Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_filters::BuriedSurfaceAreaFilter Class Reference

Calculates buried surface area (exposed surface area minus total surface area, on a per-residue basis). Accepts a residue selector to allow buried subsets to be considered. More...

#include <BuriedSurfaceAreaFilter.hh>

Inheritance diagram for protocols::simple_filters::BuriedSurfaceAreaFilter:
Inheritance graph
[legend]

Public Member Functions

 BuriedSurfaceAreaFilter ()
 
 ~BuriedSurfaceAreaFilter () override
 
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 data to a stream More...
 
std::string name () const override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Filter in Rosetta Scripts) More...
 
protocols::filters::FilterOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::filters::FilterOP clone () const override
 required in the context of the parser/scripting scheme More...
 
void set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
 Sets the residue selector to use to select a subset of residues for which to calculate buried surface area. More...
 
void set_select_only_FAMILYVW (bool const setting)
 Set whether only hydrophobic residues and alanine (FAMILYVW) are considered. False by default. More...
 
void set_cutoff_buried_surface_area (core::Real const &setting)
 Set the cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded. More...
 
void set_filter_out_low (bool const setting)
 Set whether structures with less than the cutoff buried area or greater than the cutoff buried area are discarded. More...
 
void set_atom_mode (std::string const &setting)
 Set the atom mode (the subset of atoms to use for the calculation) by string. More...
 
void set_atom_mode (BSAF_mode const setting)
 Set the atom mode (the subset of atoms to use for the calculation). More...
 
core::select::residue_selector::ResidueSelectorCOP residue_selector () const
 Gets the residue selector to use to select a subset of residues for which to calculate buried surface area. More...
 
bool select_only_FAMILYVW () const
 Get whether only hydrophobic residues and alanine (FAMILYVW) are considered. False by default. More...
 
core::Real const & cutoff_buried_surface_area () const
 Get the cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded. More...
 
bool filter_out_low () const
 Get whether structures with less than the cutoff buried area or greater than the cutoff buried area are discarded. More...
 
BSAF_mode atom_mode () const
 Get the atom mode (the subset of atoms to use). More...
 
- 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

bool compute (std::ostream &os, core::pose::Pose const &pose, core::Real &buried_surf_area) const
 Common function called by apply(), report(), and report_sm(). More...
 
bool is_allowed_type (char const oneletter_code) const
 Is this a residue type for which we can calculate a total SASA value? More...
 
bool is_FAMILYVW (char const oneletter_code) const
 Is this a hydrophobic residue type (FAMILYVW)? More...
 
void compute_residue_selection (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset &selection) const
 Given a pose (input) and a ResidueSubset (output), compute the residues that should be operated on. More...
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP residue_selector_
 A residue selector to use to select a subset of residues for which to calculate buried surface area. Unused if not specified (i.e. all residues are used by default). More...
 
bool select_only_FAMILYVW_
 If true, only hydrophobic residues and alanine (FAMILYVW) are considered. False by default. More...
 
BSAF_mode atom_mode_
 The subset of atoms to consider. Default is all atoms, but only hydrophobic atoms or only polar atoms are both possible, too. More...
 
core::Real cutoff_area_
 The cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded. More...
 
bool filter_out_low_
 If true, structures with less than the cutoff buried area are discrded. More...
 

Additional Inherited Members

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

Detailed Description

Calculates buried surface area (exposed surface area minus total surface area, on a per-residue basis). Accepts a residue selector to allow buried subsets to be considered.

Constructor & Destructor Documentation

protocols::simple_filters::BuriedSurfaceAreaFilter::BuriedSurfaceAreaFilter ( )
protocols::simple_filters::BuriedSurfaceAreaFilter::~BuriedSurfaceAreaFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::BuriedSurfaceAreaFilter::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 protocols::simple_filters::TR().

BSAF_mode protocols::simple_filters::BuriedSurfaceAreaFilter::atom_mode ( ) const
inline

Get the atom mode (the subset of atoms to use).

References atom_mode_.

Referenced by compute().

std::string protocols::simple_filters::BuriedSurfaceAreaFilter::class_name ( )
static
protocols::filters::FilterOP protocols::simple_filters::BuriedSurfaceAreaFilter::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

bool protocols::simple_filters::BuriedSurfaceAreaFilter::compute ( std::ostream &  os,
core::pose::Pose const &  pose,
core::Real buried_surf_area 
) const
private
void protocols::simple_filters::BuriedSurfaceAreaFilter::compute_residue_selection ( core::pose::Pose const &  pose,
core::select::residue_selector::ResidueSubset selection 
) const
private

Given a pose (input) and a ResidueSubset (output), compute the residues that should be operated on.

References is_allowed_type(), is_FAMILYVW(), core::chemical::ResidueTypeBase::name1(), residue_selector(), core::pose::Pose::residue_type(), select_only_FAMILYVW(), and core::pose::Pose::total_residue().

Referenced by compute().

core::Real const& protocols::simple_filters::BuriedSurfaceAreaFilter::cutoff_buried_surface_area ( ) const
inline

Get the cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded.

References cutoff_area_.

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::BuriedSurfaceAreaFilter::filter_out_low ( ) const
inline

Get whether structures with less than the cutoff buried area or greater than the cutoff buried area are discarded.

If true, structures with less than the cutoff buried area are discrded.

References filter_out_low_.

Referenced by compute(), and parse_my_tag().

protocols::filters::FilterOP protocols::simple_filters::BuriedSurfaceAreaFilter::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

bool protocols::simple_filters::BuriedSurfaceAreaFilter::is_allowed_type ( char const  oneletter_code) const
private

Is this a residue type for which we can calculate a total SASA value?

Referenced by compute(), and compute_residue_selection().

bool protocols::simple_filters::BuriedSurfaceAreaFilter::is_FAMILYVW ( char const  oneletter_code) const
private

Is this a hydrophobic residue type (FAMILYVW)?

Referenced by compute_residue_selection().

std::string protocols::simple_filters::BuriedSurfaceAreaFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

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

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

References compute().

core::Real protocols::simple_filters::BuriedSurfaceAreaFilter::report_sm ( core::pose::Pose const &  pose) const
overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References compute(), and protocols::simple_filters::TR().

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::BuriedSurfaceAreaFilter::residue_selector ( ) const
inline

Gets the residue selector to use to select a subset of residues for which to calculate buried surface area.

References residue_selector_.

Referenced by compute_residue_selection().

bool protocols::simple_filters::BuriedSurfaceAreaFilter::select_only_FAMILYVW ( ) const
inline

Get whether only hydrophobic residues and alanine (FAMILYVW) are considered. False by default.

The selection FAMILYVW is combined with the residue selector, if specified, using AND logic.

References select_only_FAMILYVW_.

Referenced by compute_residue_selection(), and parse_my_tag().

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_atom_mode ( std::string const &  setting)

Set the atom mode (the subset of atoms to use for the calculation) by string.

References protocols::simple_filters::BSAF_all_atoms, protocols::simple_filters::BSAF_hydrophobic_atoms, and protocols::simple_filters::BSAF_polar_atoms.

Referenced by parse_my_tag().

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_atom_mode ( BSAF_mode const  setting)

Set the atom mode (the subset of atoms to use for the calculation).

References atom_mode_, and protocols::simple_filters::BSAF_end_of_list.

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_cutoff_buried_surface_area ( core::Real const &  setting)

Set the cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded.

References cutoff_area_.

Referenced by parse_my_tag().

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_filter_out_low ( bool const  setting)

Set whether structures with less than the cutoff buried area or greater than the cutoff buried area are discarded.

If true, structures with less than the cutoff buried area are discrded.

References filter_out_low_.

Referenced by parse_my_tag().

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP  selector_in)

Sets the residue selector to use to select a subset of residues for which to calculate buried surface area.

Copies the input owning pointer; does not clone. This means that residue selectors could be shared with other Rosetta modules.

References residue_selector_.

Referenced by parse_my_tag().

void protocols::simple_filters::BuriedSurfaceAreaFilter::set_select_only_FAMILYVW ( bool const  setting)

Set whether only hydrophobic residues and alanine (FAMILYVW) are considered. False by default.

The selection FAMILYVW is combined with the residue selector, if specified, using AND logic.

References select_only_FAMILYVW_.

Referenced by parse_my_tag().

Member Data Documentation

BSAF_mode protocols::simple_filters::BuriedSurfaceAreaFilter::atom_mode_
private

The subset of atoms to consider. Default is all atoms, but only hydrophobic atoms or only polar atoms are both possible, too.

Referenced by atom_mode(), and set_atom_mode().

core::Real protocols::simple_filters::BuriedSurfaceAreaFilter::cutoff_area_
private

The cutoff buried surface area below which (or above which, if filter_out_low_ is false) structures are discarded.

Defaults to 500 square Angstroms (arbitrarily chosen).

Referenced by cutoff_buried_surface_area(), and set_cutoff_buried_surface_area().

bool protocols::simple_filters::BuriedSurfaceAreaFilter::filter_out_low_
private

If true, structures with less than the cutoff buried area are discrded.

True by default.

Referenced by filter_out_low(), and set_filter_out_low().

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::BuriedSurfaceAreaFilter::residue_selector_
private

A residue selector to use to select a subset of residues for which to calculate buried surface area. Unused if not specified (i.e. all residues are used by default).

Referenced by residue_selector(), and set_residue_selector().

bool protocols::simple_filters::BuriedSurfaceAreaFilter::select_only_FAMILYVW_
private

If true, only hydrophobic residues and alanine (FAMILYVW) are considered. False by default.

The selection FAMILYVW is combined with the residue selector, if specified, using AND logic.

Referenced by select_only_FAMILYVW(), and set_select_only_FAMILYVW().


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