A metric for estimating the probability of a given residue(s) to be modified, as predicted by a pre-trained neural network. More...

#include <PTMPredictionMetric.hh>

Inheritance diagram for protocols::ptm_prediction::PTMPredictionMetric:

[legend]

Public Types
enum class	PTMPredictionMetricModes { INVALID_MODE = 0 , ACETYLATION , ARG_METHYLATION , CITRULLINATION , CROTONYLATION , DEAMIDATION , GAMMA_CARBOXY_GLUTAMIC_ACID , GLUTARYLATION , GLUTATHIONYLATION , HYDROXYLATION , LYS_METHYLATION , MALONYLATION , N_LINKED_GLYCOSYLATION , O_LINKED_GLYCOSYLATION , PHOSPHORYLATION , S_NITROSYLATION , SUCCINYLATION , SUMOYLATION , UBIQUITINATION , N_MODES = UBIQUITINATION }
	enum class to define the different modifications that can be predicted More...

Public Member Functions
	PTMPredictionMetric ()
	Constructors ///. More...

	PTMPredictionMetric (PTMPredictionMetric const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~PTMPredictionMetric () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

std::map< core::Size, core::Real >	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

std::string	name () const override
	Name of the class. More...

std::string	metric () const override
	Name of the metric. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	called by parse_my_tag – should not be used directly More...

core::simple_metrics::SimpleMetricOP	clone () const override

std::string	modification () const
	Get the modification type that should be predicted. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector_in)
	Set the residue selector that we'll be using. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector () const
	Get the residue selector. More...

PTMPredictionMetric::PTMPredictionMetricModes	ptm_mode () const
	Get the modification type that should be predicted as enum class type. More...

Public Member Functions inherited from core::simple_metrics::PerResidueRealMetric
	PerResidueRealMetric ()

	~PerResidueRealMetric () override

	PerResidueRealMetric (PerResidueRealMetric const &other)

PerResidueRealMetric &	operator= (PerResidueRealMetric const &)

void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const override
	Calculate the metric and add it to the pose as a score. labeled as out_label. More...

void	set_residue_selector (select::residue_selector::ResidueSelectorCOP selector)
	Set a ResidueSelector for which we will calculate values over. More...

void	set_output_as_pdb_nums (bool output_as_pdb_nums)
	Set to output in PDB numbering instead of Rosetta during the Apply function, which adds the data to pose as extra scores. More...

std::map< core::Size, core::Real >	cached_calculate (pose::Pose const &pose, bool use_cache, std::string prefix="", std::string suffix="", bool fail_on_missing_cache=true, bool use_ref_pose_for_cache=true) const
	Grab the data from the pose if it exists or calculate the metric. More...

utility::vector1< std::string >	get_metric_names () const override
	Get the submetric names that this Metric will calculate. More...

select::residue_selector::ResidueSelectorCOP	get_selector () const
	Get the set residue selector of this class. More...

virtual void	parse_per_residue_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

virtual void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const=0
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as `label` Must be implemented by derived classes. More...

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

Public Member Functions inherited from core::simple_metrics::SimpleMetric
	SimpleMetric (std::string const &simple_metric_type)

	~SimpleMetric () override

	SimpleMetric (SimpleMetric const &other)

SimpleMetric &	operator= (SimpleMetric const &)

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

void	set_custom_type (std::string const &custom_type)

std::string	get_custom_type () const
	Additional setting to prefix/suffix. More...

virtual void	parse_base_tag (utility::tag::TagCOP tag)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

std::string	simple_metric_type () const

std::string	get_final_sm_type () const
	Get the final name of this metric including its simple_metric_type_ name and any set custom type. More...

Static Public Member Functions
static std::string	name_static ()
	Name of the class for creator. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	enum_to_string (PTMPredictionMetric::PTMPredictionMetricModes &ptm_mode)
	Convert an enum modification type into the respective string modification type. More...

static PTMPredictionMetric::PTMPredictionMetricModes	string_to_enum (std::string &modification_type)
	Convert an string modification type into an enum modification type. More...

Static Public Member Functions inherited from core::simple_metrics::PerResidueRealMetric
static void	add_schema (utility::tag::XMLSchemaComplexTypeGeneratorOP complex_schema)
	Add options to the schema from this base class. More...

Static Public Member Functions inherited from core::simple_metrics::SimpleMetric
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)

Private Member Functions
void	provide_citation_info (basic::citation_manager::CitationCollectionList &citations) const override
	This metric is unpublished. It returns Moritz Ertelt as its author. More...

Private Attributes
std::string	modification_
	The kind of post-translational modification to be predicted. More...

PTMPredictionMetric::PTMPredictionMetricModes	ptm_mode_
	The kind of post-translational modification to be predicted as enum class. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector_ = nullptr
	An optional residue selector. More...

PTMPredictionTensorflowProtocolBaseCOP	tensorflow_protocol_ = nullptr
	The tensorflow protocol used to predict post-translational modifications. More...

Detailed Description

A metric for estimating the probability of a given residue(s) to be modified, as predicted by a pre-trained neural network.

Member Enumeration Documentation

◆ PTMPredictionMetricModes

enum protocols::ptm_prediction::PTMPredictionMetric::PTMPredictionMetricModes

strong

enum class to define the different modifications that can be predicted

Enumerator
INVALID_MODE
ACETYLATION
ARG_METHYLATION
CITRULLINATION
CROTONYLATION
DEAMIDATION
GAMMA_CARBOXY_GLUTAMIC_ACID
GLUTARYLATION
GLUTATHIONYLATION
HYDROXYLATION
LYS_METHYLATION
MALONYLATION
N_LINKED_GLYCOSYLATION
O_LINKED_GLYCOSYLATION
PHOSPHORYLATION
S_NITROSYLATION
SUCCINYLATION
SUMOYLATION
UBIQUITINATION
N_MODES

Constructor & Destructor Documentation

◆ PTMPredictionMetric() [1/2]

protocols::ptm_prediction::PTMPredictionMetric::PTMPredictionMetric ( )

Constructors ///.

Default constructor

◆ PTMPredictionMetric() [2/2]

protocols::ptm_prediction::PTMPredictionMetric::PTMPredictionMetric ( PTMPredictionMetric const & src )

default

Copy constructor (not needed unless you need deep copies)

Copy constructor.

◆ ~PTMPredictionMetric()

protocols::ptm_prediction::PTMPredictionMetric::~PTMPredictionMetric ( )

override

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

Member Function Documentation

◆ calculate()

std::map< core::Size, core::Real > protocols::ptm_prediction::PTMPredictionMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Calculate the metric.

Implements core::simple_metrics::PerResidueRealMetric.

References modification_, ptm_mode_, residue_selector_, tensorflow_protocol_, and core::pose::Pose::total_residue().

◆ clone()

core::simple_metrics::SimpleMetricOP protocols::ptm_prediction::PTMPredictionMetric::clone ( ) const

overridevirtual

Implements core::simple_metrics::PerResidueRealMetric.

◆ enum_to_string()

std::string protocols::ptm_prediction::PTMPredictionMetric::enum_to_string ( PTMPredictionMetric::PTMPredictionMetricModes & ptm_mode )

static

Convert an enum modification type into the respective string modification type.

convert the type of modification enum to a string

References ACETYLATION, ARG_METHYLATION, CITRULLINATION, CROTONYLATION, DEAMIDATION, GAMMA_CARBOXY_GLUTAMIC_ACID, GLUTARYLATION, GLUTATHIONYLATION, HYDROXYLATION, INVALID_MODE, LYS_METHYLATION, MALONYLATION, N_LINKED_GLYCOSYLATION, O_LINKED_GLYCOSYLATION, PHOSPHORYLATION, ptm_mode(), S_NITROSYLATION, SUCCINYLATION, SUMOYLATION, and UBIQUITINATION.

Referenced by provide_xml_schema(), and string_to_enum().

◆ metric()

std::string protocols::ptm_prediction::PTMPredictionMetric::metric ( ) const

overridevirtual

Name of the metric.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

◆ modification()

std::string protocols::ptm_prediction::PTMPredictionMetric::modification ( ) const

inline

Get the modification type that should be predicted.

References modification_.

◆ name()

std::string protocols::ptm_prediction::PTMPredictionMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::PerResidueRealMetric.

References name_static().

◆ name_static()

std::string protocols::ptm_prediction::PTMPredictionMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::ptm_prediction::PTMPredictionMetricCreator::keyname(), metric(), name(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::ptm_prediction::PTMPredictionMetric::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

called by parse_my_tag – should not be used directly

Implements core::simple_metrics::PerResidueRealMetric.

References modification_, core::select::residue_selector::parse_residue_selector(), ptm_mode_, set_residue_selector(), string_to_enum(), and tensorflow_protocol_.

◆ provide_citation_info()

void protocols::ptm_prediction::PTMPredictionMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overrideprivatevirtual

This metric is unpublished. It returns Moritz Ertelt as its author.

Reimplemented from core::simple_metrics::SimpleMetric.

◆ provide_xml_schema()

void protocols::ptm_prediction::PTMPredictionMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), enum_to_string(), N_MODES, name_static(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by protocols::ptm_prediction::PTMPredictionMetricCreator::provide_xml_schema().

◆ ptm_mode()

PTMPredictionMetric::PTMPredictionMetricModes protocols::ptm_prediction::PTMPredictionMetric::ptm_mode ( ) const

inline

Get the modification type that should be predicted as enum class type.

References ptm_mode_.

Referenced by enum_to_string().

◆ residue_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::ptm_prediction::PTMPredictionMetric::residue_selector ( ) const

Get the residue selector.

If this returns nullptr, it means that no residue selector is being used.

References residue_selector_.

◆ set_residue_selector()

void protocols::ptm_prediction::PTMPredictionMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector_in )

Set the residue selector that we'll be using.

Set the residue selector that we'll be using, OP is used directly and the object is not cloned.

Passing nullptr results in no residue selector being used.

References residue_selector_.

Referenced by parse_my_tag().

◆ string_to_enum()

PTMPredictionMetric::PTMPredictionMetricModes protocols::ptm_prediction::PTMPredictionMetric::string_to_enum ( std::string & modification_type )

static

Convert an string modification type into an enum modification type.

References enum_to_string(), INVALID_MODE, and N_MODES.

Referenced by parse_my_tag().

Member Data Documentation

◆ modification_

std::string protocols::ptm_prediction::PTMPredictionMetric::modification_

private

The kind of post-translational modification to be predicted.

Referenced by calculate(), modification(), and parse_my_tag().

◆ ptm_mode_

PTMPredictionMetric::PTMPredictionMetricModes protocols::ptm_prediction::PTMPredictionMetric::ptm_mode_

private

The kind of post-translational modification to be predicted as enum class.

Referenced by calculate(), parse_my_tag(), and ptm_mode().

◆ residue_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::ptm_prediction::PTMPredictionMetric::residue_selector_ = nullptr

private

An optional residue selector.

Referenced by calculate(), residue_selector(), and set_residue_selector().

◆ tensorflow_protocol_

PTMPredictionTensorflowProtocolBaseCOP protocols::ptm_prediction::PTMPredictionMetric::tensorflow_protocol_ = nullptr

private

The tensorflow protocol used to predict post-translational modifications.

Referenced by calculate(), and parse_my_tag().

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

src/protocols/ptm_prediction/PTMPredictionMetric.hh
src/protocols/ptm_prediction/PTMPredictionMetric.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Enumeration Documentation

◆ PTMPredictionMetricModes

Constructor & Destructor Documentation

◆ PTMPredictionMetric() [1/2]

◆ PTMPredictionMetric() [2/2]

◆ ~PTMPredictionMetric()

Member Function Documentation

◆ calculate()

◆ clone()

◆ enum_to_string()

◆ metric()

◆ modification()

◆ name()

◆ name_static()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ ptm_mode()

◆ residue_selector()

◆ set_residue_selector()

◆ string_to_enum()

Member Data Documentation

◆ modification_

◆ ptm_mode_

◆ residue_selector_

◆ tensorflow_protocol_