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protocols::ptm_prediction::PTMPredictionMetric Class Reference

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:
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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::Realcalculate (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)
 
PerResidueRealMetricoperator= (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::Realcached_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)
 
SimpleMetricoperator= (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 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

◆ clone()

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

◆ enum_to_string()

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

◆ 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

◆ parse_my_tag()

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

◆ 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

◆ 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: