#include <PatchChemistry.hh>

Inheritance diagram for protocols::chemistries::PatchChemistry:

[legend]

Public Member Functions
	PatchChemistry ()

void	apply (core::chemical::MutableResidueType &) override
	Modify the passed ResidueType. More...

void	apply (core::chemical::MutableResidueType &restype, core::pose::Pose const &pose) override
	Modify the passed ResidueType, context sensitive. 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
	Initialize any data members of this instance from an input tag and a DataMap object. More...

void	patch_name (std::string const &setting)

void	patch_file (std::string const &setting)

void	add_patch_operation_line (std::string const &line)

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...

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

virtual core::chemical::MutableResidueTypeOP	get_additional_output ()
	Get additional generated ResidueTypes, if any. This allows for 1-to-many Chemistries. 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...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	class_name ()

Private Member Functions
core::chemical::MutableResidueTypeOP	apply_patches (core::chemical::MutableResidueType const &restype, utility::vector1< core::chemical::PatchCOP > const &patches) const

core::chemical::MutableResidueTypeOP	apply_patch (core::chemical::MutableResidueType const &restype, core::chemical::Patch const &patch) const

void	apply_operations (core::chemical::MutableResidueType &restype) const

void	update_type (core::chemical::MutableResidueType &restype, core::chemical::MutableResidueType const &new_restype)

Private Attributes
std::string	patch_name_
	The name of the patch from the ResidueTypeSet. More...

std::string	patch_file_
	The name of a file from which to get the patch. More...

utility::vector1< core::chemical::PatchOperationOP >	operations_
	PatchOperations. More...

core::chemical::VDVDMapping	mapping_
	The cached mapping of before to after. More...

Constructor & Destructor Documentation

◆ PatchChemistry()

protocols::chemistries::PatchChemistry::PatchChemistry ( )

inline

Member Function Documentation

◆ add_patch_operation_line()

void protocols::chemistries::PatchChemistry::add_patch_operation_line ( std::string const & line )

References core::chemical::PatchOperationFactory::newPatchOperation(), and operations_.

Referenced by parse_my_tag().

◆ apply() [1/2]

void protocols::chemistries::PatchChemistry::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 apply_operations(), apply_patch(), apply_patches(), core::chemical::MutableResidueType::clone(), core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeBase::mode(), operations_, patch_file_, patch_name_, protocols::chemistries::TR(), and update_type().

Referenced by apply().

◆ apply() [2/2]

void protocols::chemistries::PatchChemistry::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(), apply_operations(), apply_patches(), core::chemical::ResidueTypeBase::mode(), patch_name_, core::pose::Pose::residue_type_set_for_pose(), protocols::chemistries::TR(), and update_type().

◆ apply_operations()

void protocols::chemistries::PatchChemistry::apply_operations ( core::chemical::MutableResidueType & restype ) const

private

References core::chemical::ResidueTypeBase::name(), operations_, and protocols::chemistries::TR().

Referenced by apply().

◆ apply_patch()

core::chemical::MutableResidueTypeOP protocols::chemistries::PatchChemistry::apply_patch	(	core::chemical::MutableResidueType const &	restype,
		core::chemical::Patch const &	patch
	)		const

private

References core::chemical::Patch::applies_to(), core::chemical::Patch::apply(), core::chemical::Patch::name(), core::chemical::ResidueTypeBase::name(), and protocols::chemistries::TR().

Referenced by apply(), and apply_patches().

◆ apply_patches()

core::chemical::MutableResidueTypeOP protocols::chemistries::PatchChemistry::apply_patches	(	core::chemical::MutableResidueType const &	restype,
		utility::vector1< core::chemical::PatchCOP > const &	patches
	)		const

private

References apply_patch().

Referenced by apply().

◆ class_name()

std::string protocols::chemistries::PatchChemistry::class_name ( )

static

Referenced by protocols::chemistries::PatchChemistryCreator::keyname(), and provide_xml_schema().

◆ get_mapping()

core::chemical::VDVDMapping protocols::chemistries::PatchChemistry::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 mapping_.

◆ parse_my_tag()

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

overridevirtual

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

Implements protocols::chemistries::Chemistry.

References add_patch_operation_line(), operations_, patch_file(), patch_file_, patch_name(), patch_name_, and protocols::chemistries::TR().

◆ patch_file()

void protocols::chemistries::PatchChemistry::patch_file ( std::string const & setting )

inline

References patch_file_.

Referenced by parse_my_tag().

◆ patch_name()

void protocols::chemistries::PatchChemistry::patch_name ( std::string const & setting )

inline

References patch_name_.

Referenced by parse_my_tag().

◆ provide_xml_schema()

void protocols::chemistries::PatchChemistry::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References class_name(), and protocols::chemistries::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::chemistries::PatchChemistryCreator::provide_xml_schema().

◆ update_type()

void protocols::chemistries::PatchChemistry::update_type	(	core::chemical::MutableResidueType &	restype,
		core::chemical::MutableResidueType const &	new_restype
	)

private

References mapping_.

Referenced by apply().

Member Data Documentation

◆ mapping_

core::chemical::VDVDMapping protocols::chemistries::PatchChemistry::mapping_

private

The cached mapping of before to after.

Referenced by get_mapping(), and update_type().

◆ operations_

utility::vector1< core::chemical::PatchOperationOP > protocols::chemistries::PatchChemistry::operations_

private

PatchOperations.

Referenced by add_patch_operation_line(), apply(), apply_operations(), and parse_my_tag().

◆ patch_file_

std::string protocols::chemistries::PatchChemistry::patch_file_

private

The name of a file from which to get the patch.

Referenced by apply(), parse_my_tag(), and patch_file().

◆ patch_name_

std::string protocols::chemistries::PatchChemistry::patch_name_

private

The name of the patch from the ResidueTypeSet.

Referenced by apply(), parse_my_tag(), and patch_name().

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

src/protocols/chemistries/PatchChemistry.hh
src/protocols/chemistries/PatchChemistry.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ PatchChemistry()

Member Function Documentation

◆ add_patch_operation_line()

◆ apply() [1/2]

◆ apply() [2/2]

◆ apply_operations()

◆ apply_patch()

◆ apply_patches()

◆ class_name()

◆ get_mapping()

◆ parse_my_tag()

◆ patch_file()

◆ patch_name()

◆ provide_xml_schema()

◆ update_type()

Member Data Documentation

◆ mapping_

◆ operations_

◆ patch_file_

◆ patch_name_