#include <ReactionFragment.hh>

Inheritance diagram for protocols::drug_design::ReactionFragment:

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Public Member Functions
	ReactionFragment ()

void	keep_bigger (bool setting)

void	keep_random (bool setting)

void	keep_atom (std::string const &keep_atom)

bool	keep_bigger () const

bool	keep_random () const

std::string	keep_atom () const

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datacache) override
	Initialize any data members of this instance from an input tag and a DataMap object. 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	add_reaction (::RDKit::ChemicalReactionOP rxn, core::Real weight) override
	Add a reaction to the list of reactions to use. Reaction should be written in the synthetic direction with a single product. More...

Public Member Functions inherited from protocols::drug_design::ReactionChemistry
	ReactionChemistry (std::string const &type)

virtual void	reaction_file (std::string filename, bool append=false)
	The file which contains the reactions which to use. More...

void	prefilter_reactions (utility::vector1< ::RDKit::ROMolOP > const &reactants, bool exclude_first=true)
	Filter reaction list for those compatible with the given reactants. More...

Public Member Functions inherited from protocols::chemistries::Chemistry
	Chemistry (std::string const &name)

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

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 std::string	class_name ()

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

Private Attributes
bool	keep_bigger_
	Keep the fragment which is bigger. More...

bool	keep_random_
	Keep a random fragment. More...

std::string	keep_atom_
	Keep the fragment which contains the given atom. More...

core::chemical::VDVDMapping	mapping_

Additional Inherited Members
Protected Member Functions inherited from protocols::drug_design::ReactionChemistry
void	filter_reactions (::RDKit::ROMol const &rdmol, utility::vector1< ::RDKit::ChemicalReactionOP > &rxns, numeric::random::WeightedSampler &rxn_sampler) const
	Filter the reactions to just the ones which can be applied to rdmol If the reactions are multi-component, is assumed that the rdmol (derived from input residue passed to apply()) will be passed as the first reactant to the reaction. More...

bool	cleanup_product (::RDKit::RWMol &prod) const
	attempt to clean up the product of an RDKit reaction Modifies the RWMol in place - if modification unsuccessful, it will return true. More...

utility::vector1< std::pair< ::RDKit::ChemicalReactionOP, core::Real > > const &	get_reactions () const

Constructor & Destructor Documentation

◆ ReactionFragment()

protocols::drug_design::ReactionFragment::ReactionFragment ( )

Member Function Documentation

◆ add_reaction()

void protocols::drug_design::ReactionFragment::add_reaction	(	::RDKit::ChemicalReactionOP	rxn,
		core::Real	weight
	)

overridevirtual

Add a reaction to the list of reactions to use. Reaction should be written in the synthetic direction with a single product.

Reimplemented from protocols::drug_design::ReactionChemistry.

References protocols::drug_design::ReactionChemistry::add_reaction(), and protocols::drug_design::TR().

◆ apply()

void protocols::drug_design::ReactionFragment::apply ( core::chemical::MutableResidueType & )

overridevirtual

Modify the passed ResidueType.

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

Implements protocols::drug_design::ReactionChemistry.

References core::chemical::MutableResidueType::atom_vertex(), protocols::drug_design::ReactionChemistry::cleanup_product(), core::chemical::AtomRefMapping< FromRef, ToRef >::clear(), core::chemical::combine(), core::chemical::AtomRefMapping< FromRef, ToRef >::empty(), core::chemical::modifications::FAIL_DO_NOT_RETRY, core::chemical::modifications::FAIL_RETRY, protocols::drug_design::ReactionChemistry::filter_reactions(), core::chemical::rdkit::find_mapping(), core::chemical::rdkit::RDMolToRestype::generate_restype(), core::chemical::MutableResidueType::has(), core::chemical::AtomRefMapping< FromRef, ToRef >::identity(), core::chemical::rdkit::RDMolToRestype::index_to_vd(), protocols::drug_design::invalid_products(), keep_atom_, keep_bigger_, keep_random_, core::chemical::rdkit::label_with_index(), mapping_, core::chemical::rdkit::RestypeToRDMol::Mol(), core::chemical::ResidueTypeBase::name(), core::chemical::MutableResidueType::nbr_vertex(), core::chemical::MutableResidueType::nheavyatoms(), core::chemical::modifications::ChemistryBase::set_last_status(), core::chemical::rdkit::RDMolToRestype::set_nbr(), core::chemical::modifications::SUCCESS, protocols::drug_design::TR(), and core::chemical::rdkit::RestypeToRDMol::vd_to_index().

◆ class_name()

std::string protocols::drug_design::ReactionFragment::class_name ( )

static

Referenced by protocols::drug_design::ReactionFragmentCreator::keyname(), and provide_xml_schema().

◆ get_mapping()

core::chemical::VDVDMapping protocols::drug_design::ReactionFragment::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.

Implements protocols::drug_design::ReactionChemistry.

References mapping_.