core::scoring::aa_composition_energy::AACompositionPropertiesSet Class Reference

AACompositionPropertiesSet, a helper class that stores: More...

#include <AACompositionEnergySetup.hh>

Inheritance diagram for core::scoring::aa_composition_energy::AACompositionPropertiesSet:

Public Member Functions
	AACompositionPropertiesSet ()
	Default constructor for AACompositionPropertiesSet. More...
	AACompositionPropertiesSet (utility::vector1< std::string > const &included_type_strings, utility::vector1< std::string > const &excluded_type_strings, utility::vector1< std::string > const &included_properties_strings, utility::vector1< std::string > const &or_properties_strings, utility::vector1< std::string > const &excluded_properties_strings)
	Constructor for AACompositionPropertiesSet that takes lists of included and excluded properties. More...
	AACompositionPropertiesSet (AACompositionPropertiesSet const &src)
	Copy constructor for AACompositionPropertiesSet. More...
	~AACompositionPropertiesSet () override
	Default destructor for AACompositionPropertiesSet. More...
virtual AACompositionPropertiesSetOP	clone () const
	Clone: create a copy of this object, and return an owning pointer to the copy. More...
bool	properties_match_this (core::chemical::ResidueType const &rsd_type) const
	Check whether the properties of a residue type match those of this set. More...
void	parse_included_types (utility::vector1< std::string > const &typelist)
	Take a list of included type strings and add it to the list of included types, checking that none of the types has already been added. More...
void	parse_excluded_types (utility::vector1< std::string > const &typelist)
	Take a list of excluded type strings and add it to the list of excluded types, checking that none of the types has already been added. More...
void	parse_included_properites (utility::vector1< std::string > const &proplist)
	Take a list of included property strings and parse it. More...
void	parse_or_properties (utility::vector1< std::string > const &proplist)
	Take a list of included property strings and parse it. More...
void	parse_excluded_properites (utility::vector1< std::string > const &proplist)
	Take a list of excluded property strings and parse it. More...
std::string	one_line_report () const
	Generate a one-line summary of the properties stored in this AACompositionPropertySet. More...

Private Member Functions
void	add_included_type (std::string const &type)
	Add a type to the list of types that are always counted. More...
void	add_excluded_type (std::string const &type)
	Add a type to the list of types that are never counted. More...
void	add_included_property (core::chemical::ResidueProperty const property)
	Add a property to the list of properties that must be present. More...
void	add_or_property (core::chemical::ResidueProperty const property)
	Add a property to the list of properties that, if present, result in the residue being counted if it's not in the excluded_types_ or excluded_properties_ lists. More...
void	add_excluded_property (core::chemical::ResidueProperty const property)
	Add a property to the list of properties that must not be present. More...
core::chemical::ResidueProperty	parse_property (std::string const &name) const
	Convert a property name to a ResidueProperty enum. More...

Private Attributes
utility::vector1< std::string >	included_types_
	Residue names that are counted. More...
utility::vector1< std::string >	excluded_types_
	Residue names that are not counted. More...
utility::vector1 < core::chemical::ResidueProperty >	included_properties_
	Properties that a residue MUST have. More...
utility::vector1 < core::chemical::ResidueProperty >	or_properties_
	Properties, any of which is sufficient for a residue to be counted if it's not in the NOT_TYPE or NOT_PROPERTIES lists. More...
utility::vector1 < core::chemical::ResidueProperty >	excluded_properties_
	Properties that a residue MUST NOT have. More...

Detailed Description

AACompositionPropertiesSet, a helper class that stores:

• names of residue types that WILL be counted (TYPE)
• names of residue types that WILL NOT be counted (NOT_TYPE)
• properties that MUST be present in order for a residue to be counted (PROPERTIES).
• properties, any of which is sufficient for a residue to be counted (OR_PROPERTIES).
• properties that MUST NOT be present in order for a residue to be counted (NOT_PROPERTIES).

The logic is as follows: a residue is counted if and only if [any TYPE matches] OR [ (no NOT_TYPE matches) AND ( {all PROPERTIES match} OR {any OR_PROPERTIES match} OR {no TYPEs defined AND no PROPERTIES defined AND no OR_PROPERTIES defined } ) AND ( no NOT_PROPERTIES match) ]

Constructor & Destructor Documentation

core::scoring::aa_composition_energy::AACompositionPropertiesSet::AACompositionPropertiesSet

(

)

Default constructor for AACompositionPropertiesSet.

core::scoring::aa_composition_energy::AACompositionPropertiesSet::AACompositionPropertiesSet	(	utility::vector1< std::string > const &	included_type_strings,
		utility::vector1< std::string > const &	excluded_type_strings,
		utility::vector1< std::string > const &	included_properties_strings,
		utility::vector1< std::string > const &	or_properties_strings,
		utility::vector1< std::string > const &	excluded_properties_strings
	)

Constructor for AACompositionPropertiesSet that takes lists of included and excluded properties.

References parse_excluded_properites(), parse_excluded_types(), parse_included_properites(), parse_included_types(), and parse_or_properties().

core::scoring::aa_composition_energy::AACompositionPropertiesSet::AACompositionPropertiesSet

(

AACompositionPropertiesSet const &

src

)

Copy constructor for AACompositionPropertiesSet.

core::scoring::aa_composition_energy::AACompositionPropertiesSet::~AACompositionPropertiesSet ( )

overridedefault

Default destructor for AACompositionPropertiesSet.

Member Function Documentation

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::add_excluded_property ( core::chemical::ResidueProperty const  property )

private

Add a property to the list of properties that must not be present.

Checks that it hasn't yet been added to any list.

References excluded_properties_, included_properties_, and or_properties_.

Referenced by parse_excluded_properites().

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::add_excluded_type ( std::string const &  type )

private

Add a type to the list of types that are never counted.

Checks that it hasn't yet been added to any list.

References excluded_types_, and included_types_.

Referenced by parse_excluded_types().

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::add_included_property ( core::chemical::ResidueProperty const  property )

private

Add a property to the list of properties that must be present.

Checks that it hasn't yet been added to any list.

References excluded_properties_, included_properties_, and or_properties_.

Referenced by parse_included_properites().

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::add_included_type ( std::string const &  type )

private

Add a type to the list of types that are always counted.

Checks that it hasn't yet been added to any list.

References excluded_types_, and included_types_.

Referenced by parse_included_types().

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::add_or_property ( core::chemical::ResidueProperty const  property )

private

Add a property to the list of properties that, if present, result in the residue being counted if it's not in the excluded_types_ or excluded_properties_ lists.

Checks that it hasn't yet been added to any list.

References excluded_properties_, included_properties_, and or_properties_.

Referenced by parse_or_properties().

AACompositionPropertiesSetOP core::scoring::aa_composition_energy::AACompositionPropertiesSet::clone ( ) const

virtual

Clone: create a copy of this object, and return an owning pointer to the copy.

std::string core::scoring::aa_composition_energy::AACompositionPropertiesSet::one_line_report

(

)

const

Generate a one-line summary of the properties stored in this AACompositionPropertySet.

References excluded_properties_, excluded_types_, core::chemical::ResidueProperties::get_string_from_property(), included_properties_, included_types_, and or_properties_.

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_excluded_properites

(

utility::vector1< std::string > const &

proplist

)

Take a list of excluded property strings and parse it.

Populates the excluded_properties_ vector based on the properties named in the list.

References add_excluded_property(), excluded_properties_, and parse_property().

Referenced by AACompositionPropertiesSet().

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_excluded_types

(

utility::vector1< std::string > const &

typelist

)

Take a list of excluded type strings and add it to the list of excluded types, checking that none of the types has already been added.

Populates the excluded_types_ vector based on the types named in the list.

References add_excluded_type(), and excluded_types_.

Referenced by AACompositionPropertiesSet().

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_included_properites

(

utility::vector1< std::string > const &

proplist

)

Take a list of included property strings and parse it.

Populates the included_properties_ vector based on the properties named in the list.

References add_included_property(), included_properties_, and parse_property().

Referenced by AACompositionPropertiesSet().

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_included_types

(

utility::vector1< std::string > const &

typelist

)

Take a list of included type strings and add it to the list of included types, checking that none of the types has already been added.

Populates the included_types_ vector based on the types named in the list.

References add_included_type(), and included_types_.

Referenced by AACompositionPropertiesSet().

void core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_or_properties

(

utility::vector1< std::string > const &

proplist

)

Take a list of included property strings and parse it.

Populates the included_properties_ vector based on the properties named in the list.

References add_or_property(), or_properties_, and parse_property().

Referenced by AACompositionPropertiesSet().

core::chemical::ResidueProperty core::scoring::aa_composition_energy::AACompositionPropertiesSet::parse_property ( std::string const &  name ) const

private

Convert a property name to a ResidueProperty enum.

Throws an error if the property name is not recognized.

References core::chemical::ResidueProperties::get_property_from_string(), and core::chemical::NO_PROPERTY.

Referenced by parse_excluded_properites(), parse_included_properites(), and parse_or_properties().

bool core::scoring::aa_composition_energy::AACompositionPropertiesSet::properties_match_this ( core::chemical::ResidueType const &  rsd_type ) const

inline

Check whether the properties of a residue type match those of this set.

This checks:

1. Whether the residue name matches an exlcuded name -> return false.
2. Whether the residue name matches an included name -> return true.
3. Whether the residue properties match an excluded property -> return false.
4. Whether all three of the included_types and or_properties and included_property lists are empty -> return true.
5. Whether any or_property is matched -> return true.
6. Whether there exist any proprties to match -> if not, return false.
7. Whether any properties are not matched -> return false. Returns true

References excluded_properties_, excluded_types_, core::chemical::ResidueTypeBase::has_property(), included_properties_, included_types_, core::chemical::ResidueTypeBase::name3(), and or_properties_.

Member Data Documentation

utility::vector1< core::chemical::ResidueProperty > core::scoring::aa_composition_energy::AACompositionPropertiesSet::excluded_properties_

private

Properties that a residue MUST NOT have.

Referenced by add_excluded_property(), add_included_property(), add_or_property(), one_line_report(), parse_excluded_properites(), and properties_match_this().

utility::vector1< std::string > core::scoring::aa_composition_energy::AACompositionPropertiesSet::excluded_types_

private

Residue names that are not counted.

Referenced by add_excluded_type(), add_included_type(), one_line_report(), parse_excluded_types(), and properties_match_this().

utility::vector1< core::chemical::ResidueProperty > core::scoring::aa_composition_energy::AACompositionPropertiesSet::included_properties_

private

Properties that a residue MUST have.

Referenced by add_excluded_property(), add_included_property(), add_or_property(), one_line_report(), parse_included_properites(), and properties_match_this().

utility::vector1< std::string > core::scoring::aa_composition_energy::AACompositionPropertiesSet::included_types_

private

Residue names that are counted.

Referenced by add_excluded_type(), add_included_type(), one_line_report(), parse_included_types(), and properties_match_this().

utility::vector1< core::chemical::ResidueProperty > core::scoring::aa_composition_energy::AACompositionPropertiesSet::or_properties_

private

Properties, any of which is sufficient for a residue to be counted if it's not in the NOT_TYPE or NOT_PROPERTIES lists.

Referenced by add_excluded_property(), add_included_property(), add_or_property(), one_line_report(), parse_or_properties(), and properties_match_this().

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

• src/core/scoring/aa_composition_energy/AACompositionEnergySetup.hh
• src/core/scoring/aa_composition_energy/AACompositionEnergySetup.cc