AACompositionEnergySetup, a helper class for the AACompositionEnergy energy method that stores all of its setup data. More...

#include <AACompositionEnergySetup.hh>

Inheritance diagram for core::scoring::aa_composition_energy::AACompositionEnergySetup:

[legend]

Public Member Functions
	AACompositionEnergySetup ()
	Default constructor for AACompositionEnergySetup. More...

	AACompositionEnergySetup (AACompositionEnergySetup const &src)
	Copy constructor for AACompositionEnergySetup. More...

	~AACompositionEnergySetup () override
	Default destructor for AACompositionEnergySetup. More...

virtual AACompositionEnergySetupOP	clone () const
	Clone: create a copy of this object, and return an owning pointer to the copy. More...

void	reset ()
	Reset all data in this data storage object. More...

void	initialize_from_file (std::string const &filename)
	Initialize from a .comp file. More...

void	initialize_from_file_contents (std::string const &filecontents)
	Initialize from a string in the format of a .comp file. More...

std::string	get_tailfunction_name (TailFunction const tf) const
	Get tail function name from enum. More...

TailFunction	get_tailfunction_from_name (std::string const &name) const
	Get tail function enum from name. More...

bool	use_fract_ranges (core::Size const index) const
	Look up whether we're using absolute (return false) or fractional (return true) penalty ranges. More...

bool	use_fract_ranges_any () const
	Determine whether ANY of the property sets of this helper object use fractional ranges. More...

bool	use_fract_expected_values_any () const
	Determine whether ANY of the property sets of this helper object use fractional expected values. More...

core::Real	property_penalty (signed long const delta_expected, core::Size const property_set_index) const
	Look up the penalty for a property set of internal index property_set_index, given a deviation from the desired count given by delta_expected. More...

core::Real	fract_property_penalty (core::Real const delta_fract, core::Size const property_set_index) const
	Look up the penalty for a property set of internal index property_set_index, given a fractional content given by fract. More...

core::Size	n_property_sets () const
	Get the number of sets of properties that we'll be counting. More...

signed long	expected_by_properties_absolute (core::Size const index) const
	Get the expected absolute number of residues for a given set of properties, by property set index. More...

core::Real	expected_by_properties_fraction (core::Size const index) const
	Get the expected fractional number of residues for a given set of properties, by property set index. More...

void	property_set_indices_matching_residue (core::chemical::ResidueType const &rsd_type, utility::vector1< core::Size > &indices_out) const
	Get the indices of all of the property sets corresponding to the current residue. More...

std::string	report () const
	Get a summary of the data stored in this object. More...

Private Member Functions
void	parse_penalty_definitions (utility::vector1< std::string > const &lines)
	Parse out penalty definition blocks from the data read from file. More...

void	parse_a_penalty_definition (utility::vector1< std::string > const &lines)
	Parse out penalty definition from a single block of lines from file. More...

void	check_data () const
	Do some final checks to ensure that data were loaded properly. More...

core::Real	interpolate_property_penalties (core::Real const &delta_fract, core::Size const index) const
	Calculate a penalty, linearly interpolating between penalty values. More...

core::Real	out_of_bounds_func (core::Size const index, signed long const delta_expected, bool const before) const
	Calculate the out-of-bounds behaviour of the penalty function and return the penalty value. More...

core::Real	fract_out_of_bounds_func (core::Size const index, core::Real const &delta_fract, bool const before) const
	Calculate the out-of-bounds behaviour of the penalty function and return the penalty value. This version is for cases with fractional desired contents. More...

core::Real	const_out_of_bounds_func (bool const before, core::Size const index) const
	Return a constant value for an out-of-bounds behaviour. More...

core::Real	linear_fract_out_of_bounds_func (bool const before, core::Size const index, core::Real const &delta_fract) const
	Return a linear value for an out-of-bounds behaviour. This version is for fractional penalty ranges. More...

core::Real	linear_out_of_bounds_func (bool const before, core::Size const index, signed long const delta_expected) const
	Return a linear value for an out-of-bounds behaviour. More...

core::Real	quadratic_fract_out_of_bounds_func (bool const before, core::Size const index, core::Real const &delta_fract) const
	Return a quadratic value for an out-of-bounds behaviour. This version is for fractional penalty ranges. More...

core::Real	quadratic_out_of_bounds_func (bool const before, core::Size const index, signed long const delta_expected) const
	Return a quadratic value for an out-of-bounds behaviour. More...

Private Attributes
utility::vector1 < AACompositionPropertiesSetOP >	property_sets_
	The residue property sets that we'll be counting. More...

utility::vector1< core::Real >	expected_by_properties_fraction_
	The expected number of residues for each set of properties (by property set index), as a fraction (from 0 to 1) of total. More...

utility::vector1< signed long >	expected_by_properties_absolute_
	The expected number of residues for each set of properties (by property set index), as an absolute number. More...

utility::vector1 < utility::vector1< core::Real > >	property_penalties_
	Penalties for each residue count (relative to expected) and each property set. More...

utility::vector1 < utility::vector1< core::Real > >	property_penalty_fracts_
	For each set of property penalties, this is the corresponding fractional abundance. More...

utility::vector1< bool >	use_fract_ranges_
	For a given property set, should we use absolute ranges (false) or fractional ranges (true)? More...

utility::vector1< std::pair < signed long, signed long > >	property_deviation_ranges_
	Deviation ranges for each property set. More...

utility::vector1< std::pair < core::Real, core::Real > >	fract_property_deviation_ranges_
	Deviation ranges for each property set, expressed as a fraction of total residues. More...

utility::vector1< std::pair < TailFunction, TailFunction > >	property_tailfunctions_
	The behaviours at the end of the user-defined range for each property set. More...

Detailed Description

AACompositionEnergySetup, a helper class for the AACompositionEnergy energy method that stores all of its setup data.

Constructor & Destructor Documentation

core::scoring::aa_composition_energy::AACompositionEnergySetup::AACompositionEnergySetup ( )

Default constructor for AACompositionEnergySetup.

core::scoring::aa_composition_energy::AACompositionEnergySetup::AACompositionEnergySetup ( AACompositionEnergySetup const & src )

Copy constructor for AACompositionEnergySetup.

References check_data(), and property_sets_.

core::scoring::aa_composition_energy::AACompositionEnergySetup::~AACompositionEnergySetup ( )

overridedefault

Default destructor for AACompositionEnergySetup.

Member Function Documentation

void core::scoring::aa_composition_energy::AACompositionEnergySetup::check_data ( ) const

private

Do some final checks to ensure that data were loaded properly.

References expected_by_properties_absolute_, expected_by_properties_fraction_, fract_property_deviation_ranges_, property_deviation_ranges_, property_penalties_, property_penalty_fracts_, property_sets_, property_tailfunctions_, core::scoring::aa_composition_energy::TR(), and use_fract_ranges_.

Referenced by AACompositionEnergySetup(), initialize_from_file(), and initialize_from_file_contents().

AACompositionEnergySetupOP core::scoring::aa_composition_energy::AACompositionEnergySetup::clone ( ) const

virtual

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

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::const_out_of_bounds_func	(	bool const	before,
		core::Size const	index
	)		const

inlineprivate

Return a constant value for an out-of-bounds behaviour.

Inputs are:

Parameters

[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.
[in]	property	If true, we're counting property sets. If false, we're counting residue types.
[in]	index	The index in the list of properties or residue types that we're counting.

References property_penalties_.

Referenced by fract_out_of_bounds_func(), and out_of_bounds_func().

signed long core::scoring::aa_composition_energy::AACompositionEnergySetup::expected_by_properties_absolute ( core::Size const index ) const

inline

Get the expected absolute number of residues for a given set of properties, by property set index.

Warning! For speed, there's no check that the index is in range!

References expected_by_properties_absolute_.

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::expected_by_properties_fraction ( core::Size const index ) const

inline

Get the expected fractional number of residues for a given set of properties, by property set index.

Warning! For speed, there's no check that the index is in range!

References expected_by_properties_fraction_.

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::fract_out_of_bounds_func	(	core::Size const	index,
		core::Real const &	delta_fract,
		bool const	before
	)		const

inlineprivate

Calculate the out-of-bounds behaviour of the penalty function and return the penalty value. This version is for cases with fractional desired contents.

Inputs are:

Parameters

[in]	index	The index in the list of properties or residue types that we're counting.
[in]	delta_fract	The fractional deviation from the expected count (e.g. if expected is 5% and observed is 3%, this is -0.02).
[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.

References const_out_of_bounds_func(), linear_fract_out_of_bounds_func(), property_tailfunctions_, quadratic_fract_out_of_bounds_func(), core::scoring::aa_composition_energy::tf_constant, core::scoring::aa_composition_energy::tf_linear, core::scoring::aa_composition_energy::tf_quadratic, and core::scoring::aa_composition_energy::tf_unknown.

Referenced by fract_property_penalty().

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::fract_property_penalty	(	core::Real const	delta_fract,
		core::Size const	property_set_index
	)		const

inline

Look up the penalty for a property set of internal index property_set_index, given a fractional content given by fract.

This version is for fractional property penalties.

Parameters

[in]	delta_fract	The measured fractional content of amino acids matching this property set in the pose or pose subset minus the expected.
[in]	property_set_index	The index of this property set.

References fract_out_of_bounds_func(), fract_property_deviation_ranges_, and interpolate_property_penalties().

TailFunction core::scoring::aa_composition_energy::AACompositionEnergySetup::get_tailfunction_from_name ( std::string const & name ) const

Get tail function enum from name.

This is slow; it calls get_tailfunction_name repeatedly. Intended only for use during setup.

References get_tailfunction_name(), core::scoring::aa_composition_energy::tf_end_of_list, and core::scoring::aa_composition_energy::tf_unknown.

Referenced by parse_a_penalty_definition().

std::string core::scoring::aa_composition_energy::AACompositionEnergySetup::get_tailfunction_name ( TailFunction const tf ) const

Get tail function name from enum.

References core::scoring::aa_composition_energy::tf_constant, core::scoring::aa_composition_energy::tf_linear, and core::scoring::aa_composition_energy::tf_quadratic.

Referenced by get_tailfunction_from_name().

void core::scoring::aa_composition_energy::AACompositionEnergySetup::initialize_from_file ( std::string const & filename )

Initialize from a .comp file.

References check_data(), protocols::abinitio::filename(), parse_penalty_definitions(), reset(), and core::scoring::aa_composition_energy::TR().

void core::scoring::aa_composition_energy::AACompositionEnergySetup::initialize_from_file_contents ( std::string const & filecontents )

Initialize from a string in the format of a .comp file.

Allows external code to initialize object without having it read directly from disk.

References check_data(), parse_penalty_definitions(), reset(), and core::scoring::aa_composition_energy::TR().

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::interpolate_property_penalties	(	core::Real const &	delta_fract,
		core::Size const	index
	)		const

inlineprivate

Calculate a penalty, linearly interpolating between penalty values.

Used only in the case of fractional penalty ranges.

Parameters

[in]	delta_fract	The fractional deviation from the expected count (e.g. if expected is 5% and observed is 3%, this is -0.02).
[in]	index	The index of the property set that we're counting. Note that, for speed, there is no check that this is in range.

References property_penalties_, and property_penalty_fracts_.

Referenced by fract_property_penalty().

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::linear_fract_out_of_bounds_func	(	bool const	before,
		core::Size const	index,
		core::Real const &	delta_fract
	)		const

inlineprivate

Return a linear value for an out-of-bounds behaviour. This version is for fractional penalty ranges.

This fits the first two or last two points to a straight line, then extends it. Inputs are:

Parameters

[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.
[in]	property	If true, we're counting property sets. If false, we're counting residue types.
[in]	index	The index in the list of properties or residue types that we're counting.
[in]	delta_fract	The fractional deviation from the expected count (e.g. if expected is 5% and observed is 3%, this is -0.02).

References protocols::match::upstream::b, fract_property_deviation_ranges_, property_penalties_, and property_penalty_fracts_.

Referenced by fract_out_of_bounds_func().

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::linear_out_of_bounds_func	(	bool const	before,
		core::Size const	index,
		signed long const	delta_expected
	)		const

inlineprivate

Return a linear value for an out-of-bounds behaviour.

This fits the first two or last two points to a straight line, then extends it. Inputs are:

Parameters

[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.
[in]	property	If true, we're counting property sets. If false, we're counting residue types.
[in]	index	The index in the list of properties or residue types that we're counting.
[in]	delta_expected	The deviation from the expected count.

References protocols::match::upstream::b, property_deviation_ranges_, and property_penalties_.

Referenced by out_of_bounds_func().

core::Size core::scoring::aa_composition_energy::AACompositionEnergySetup::n_property_sets ( ) const

inline

Get the number of sets of properties that we'll be counting.

References property_sets_.

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::out_of_bounds_func	(	core::Size const	index,
		signed long const	delta_expected,
		bool const	before
	)		const

inlineprivate

Calculate the out-of-bounds behaviour of the penalty function and return the penalty value.

Inputs are:

Parameters

[in]	index	The index in the list of properties or residue types that we're counting.
[in]	delta_expected	The deviation from the expected count.
[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.

References const_out_of_bounds_func(), linear_out_of_bounds_func(), property_tailfunctions_, quadratic_out_of_bounds_func(), core::scoring::aa_composition_energy::tf_constant, core::scoring::aa_composition_energy::tf_linear, core::scoring::aa_composition_energy::tf_quadratic, and core::scoring::aa_composition_energy::tf_unknown.

Referenced by property_penalty().

void core::scoring::aa_composition_energy::AACompositionEnergySetup::parse_a_penalty_definition ( utility::vector1< std::string > const & lines )

private

Parse out penalty definition from a single block of lines from file.

The lines vector should be the lines BETWEEN the PENALTY_DEFINITION and END_PENALTY_DEFINITION lines.

References expected_by_properties_absolute_, expected_by_properties_fraction_, fract_property_deviation_ranges_, get_tailfunction_from_name(), property_deviation_ranges_, property_penalties_, property_penalty_fracts_, property_sets_, property_tailfunctions_, core::scoring::aa_composition_energy::tf_quadratic, core::scoring::aa_composition_energy::tf_unknown, and use_fract_ranges_.

Referenced by parse_penalty_definitions().

void core::scoring::aa_composition_energy::AACompositionEnergySetup::parse_penalty_definitions ( utility::vector1< std::string > const & lines )

private

Parse out penalty definition blocks from the data read from file.

References parse_a_penalty_definition().

Referenced by initialize_from_file(), and initialize_from_file_contents().

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::property_penalty	(	signed long const	delta_expected,
		core::Size const	property_set_index
	)		const

inline

Look up the penalty for a property set of internal index property_set_index, given a deviation from the desired count given by delta_expected.

References out_of_bounds_func(), property_deviation_ranges_, and property_penalties_.

void core::scoring::aa_composition_energy::AACompositionEnergySetup::property_set_indices_matching_residue	(	core::chemical::ResidueType const &	rsd_type,
		utility::vector1< core::Size > &	indices_out
	)		const

inline

Get the indices of all of the property sets corresponding to the current residue.

Returns empty vector if none of the property sets that we're counting corresponds to the current residue.

References property_sets_.

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::quadratic_fract_out_of_bounds_func	(	bool const	before,
		core::Size const	index,
		core::Real const &	delta_fract
	)		const

inlineprivate

Return a quadratic value for an out-of-bounds behaviour. This version is for fractional penalty ranges.

This fits the first two or the last two values to a parabola centred on the origin, then extends it. Inputs are:

Parameters

[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.
[in]	property	If true, we're counting property sets. If false, we're counting residue types.
[in]	index	The index in the list of properties or residue types that we're counting.
[in]	delta_fract	The fractional deviation from the expected count (e.g. if expected is 5% and observed is 3%, this is -0.02).

References core::pose::motif::a(), protocols::match::upstream::b, property_penalties_, and property_penalty_fracts_.

Referenced by fract_out_of_bounds_func().

core::Real core::scoring::aa_composition_energy::AACompositionEnergySetup::quadratic_out_of_bounds_func	(	bool const	before,
		core::Size const	index,
		signed long const	delta_expected
	)		const

inlineprivate

Return a quadratic value for an out-of-bounds behaviour.

This fits the first two or the last two values to a parabola centred on the origin, then extends it. Inputs are:

Parameters

[in]	before	If true, this is beyond the low range of penalty values. If false, we're beyond the high range.
[in]	property	If true, we're counting property sets. If false, we're counting residue types.
[in]	index	The index in the list of properties or residue types that we're counting.
[in]	delta_expected	The deviation from the expected count.

References core::pose::motif::a(), protocols::match::upstream::b, property_deviation_ranges_, and property_penalties_.

Referenced by out_of_bounds_func().

std::string core::scoring::aa_composition_energy::AACompositionEnergySetup::report ( ) const

Get a summary of the data stored in this object.

References expected_by_properties_absolute_, expected_by_properties_fraction_, fract_property_deviation_ranges_, property_deviation_ranges_, property_penalties_, property_penalty_fracts_, property_sets_, and use_fract_ranges_.

void core::scoring::aa_composition_energy::AACompositionEnergySetup::reset ( )

Reset all data in this data storage object.

References expected_by_properties_absolute_, expected_by_properties_fraction_, fract_property_deviation_ranges_, property_deviation_ranges_, property_penalties_, property_penalty_fracts_, property_sets_, property_tailfunctions_, and use_fract_ranges_.

Referenced by initialize_from_file(), and initialize_from_file_contents().

bool core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_expected_values_any ( ) const

Determine whether ANY of the property sets of this helper object use fractional expected values.

References expected_by_properties_absolute_.

bool core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_ranges ( core::Size const index ) const

inline

Look up whether we're using absolute (return false) or fractional (return true) penalty ranges.

References use_fract_ranges_.

bool core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_ranges_any ( ) const

Determine whether ANY of the property sets of this helper object use fractional ranges.

References use_fract_ranges_.

Member Data Documentation

utility::vector1< signed long > core::scoring::aa_composition_energy::AACompositionEnergySetup::expected_by_properties_absolute_

private

The expected number of residues for each set of properties (by property set index), as an absolute number.

If this is negative, the fraction is used instead.

Referenced by check_data(), expected_by_properties_absolute(), parse_a_penalty_definition(), report(), reset(), and use_fract_expected_values_any().

utility::vector1< core::Real > core::scoring::aa_composition_energy::AACompositionEnergySetup::expected_by_properties_fraction_

private

The expected number of residues for each set of properties (by property set index), as a fraction (from 0 to 1) of total.

Referenced by check_data(), expected_by_properties_fraction(), parse_a_penalty_definition(), report(), and reset().

utility::vector1< std::pair < core::Real, core::Real > > core::scoring::aa_composition_energy::AACompositionEnergySetup::fract_property_deviation_ranges_

private

Deviation ranges for each property set, expressed as a fraction of total residues.

Outer vector is the property set, by internal index. Inner vector is pairs of deviation ranges (e.g. 0.05,0.09 indicating that we are storing penalties for having 5% of a residue type to 9% of a residue type for a given property set). Deviations outside of this range are assigned a value given by the begin function or end function.

Referenced by check_data(), fract_property_penalty(), linear_fract_out_of_bounds_func(), parse_a_penalty_definition(), report(), and reset().

utility::vector1< std::pair < signed long, signed long > > core::scoring::aa_composition_energy::AACompositionEnergySetup::property_deviation_ranges_

private

Deviation ranges for each property set.

Outer vector is the property set, by internal index. Inner vector is pairs of deviation ranges (e.g. -10,5 indicating that we are storing penalties for having 10 residues too few up to 5 residues too many for a given property set). Deviations outside of this range are assigned a value given by the begin function or end function.

Referenced by check_data(), linear_out_of_bounds_func(), parse_a_penalty_definition(), property_penalty(), quadratic_out_of_bounds_func(), report(), and reset().

utility::vector1< utility::vector1 < core::Real > > core::scoring::aa_composition_energy::AACompositionEnergySetup::property_penalties_

private

Penalties for each residue count (relative to expected) and each property set.

Outer vector is the property set, by internal index. Inner vector is the penalty value for a given deviation from the ideal count, by internal index.

Referenced by check_data(), const_out_of_bounds_func(), interpolate_property_penalties(), linear_fract_out_of_bounds_func(), linear_out_of_bounds_func(), parse_a_penalty_definition(), property_penalty(), quadratic_fract_out_of_bounds_func(), quadratic_out_of_bounds_func(), report(), and reset().

utility::vector1< utility::vector1 < core::Real > > core::scoring::aa_composition_energy::AACompositionEnergySetup::property_penalty_fracts_

private

For each set of property penalties, this is the corresponding fractional abundance.

Outer vector is the property set, by internal index. Inner vector is the fractional abundance corresponding to each penalty value in property_penalties_. Inner vector will be an empty vector if use_fract_ranges_ is false (i.e. only used if fractional ranges are used).

Referenced by check_data(), interpolate_property_penalties(), linear_fract_out_of_bounds_func(), parse_a_penalty_definition(), quadratic_fract_out_of_bounds_func(), report(), and reset().

utility::vector1< AACompositionPropertiesSetOP > core::scoring::aa_composition_energy::AACompositionEnergySetup::property_sets_

private

The residue property sets that we'll be counting.

Referenced by AACompositionEnergySetup(), check_data(), n_property_sets(), parse_a_penalty_definition(), property_set_indices_matching_residue(), report(), and reset().

utility::vector1< std::pair <TailFunction, TailFunction > > core::scoring::aa_composition_energy::AACompositionEnergySetup::property_tailfunctions_

private

The behaviours at the end of the user-defined range for each property set.

By default, past the user-defined range, the energy increases quadratically with increasing deviations from ideal sequence composition. The user can set this to be linear or constant, though. The vector index corresponds to the property set index, and the internal std::pair represents the behaviour below the range and the behaviour above the range.

Referenced by check_data(), fract_out_of_bounds_func(), out_of_bounds_func(), parse_a_penalty_definition(), and reset().

utility::vector1< bool > core::scoring::aa_composition_energy::AACompositionEnergySetup::use_fract_ranges_

private

For a given property set, should we use absolute ranges (false) or fractional ranges (true)?

Referenced by check_data(), parse_a_penalty_definition(), report(), reset(), use_fract_ranges(), and use_fract_ranges_any().

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

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation