#include <Chemistry.hh>

Inheritance diagram for protocols::chemistries::Chemistry:

[legend]

Public Member Functions
	Chemistry (std::string const &name)

void	apply (core::chemical::MutableResidueType &) override=0
	Modify the passed ResidueType. More...

virtual void	apply (core::chemical::MutableResidueType &restype, core::pose::Pose const &)
	Modify the passed ResidueType, context sensitive. More...

virtual void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &)=0
	Initialize any data members of this instance from an input tag and a DataMap object. More...

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...

virtual VDVDMapping	get_mapping () const
	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...

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...

Constructor & Destructor Documentation

◆ Chemistry()

protocols::chemistries::Chemistry::Chemistry ( std::string const & name )

inline

Member Function Documentation

◆ apply() [1/2]

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

overridepure virtual

Modify the passed ResidueType.

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

Implements core::chemical::modifications::ChemistryBase.

Referenced by apply(), protocols::drug_design::DrugDesignMover::apply(), and protocols::drug_design::DrugPolishMover::apply().

◆ apply() [2/2]

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

inlinevirtual

Modify the passed ResidueType, context sensitive.

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

Reimplemented in protocols::chemistries::PatchChemistry, and protocols::chemistries::WrappedBaseChemistry.

References apply().

◆ parse_my_tag()

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

pure virtual

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

Implemented in protocols::chemistries::WrappedBaseChemistry, protocols::rotamer_gen::RDKitRotamers, protocols::rotamer_gen::FragmentRotamers, protocols::drug_design::RandomFragmentLigand, protocols::chemistries::ReprotonateChemistry, protocols::chemistries::PatchChemistry, protocols::drug_design::ReactionChemistry, protocols::drug_design::SubstructureReplace, protocols::drug_design::SubstituentReplace, protocols::drug_design::ReactionMultiTransform, protocols::drug_design::ReactionGrow, protocols::drug_design::ReactionFragment, and protocols::drug_design::ReactionBasedAnalogSampler.

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