interface_design::filters::HbondsToResidueFilter::set_sidechain ( bool const  val)
inline

Set whether to include backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References sidechain_, and protocols::hybridization::val.

Referenced by parse_my_tag().

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::sidechain ( ) const
inline

Get whether to include backbone hydrogen bonds.

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

References sidechain_.

Member Data Documentation

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::backbone_
private

Include backbone hydrogen bonds?

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

Referenced by backbone(), compute(), and set_backbone().

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::bb_bb_
private

Include backbone-backbone hydrogen bonds?

I'm pretty sure that this is not implemented properly. (VKM – 6 July 2015).

Referenced by bb_bb(), compute(), and set_bb_bb().

Real protocols::protein_interface_design::filters::HbondsToResidueFilter::energy_cutoff_
private

The threshold for the hbond score term at which two residues are counted as being hydrogen bonded.

Referenced by compute(), energy_cutoff(), HbondsToResidueFilter(), and set_energy_cutoff().

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::from_other_chains_
private

If true, hydrogen bonds from other chains will be counted. True by default.

Referenced by from_other_chains(), and set_from_other_chains().

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::from_same_chain_
private

If true, hydrogen bonds from the same chain will be counted. True by default.

Referenced by from_same_chain(), and set_from_same_chain().

core::Size protocols::protein_interface_design::filters::HbondsToResidueFilter::partners_
private

The minimum number of H-bond partners that this residue must have for the filter to pass.

Referenced by apply(), partners(), and set_partners().

std::string protocols::protein_interface_design::filters::HbondsToResidueFilter::resnum_
private

The current residue, stored as a string to be parsed at apply time.

This could be a PDB number (e.g. 32A), a Rosetta number (e.g. 32), or a reference pose number (e.g. refpose(snapshot1,34).

Referenced by apply(), HbondsToResidueFilter(), resnum(), and set_resnum().

core::select::residue_selector::ResidueSelectorCOP protocols::protein_interface_design::filters::HbondsToResidueFilter::selector_
private

Owning pointer to a ResidueSelector, optionally used to select the residues to count.

Only hydrogen bonds between this residue and the residues selected by the ResidueSelector will be counted, if a ResidueSelector is provided.

Referenced by compute(), and set_selector().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::filters::HbondsToResidueFilter::sfxn_
private

Owning pointer to the scorefunction to use.

Referenced by compute(), HbondsToResidueFilter(), and set_scorefxn().

bool protocols::protein_interface_design::filters::HbondsToResidueFilter::sidechain_
private

Include sidechain hydrogen bonds?

I'm not sure that this is implemented properly. (VKM – 6 July 2015).

Referenced by compute(), set_sidechain(), and sidechain().


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