protocols::chemistries::WrappedBaseChemistry Class Reference

#include <WrappedChemistries.hh>

Inheritance diagram for protocols::chemistries::WrappedBaseChemistry:

Public Member Functions
	WrappedBaseChemistry (std::string const &name, core::chemical::modifications::ChemistryBaseOP subchem=nullptr)
void	apply (core::chemical::MutableResidueType &) override
	Modify the passed ResidueType. More...
void	apply (core::chemical::MutableResidueType &, core::pose::Pose const &) override
	Modify the passed ResidueType, context sensitive. More...
bool	has_additional_output () const override
	Are there alternate ResidueTypes which are availible from the last time we called apply? (That is, will get_addtional_output() return non-null?) More...
core::chemical::MutableResidueTypeOP	get_additional_output () override
	Get additional generated ResidueTypes, if any. This allows for 1-to-many Chemistries. More...
core::chemical::VDVDMapping	get_mapping () const override
	Get the vertex mapping that was used for the last apply() or get_additional_output() This is a mapping FROM the vds in the BEFORE MutableResidueType TO the vds in the AFTER MutableResidueType. The base class implementation defaults to an identity mapping. More...
void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override=0
	Initialize any data members of this instance from an input tag and a DataMap object. More...
void	set_subchemistry (core::chemical::modifications::ChemistryBaseOP setting)
Public Member Functions inherited from protocols::chemistries::Chemistry
	Chemistry (std::string const &name)
Public Member Functions inherited from core::chemical::modifications::ChemistryBase
	ChemistryBase (std::string const &name)
std::string	name () const
	Return the name of this Chemistry object. More...
ChemistryStatus	get_last_status () const
	What was the status of the last call to apply()/get_additional_output() More...
void	set_last_status (ChemistryStatus setting)
	Set the status of the chemistry object. More...

Private Attributes
core::chemical::modifications::ChemistryBaseOP	sub_chemistry_

Constructor & Destructor Documentation

WrappedBaseChemistry()

protocols::chemistries::WrappedBaseChemistry::WrappedBaseChemistry ( std::string const &  name, core::chemical::modifications::ChemistryBaseOP  subchem = nullptr  )

inline

Member Function Documentation

apply() [1/2]

void protocols::chemistries::WrappedBaseChemistry::apply ( core::chemical::MutableResidueType &  )

overridevirtual

Modify the passed ResidueType.

if you have a Pose, call the one which takes the Pose context

Implements protocols::chemistries::Chemistry.

References core::chemical::modifications::ChemistryBase::set_last_status(), and sub_chemistry_.

Referenced by apply().

apply() [2/2]

void protocols::chemistries::WrappedBaseChemistry::apply ( core::chemical::MutableResidueType &  restype, core::pose::Pose const &    )

overridevirtual

Modify the passed ResidueType, context sensitive.

By default, not context sensitive - will just redirect to the other function.

Reimplemented from protocols::chemistries::Chemistry.

References apply().

get_additional_output()

core::chemical::MutableResidueTypeOP protocols::chemistries::WrappedBaseChemistry::get_additional_output ( )

overridevirtual

Get additional generated ResidueTypes, if any. This allows for 1-to-many Chemistries.

Reimplemented from core::chemical::modifications::ChemistryBase.

References sub_chemistry_.

get_mapping()

core::chemical::VDVDMapping protocols::chemistries::WrappedBaseChemistry::get_mapping ( ) const

overridevirtual

Get the vertex mapping that was used for the last apply() or get_additional_output() This is a mapping FROM the vds in the BEFORE MutableResidueType TO the vds in the AFTER MutableResidueType. The base class implementation defaults to an identity mapping.

Get the vertex mapping that was used for the last apply() The base class implementation defaults to an identity mapping.

Reimplemented from core::chemical::modifications::ChemistryBase.

References sub_chemistry_.

has_additional_output()

bool protocols::chemistries::WrappedBaseChemistry::has_additional_output ( ) const

overridevirtual

Are there alternate ResidueTypes which are availible from the last time we called apply? (That is, will get_addtional_output() return non-null?)

Reimplemented from core::chemical::modifications::ChemistryBase.

References sub_chemistry_.

parse_my_tag()

void protocols::chemistries::WrappedBaseChemistry::parse_my_tag ( utility::tag::TagCOP  , basic::datacache::DataMap &    )

overridepure virtual

Initialize any data members of this instance from an input tag and a DataMap object.

Implements protocols::chemistries::Chemistry.

Implemented in protocols::chemistries::ReprotonateChemistry.

set_subchemistry()

void protocols::chemistries::WrappedBaseChemistry::set_subchemistry ( core::chemical::modifications::ChemistryBaseOP  setting )

inline

References sub_chemistry_.

Referenced by protocols::chemistries::ReprotonateChemistry::ReprotonateChemistry().

Member Data Documentation

sub_chemistry_

core::chemical::modifications::ChemistryBaseOP protocols::chemistries::WrappedBaseChemistry::sub_chemistry_

private

Referenced by apply(), get_additional_output(), get_mapping(), has_additional_output(), and set_subchemistry().

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

• src/protocols/chemistries/WrappedChemistries.hh
• src/protocols/chemistries/WrappedChemistries.cc