#include <ReactionGrow.hh>

Inheritance diagram for protocols::drug_design::ReactionGrow:

[legend]

Public Member Functions
	ReactionGrow ()

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

void	fragment_database (std::string filename, bool append=false)
	The file which contains the fragments to add to input residue type. More...

void	prefilter_fragments ()
	Reduce the fragment set to those which are compatible with the reactions. More...

void	prefilter_reactions ()
	Filter reaction list for those compatible with the given fragments. More...

void	weight_by_property (std::string const &setting)
	If not empty, use property weighting based on the given property. More...

std::string const &	weight_by_property () const

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
utility::vector1< ::RDKit::ROMolOP >	fragments_
	The fragments to apply. More...

std::string	property_name_
	If not empty, pick fragments based on the weighting by the given property. 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

◆ ReactionGrow()

protocols::drug_design::ReactionGrow::ReactionGrow ( )

Member Function Documentation

◆ add_reaction()

void protocols::drug_design::ReactionGrow::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::ReactionGrow::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.

◆ class_name()

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

static

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

◆ fragment_database()

void protocols::drug_design::ReactionGrow::fragment_database	(	std::string	filename,
		bool	append = `false`
	)

The file which contains the fragments to add to input residue type.

References protocols::abinitio::filename(), fragments_, core::chemical::rdkit::load_sdf(), and protocols::drug_design::TR().

Referenced by parse_my_tag().

◆ get_mapping()

core::chemical::VDVDMapping protocols::drug_design::ReactionGrow::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_.

◆ parse_my_tag()

void protocols::drug_design::ReactionGrow::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datacache
	)

overridevirtual

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

Implements protocols::drug_design::ReactionChemistry.

References fragment_database(), prefilter_fragments(), prefilter_reactions(), protocols::drug_design::ReactionChemistry::reaction_file(), and weight_by_property().

◆ prefilter_fragments()

void protocols::drug_design::ReactionGrow::prefilter_fragments ( )

Reduce the fragment set to those which are compatible with the reactions.

Discarded fragments are discarded permanently. Only call after all reactions are finalized for this Chemistry

References fragments_, protocols::drug_design::ReactionChemistry::get_reactions(), core::id::swap(), and protocols::drug_design::TR().

Referenced by parse_my_tag().

◆ prefilter_reactions()

void protocols::drug_design::ReactionGrow::prefilter_reactions ( )

inline

Filter reaction list for those compatible with the given fragments.

Discarded reactions will be discarded permanently. Only call with the finalized fragment list.

References fragments_, and protocols::drug_design::ReactionChemistry::prefilter_reactions().

Referenced by parse_my_tag().

◆ provide_xml_schema()

void protocols::drug_design::ReactionGrow::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::drug_design::ReactionGrowCreator::provide_xml_schema().

◆ weight_by_property() [1/2]

std::string const& protocols::drug_design::ReactionGrow::weight_by_property ( ) const

inline

References property_name_.

Referenced by parse_my_tag().

◆ weight_by_property() [2/2]

void protocols::drug_design::ReactionGrow::weight_by_property ( std::string const & setting )

inline

If not empty, use property weighting based on the given property.

References property_name_.

Member Data Documentation

◆ fragments_

utility::vector1< ::RDKit::ROMolOP > protocols::drug_design::ReactionGrow::fragments_

private

The fragments to apply.

Referenced by apply(), fragment_database(), prefilter_fragments(), and prefilter_reactions().

◆ mapping_

core::chemical::VDVDMapping protocols::drug_design::ReactionGrow::mapping_

private

Referenced by apply(), and get_mapping().

◆ property_name_

std::string protocols::drug_design::ReactionGrow::property_name_

private

If not empty, pick fragments based on the weighting by the given property.

Referenced by apply(), and weight_by_property().

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

src/protocols/drug_design/ReactionGrow.hh
src/protocols/drug_design/ReactionGrow.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ReactionGrow()

Member Function Documentation

◆ add_reaction()

◆ apply()

◆ class_name()

◆ fragment_database()

◆ get_mapping()

◆ parse_my_tag()

◆ prefilter_fragments()

◆ prefilter_reactions()

◆ provide_xml_schema()

◆ weight_by_property() [1/2]

◆ weight_by_property() [2/2]

Member Data Documentation

◆ fragments_

◆ mapping_

◆ property_name_